Title: Spatial Empirical Dynamic Modeling
Description: Inferring causation from spatial cross-sectional data through empirical dynamic modeling (EDM), with methodological extensions including geographical convergent cross mapping from Gao et al. (2023) <doi:10.1038/s41467-023-41619-6>, as well as the spatial causality test following the approach of Herrera et al. (2016) <doi:10.1111/pirs.12144>.
Author: Wenbo Lv [aut, cre, cph]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between spEDM versions 1.6 dated 2025-05-16 and 1.7 dated 2025-06-24
spEDM-1.6/spEDM/R/variable_check_prepare.R |only spEDM-1.6/spEDM/R/xmapdf.R |only spEDM-1.6/spEDM/inst/doc/spEDM.Rmd |only spEDM-1.6/spEDM/inst/doc/spEDM.html |only spEDM-1.6/spEDM/vignettes/spEDM.Rmd |only spEDM-1.6/spEDM/vignettes/spEDM.Rmd.orig |only spEDM-1.7/spEDM/DESCRIPTION | 6 spEDM-1.7/spEDM/MD5 | 207 +++--- spEDM-1.7/spEDM/NAMESPACE | 5 spEDM-1.7/spEDM/NEWS.md | 32 - spEDM-1.7/spEDM/R/Agenerics.R |only spEDM-1.7/spEDM/R/RcppExports.R | 92 ++ spEDM-1.7/spEDM/R/embedded.R | 80 +- spEDM-1.7/spEDM/R/fnn.R | 19 spEDM-1.7/spEDM/R/formatoutput.R | 96 ++- spEDM-1.7/spEDM/R/gccm.R | 44 - spEDM-1.7/spEDM/R/gcmc.R | 64 -- spEDM-1.7/spEDM/R/globals.R | 4 spEDM-1.7/spEDM/R/ic.R |only spEDM-1.7/spEDM/R/internal_utility.R |only spEDM-1.7/spEDM/R/multiview.R | 27 spEDM-1.7/spEDM/R/sctest.R | 45 - spEDM-1.7/spEDM/R/simplex.R | 45 - spEDM-1.7/spEDM/R/slm.R |only spEDM-1.7/spEDM/R/smap.R | 37 - spEDM-1.7/spEDM/R/zzz.R | 9 spEDM-1.7/spEDM/build/vignette.rds |binary spEDM-1.7/spEDM/inst/CITATION |only spEDM-1.7/spEDM/inst/doc/GCCM.Rmd | 89 +- spEDM-1.7/spEDM/inst/doc/GCCM.html | 213 +++--- spEDM-1.7/spEDM/inst/doc/GCMC.Rmd | 119 +-- spEDM-1.7/spEDM/inst/doc/GCMC.html | 370 +++++------ spEDM-1.7/spEDM/inst/doc/PkgIntro.Rmd |only spEDM-1.7/spEDM/inst/doc/PkgIntro.html |only spEDM-1.7/spEDM/inst/doc/SCT.Rmd | 28 spEDM-1.7/spEDM/inst/doc/SCT.html | 32 - spEDM-1.7/spEDM/inst/doc/SLM.Rmd |only spEDM-1.7/spEDM/inst/doc/SLM.html |only spEDM-1.7/spEDM/inst/doc/SSR.Rmd | 36 - spEDM-1.7/spEDM/inst/doc/SSR.html | 38 - spEDM-1.7/spEDM/man/embedded.Rd | 16 spEDM-1.7/spEDM/man/figures/gccm/fig1-1.png |binary spEDM-1.7/spEDM/man/figures/gccm/fig2-1.png |binary spEDM-1.7/spEDM/man/figures/gcmc/fig1-1.png |binary spEDM-1.7/spEDM/man/figures/gcmc/fig2-1.png |binary spEDM-1.7/spEDM/man/figures/slm |only spEDM-1.7/spEDM/man/fnn.Rd | 146 ++-- spEDM-1.7/spEDM/man/gccm.Rd | 38 - spEDM-1.7/spEDM/man/gcmc.Rd | 181 ++--- spEDM-1.7/spEDM/man/ic.Rd |only spEDM-1.7/spEDM/man/multiview.Rd | 36 - spEDM-1.7/spEDM/man/sc.test.Rd | 186 ++--- spEDM-1.7/spEDM/man/simplex.Rd | 34 - spEDM-1.7/spEDM/man/slm.Rd |only spEDM-1.7/spEDM/man/smap.Rd | 35 - spEDM-1.7/spEDM/src/CppGridUtils.cpp | 177 ++++- spEDM-1.7/spEDM/src/CppGridUtils.h | 76 +- spEDM-1.7/spEDM/src/CppLatticeUtils.cpp | 47 - spEDM-1.7/spEDM/src/CppLatticeUtils.h | 13 spEDM-1.7/spEDM/src/CppStats.cpp | 270 ++++++++ spEDM-1.7/spEDM/src/CppStats.h | 21 spEDM-1.7/spEDM/src/CrossMappingCardinality.cpp | 645 +++++++++++--------- spEDM-1.7/spEDM/src/CrossMappingCardinality.h | 104 +-- spEDM-1.7/spEDM/src/DeLongPlacements.cpp | 20 spEDM-1.7/spEDM/src/DeLongPlacements.h | 1 spEDM-1.7/spEDM/src/EntropyExp.cpp | 16 spEDM-1.7/spEDM/src/Forecast4Grid.cpp | 262 ++++++-- spEDM-1.7/spEDM/src/Forecast4Grid.h | 68 +- spEDM-1.7/spEDM/src/Forecast4Lattice.cpp | 237 ++++++- spEDM-1.7/spEDM/src/Forecast4Lattice.h | 78 ++ spEDM-1.7/spEDM/src/ForecastExp.cpp | 106 +-- spEDM-1.7/spEDM/src/GCCM4Grid.cpp | 184 +---- spEDM-1.7/spEDM/src/GCCM4Grid.h | 14 spEDM-1.7/spEDM/src/GCCM4Lattice.cpp | 89 -- spEDM-1.7/spEDM/src/GCCM4Lattice.h | 10 spEDM-1.7/spEDM/src/GridExp.cpp | 755 +++++++++++++++++++----- spEDM-1.7/spEDM/src/HelperFuns.cpp | 312 +++++++-- spEDM-1.7/spEDM/src/HelperFuns.h | 49 + spEDM-1.7/spEDM/src/IntersectionCardinality.cpp | 492 ++++++++++++--- spEDM-1.7/spEDM/src/IntersectionCardinality.h | 123 +++ spEDM-1.7/spEDM/src/LatticeExp.cpp | 581 +++++++++++++----- spEDM-1.7/spEDM/src/MultiViewEmbedding.cpp | 16 spEDM-1.7/spEDM/src/MultiViewEmbedding.h | 8 spEDM-1.7/spEDM/src/RcppExports.cpp | 406 ++++++++---- spEDM-1.7/spEDM/src/SCPCM4Grid.cpp | 229 ++----- spEDM-1.7/spEDM/src/SCPCM4Grid.h | 52 - spEDM-1.7/spEDM/src/SCPCM4Lattice.cpp | 118 +-- spEDM-1.7/spEDM/src/SCPCM4Lattice.h | 46 - spEDM-1.7/spEDM/src/SGC4Grid.cpp | 35 - spEDM-1.7/spEDM/src/SGC4Grid.h | 1 spEDM-1.7/spEDM/src/SGC4Lattice.cpp | 77 +- spEDM-1.7/spEDM/src/SGC4Lattice.h | 1 spEDM-1.7/spEDM/src/SLM4Grid.cpp |only spEDM-1.7/spEDM/src/SLM4Grid.h |only spEDM-1.7/spEDM/src/SLM4Lattice.cpp |only spEDM-1.7/spEDM/src/SLM4Lattice.h |only spEDM-1.7/spEDM/src/SMap.cpp | 226 +++---- spEDM-1.7/spEDM/src/SMap.h | 55 - spEDM-1.7/spEDM/src/SimplexProjection.cpp | 103 +-- spEDM-1.7/spEDM/src/SimplexProjection.h | 24 spEDM-1.7/spEDM/src/SpatialBlockBootstrap.cpp | 55 + spEDM-1.7/spEDM/src/SpatialBlockBootstrap.h | 23 spEDM-1.7/spEDM/src/StatsExp.cpp | 151 +++- spEDM-1.7/spEDM/src/spEDMDataStruct.h | 24 spEDM-1.7/spEDM/vignettes/GCCM.Rmd | 89 +- spEDM-1.7/spEDM/vignettes/GCCM.Rmd.orig | 24 spEDM-1.7/spEDM/vignettes/GCMC.Rmd | 119 +-- spEDM-1.7/spEDM/vignettes/GCMC.Rmd.orig | 46 - spEDM-1.7/spEDM/vignettes/PkgIntro.Rmd |only spEDM-1.7/spEDM/vignettes/PkgIntro.Rmd.orig |only spEDM-1.7/spEDM/vignettes/SCPCM.Rmd.orig | 9 spEDM-1.7/spEDM/vignettes/SCT.Rmd | 28 spEDM-1.7/spEDM/vignettes/SCT.Rmd.orig | 2 spEDM-1.7/spEDM/vignettes/SLM.Rmd |only spEDM-1.7/spEDM/vignettes/SLM.Rmd.orig |only spEDM-1.7/spEDM/vignettes/SSR.Rmd | 36 - spEDM-1.7/spEDM/vignettes/SSR.Rmd.orig | 22 117 files changed, 5789 insertions(+), 3395 deletions(-)
Title: Ensemble Methods for Multiple Change-Point Detection
Description: Implements a segmentation algorithm for multiple change-point detection in univariate time series using the Ensemble Binary Segmentation of Korkas (2022) <Journal of the Korean Statistical Society, 51(1), pp.65-86.>.
Author: Karolos K. Korkas [aut, cre]
Maintainer: Karolos K. Korkas <kkorkas@yahoo.co.uk>
Diff between eNchange versions 1.0 dated 2020-03-20 and 1.1 dated 2025-06-24
DESCRIPTION | 15 +-- MD5 | 40 ++++---- NAMESPACE | 2 R/BinSeg.R | 11 +- R/EnBinSeg.R | 8 - R/Z_trans.R | 4 R/boot_thresh.R | 12 +- R/pc_acdsim.R | 9 - R/pc_hawkessim.R | 8 - R/simACD.R | 14 +- R/simHawkes.R | 8 - man/BinSeg-methods.Rd | 180 ++++++++++++++++++------------------ man/EnBinSeg-methods.Rd | 218 ++++++++++++++++++++++---------------------- man/Z_trans-methods.Rd | 142 ++++++++++++++-------------- man/boot_thresh-methods.Rd | 168 ++++++++++++++++----------------- man/eNchange-package.Rd | 6 - man/pc_acdsim-methods.Rd | 76 +++++++-------- man/pc_hawkessim-methods.Rd | 76 +++++++-------- man/simACD-class.Rd | 102 ++++++++++---------- man/simHawkes-class.Rd | 96 +++++++++---------- src/RcppExports.cpp | 5 + 21 files changed, 603 insertions(+), 597 deletions(-)
Title: "Smith-Pittman Community Detection Algorithm for 'igraph'
Objects (2024)"
Description: Implements the "Smith-Pittman" community detection algorithm
for network analysis using 'igraph' objects. This algorithm combines node
degree and betweenness centrality measures to identify communities within
networks, with a gradient evident in social partitioning. The package
provides functions for community detection, visualization, and analysis of
the resulting community structure. Methods are based on results from Smith,
Pittman and Xu (2024) <doi:10.48550/arXiv.2411.01394>.
Author: Benjamin Smith [aut, cre] ,
Tyler Pittman [aut] ,
Wei Xu [aut]
Maintainer: Benjamin Smith <benyamin.smith@mail.utoronto.ca>
Diff between ig.degree.betweenness versions 0.1.1 dated 2025-03-11 and 0.2.0 dated 2025-06-24
DESCRIPTION | 17 ++++++++++------- MD5 | 11 +++++++++-- NAMESPACE | 1 + R/oncology_network.R |only R/plot_node_degrees.R |only R/zzz.R |only data |only inst |only man/oncology_network.Rd |only man/plot_node_degrees.Rd |only 10 files changed, 20 insertions(+), 9 deletions(-)
More information about ig.degree.betweenness at CRAN
Permanent link
Title: Tools for Analyzing Cross-National Military Deployment and
Basing Data
Description: These functions generate data frames on troop deployments and military basing using U.S. Department of Defense data on overseas military deployments. This package provides functions for pulling country-year troop deployment and basing data. Subsequent versions will hopefully include cross-national data on deploying countries.
Author: Michael Flynn [aut, cre]
Maintainer: Michael Flynn <meflynn@ksu.edu>
Diff between troopdata versions 1.0.2 dated 2024-09-10 and 1.0.3 dated 2025-06-24
DESCRIPTION | 15 +++++++------ MD5 | 20 +++++++++-------- NEWS.md | 10 ++++++++ R/data.R | 1 R/get_troopdata.R | 42 ++++++++++++++++++------------------- README.md | 2 - build/partial.rdb |binary data/troopdata_rebuild_long.rda |binary data/troopdata_rebuild_reports.rda |binary man/troopdata_rebuild_long.Rd | 1 tests/testthat |only tests/testthat.R |only 12 files changed, 53 insertions(+), 38 deletions(-)
Title: Fake Web Apps for HTTP Testing
Description: Create a web app that makes it easier to test web clients
without using the internet. It includes a web app framework with path
matching, parameters and templates. Can parse various 'HTTP' request
bodies. Can send 'JSON' data or files from the disk. Includes a web
app that implements the 'httpbin.org' web service.
Author: Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd] ,
Civetweb contributors [ctb] ,
Redoc contributors [ctb] ,
L. Peter Deutsch [ctb] ,
Martin Purschke [ctb] ,
Aladdin Enterprises [cph] ,
Maelle Salmon [ctb]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between webfakes versions 1.3.2 dated 2025-01-11 and 1.4.0 dated 2025-06-24
webfakes-1.3.2/webfakes/src/Makevars |only webfakes-1.3.2/webfakes/src/Makevars.win |only webfakes-1.3.2/webfakes/tests/testthat/fixtures/output/webfakes_app_process.txt |only webfakes-1.4.0/webfakes/DESCRIPTION | 15 webfakes-1.4.0/webfakes/LICENSE | 2 webfakes-1.4.0/webfakes/MD5 | 435 +++++++- webfakes-1.4.0/webfakes/NEWS.md | 8 webfakes-1.4.0/webfakes/R/app-process.R | 127 +- webfakes-1.4.0/webfakes/R/app.R | 80 - webfakes-1.4.0/webfakes/R/base64.R | 327 +++++- webfakes-1.4.0/webfakes/R/cleancall.R | 1 webfakes-1.4.0/webfakes/R/compat-defer.R | 119 +- webfakes-1.4.0/webfakes/R/digest.R | 5 webfakes-1.4.0/webfakes/R/docs.R | 15 webfakes-1.4.0/webfakes/R/git-app.R | 13 webfakes-1.4.0/webfakes/R/httpbin.R | 511 +++++----- webfakes-1.4.0/webfakes/R/local-app-process.R | 1 webfakes-1.4.0/webfakes/R/mime.R | 1 webfakes-1.4.0/webfakes/R/mw-authorization.R | 22 webfakes-1.4.0/webfakes/R/mw-cgi.R | 30 webfakes-1.4.0/webfakes/R/mw-cookie-parser.R | 9 webfakes-1.4.0/webfakes/R/mw-etag.R | 1 webfakes-1.4.0/webfakes/R/mw-json.R | 15 webfakes-1.4.0/webfakes/R/mw-log.R | 24 webfakes-1.4.0/webfakes/R/mw-multipart.R | 67 - webfakes-1.4.0/webfakes/R/mw-range-parser.R | 30 webfakes-1.4.0/webfakes/R/mw-raw.R | 5 webfakes-1.4.0/webfakes/R/mw-static.R | 17 webfakes-1.4.0/webfakes/R/mw-text.R | 11 webfakes-1.4.0/webfakes/R/mw-urlencoded.R | 5 webfakes-1.4.0/webfakes/R/oauth.R | 282 ++--- webfakes-1.4.0/webfakes/R/package.R | 1 webfakes-1.4.0/webfakes/R/path.R | 14 webfakes-1.4.0/webfakes/R/print.R | 8 webfakes-1.4.0/webfakes/R/rematch2.R | 15 webfakes-1.4.0/webfakes/R/request.R | 5 webfakes-1.4.0/webfakes/R/response.R | 112 +- webfakes-1.4.0/webfakes/R/server.R | 55 - webfakes-1.4.0/webfakes/R/status.R | 1 webfakes-1.4.0/webfakes/R/tmpl-glue.R | 25 webfakes-1.4.0/webfakes/R/utils.R | 19 webfakes-1.4.0/webfakes/R/uuid.R | 1 webfakes-1.4.0/webfakes/README.md | 87 - webfakes-1.4.0/webfakes/cleanup |only webfakes-1.4.0/webfakes/configure |only webfakes-1.4.0/webfakes/configure.win |only webfakes-1.4.0/webfakes/inst/cert |only webfakes-1.4.0/webfakes/inst/examples/hello/app.R | 5 webfakes-1.4.0/webfakes/inst/examples/httpbin/app.R | 1 webfakes-1.4.0/webfakes/inst/examples/send-file/app.R | 1 webfakes-1.4.0/webfakes/inst/examples/static/app.R | 1 webfakes-1.4.0/webfakes/man/how-to.Rd |only webfakes-1.4.0/webfakes/man/introduction.Rd |only webfakes-1.4.0/webfakes/man/new_app.Rd | 7 webfakes-1.4.0/webfakes/man/new_app_process.Rd | 14 webfakes-1.4.0/webfakes/man/server_opts.Rd | 6 webfakes-1.4.0/webfakes/man/webfakes-package.Rd | 2 webfakes-1.4.0/webfakes/src/Makevars.in |only webfakes-1.4.0/webfakes/src/civetweb.c | 6 webfakes-1.4.0/webfakes/src/mbedtls |only webfakes-1.4.0/webfakes/tests/testthat/_snaps/app.md |only webfakes-1.4.0/webfakes/tests/testthat/_snaps/print.md |only webfakes-1.4.0/webfakes/tests/testthat/helper.R | 50 webfakes-1.4.0/webfakes/tests/testthat/setup.R | 1 webfakes-1.4.0/webfakes/tests/testthat/teardown.R | 1 webfakes-1.4.0/webfakes/tests/testthat/test-app-process.R | 1 webfakes-1.4.0/webfakes/tests/testthat/test-app.R | 13 webfakes-1.4.0/webfakes/tests/testthat/test-base64.R | 24 webfakes-1.4.0/webfakes/tests/testthat/test-decode-url.R | 1 webfakes-1.4.0/webfakes/tests/testthat/test-delay.R | 5 webfakes-1.4.0/webfakes/tests/testthat/test-http-methods.R | 18 webfakes-1.4.0/webfakes/tests/testthat/test-httpbin.R | 67 - webfakes-1.4.0/webfakes/tests/testthat/test-https.R |only webfakes-1.4.0/webfakes/tests/testthat/test-local.R | 1 webfakes-1.4.0/webfakes/tests/testthat/test-mime.R | 1 webfakes-1.4.0/webfakes/tests/testthat/test-mw-etag.R | 32 webfakes-1.4.0/webfakes/tests/testthat/test-mw-log.R | 25 webfakes-1.4.0/webfakes/tests/testthat/test-mw-multipart.R | 5 webfakes-1.4.0/webfakes/tests/testthat/test-mw-range-parser.R | 9 webfakes-1.4.0/webfakes/tests/testthat/test-mw-raw.R | 5 webfakes-1.4.0/webfakes/tests/testthat/test-mw-static.R | 7 webfakes-1.4.0/webfakes/tests/testthat/test-mw-urlencoded.R | 1 webfakes-1.4.0/webfakes/tests/testthat/test-oauth.R | 36 webfakes-1.4.0/webfakes/tests/testthat/test-path-matching.R | 16 webfakes-1.4.0/webfakes/tests/testthat/test-print.R | 16 webfakes-1.4.0/webfakes/tests/testthat/test-request.R | 1 webfakes-1.4.0/webfakes/tests/testthat/test-response.R | 7 webfakes-1.4.0/webfakes/tests/testthat/test-threads.R |only webfakes-1.4.0/webfakes/tests/testthat/test-tmpl-glue.R | 5 webfakes-1.4.0/webfakes/tests/testthat/test-uuid.R | 5 90 files changed, 1891 insertions(+), 1026 deletions(-)
Title: Simulation-Based Power Analysis for Factorial Designs
Description: Functions to perform simulations of ANOVA designs of up to three factors. Calculates the observed power and average observed effect size for all main effects and interactions in the ANOVA, and all simple comparisons between conditions. Includes functions for analytic power calculations and additional helper functions that compute effect sizes for ANOVA designs, observed error rates in the simulations, and functions to plot power curves. Please see Lakens, D., & Caldwell, A. R. (2021). "Simulation-Based Power Analysis for Factorial Analysis of Variance Designs". <doi:10.1177/2515245920951503>.
Author: Aaron Caldwell [aut, cre],
Daniel Lakens [aut],
Lisa DeBruine [ctb],
Jonathon Love [ctb],
Frederik Aust [ctb]
Maintainer: Aaron Caldwell <arcaldwell49@gmail.com>
Diff between Superpower versions 0.2.3 dated 2025-05-15 and 0.2.4 dated 2025-06-24
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- inst/doc/ANCOVAs.html | 2 +- inst/doc/compromise_power.html | 4 ++-- inst/doc/emmeans_power.html | 2 +- inst/doc/intro_to_superpower.html | 4 ++-- inst/doc/more_anova_designs.html | 32 ++++++++++++++++---------------- tests/testthat/test-morey.R | 2 +- 8 files changed, 33 insertions(+), 33 deletions(-)
Title: Fit Hidden Markov Models using Template Model Builder
Description: Fitting hidden Markov models using automatic differentiation
and Laplace approximation, allowing for fast inference and flexible covariate
effects (including random effects and smoothing splines) on model parameters.
The package is described by Michelot (2022) <doi:10.48550/arXiv.2211.14139>.
Author: Theo Michelot [aut, cre],
Richard Glennie [aut, ctb]
Maintainer: Theo Michelot <theo.michelot@dal.ca>
Diff between hmmTMB versions 1.0.2 dated 2023-10-24 and 1.1.0 dated 2025-06-24
DESCRIPTION | 15 MD5 | 65 - NAMESPACE | 7 NEWS.md |only R/dist.R | 43 R/dist_def.R | 226 ++- R/hmm.R | 236 ++- R/make_mat.R | 38 R/markovchain.R | 36 R/observation.R | 208 ++- R/utility.R | 199 +++ README.md | 34 build/vignette.rds |binary inst/CITATION |only inst/doc/hmmTMB_list_of_online_resources.Rmd | 24 inst/doc/hmmTMB_list_of_online_resources.pdf |binary inst/examples/random_effects/fixed_effects_only_mod.hmm | 2 inst/examples/random_effects/individual_random_effects.R | 2 inst/examples/random_effects/individual_random_effects_mod.hmm | 4 inst/examples/random_effects/individual_random_effects_truemod.hmm | 4 man/Dist.Rd | 29 man/HMM.Rd | 58 man/MarkovChain.Rd | 30 man/Observation.Rd | 91 + man/check_contiguous.Rd |only man/dvm.Rd |only man/dwrpcauchy.Rd |only man/gdeterminant.Rd |only man/make_cov.Rd |only man/make_matrices.Rd | 6 man/rvm.Rd |only man/rwrpcauchy.Rd |only src/dist.hpp | 32 src/dist_def.hpp | 264 +++- src/hmmTMB.hpp | 604 ++++------ tests/testthat/test_hmm_fixedcov.R | 4 vignettes/hmmTMB_list_of_online_resources.Rmd | 24 vignettes/refs.bib | 55 38 files changed, 1609 insertions(+), 731 deletions(-)
Title: Web Application Framework for R
Description: Makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive prebuilt widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut, cre] ,
Joe Cheng [aut],
JJ Allaire [aut],
Carson Sievert [aut] ,
Barret Schloerke [aut] ,
Yihui Xie [aut],
Jeff Allen [aut],
Jonathan McPherson [aut],
Alan Dipert [aut],
Barbara Borges [aut],
Posit Software, PBC [cph, fnd],
jQuery [...truncated...]
Maintainer: Winston Chang <winston@posit.co>
Diff between shiny versions 1.10.0 dated 2024-12-13 and 1.11.0 dated 2025-06-24
DESCRIPTION | 28 MD5 | 170 NEWS.md | 54 R/bind-cache.R | 4 R/bootstrap.R | 2 R/conditions.R | 20 R/extended-task.R | 77 R/input-numeric.R | 36 R/input-password.R | 27 R/input-submit.R | 2 R/input-text.R | 34 R/input-textarea.R | 47 R/render-plot.R | 2 R/shiny-options.R | 18 R/shinyapp.R | 114 R/shinywrappers.R | 14 R/test.R | 8 R/update-input.R | 56 R/utils.R | 37 R/version_jquery.R | 2 R/version_jqueryui.R | 2 inst/app_template/tests/testthat/test-shinytest2.R | 2 inst/examples-shiny/08_html/www/index.html | 6 inst/www/shared/busy-indicators/busy-indicators.css | 4 inst/www/shared/datepicker/js/bootstrap-datepicker.min.js | 2 inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js | 2 inst/www/shared/jquery.js | 2107 inst/www/shared/jquery.min.js | 4 inst/www/shared/jquery.min.js.map | 2 inst/www/shared/jqueryui/AUTHORS.txt | 16 inst/www/shared/jqueryui/LICENSE.txt | 2 inst/www/shared/jqueryui/images/ui-icons_444444_256x240.png |binary inst/www/shared/jqueryui/images/ui-icons_555555_256x240.png |binary inst/www/shared/jqueryui/images/ui-icons_777620_256x240.png |binary inst/www/shared/jqueryui/images/ui-icons_777777_256x240.png |binary inst/www/shared/jqueryui/images/ui-icons_cc0000_256x240.png |binary inst/www/shared/jqueryui/images/ui-icons_ffffff_256x240.png |binary inst/www/shared/jqueryui/index.html | 2 inst/www/shared/jqueryui/jquery-ui.css | 42 inst/www/shared/jqueryui/jquery-ui.js | 1339 inst/www/shared/jqueryui/jquery-ui.min.css | 10 inst/www/shared/jqueryui/jquery-ui.min.js | 8 inst/www/shared/jqueryui/jquery-ui.structure.css | 35 inst/www/shared/jqueryui/jquery-ui.structure.min.css | 8 inst/www/shared/jqueryui/jquery-ui.theme.css | 21 inst/www/shared/jqueryui/jquery-ui.theme.min.css | 8 inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js | 2 inst/www/shared/shiny-autoreload.js | 5 inst/www/shared/shiny-autoreload.js.map | 8 inst/www/shared/shiny-showcase.css | 2 inst/www/shared/shiny-showcase.js | 4 inst/www/shared/shiny-showcase.js.map | 8 inst/www/shared/shiny-testmode.js | 4 inst/www/shared/shiny-testmode.js.map | 4 inst/www/shared/shiny.js |28774 +--------- inst/www/shared/shiny.js.map | 8 inst/www/shared/shiny.min.css | 4 inst/www/shared/shiny.min.js | 449 inst/www/shared/shiny.min.js.map | 8 inst/www/shared/shiny_scss/shiny.scss | 8 man/ExtendedTask.Rd | 23 man/bindCache.Rd | 4 man/downloadHandler.Rd | 10 man/numericInput.Rd | 14 man/passwordInput.Rd | 20 man/renderImage.Rd | 5 man/renderPrint.Rd | 3 man/renderUI.Rd | 2 man/shiny-package.Rd | 2 man/shinyOptions.Rd | 20 man/textAreaInput.Rd | 18 man/textInput.Rd | 20 tests/testthat/_snaps/tabPanel.md | 4 tests/testthat/test-bootstrap.r | 14 tests/testthat/test-busy-indication.R | 2 tests/testthat/test-input-select.R | 34 tests/testthat/test-plot-coordmap.R | 4 tests/testthat/test-plot-png.R | 2 tests/testthat/test-reactivity.r | 12 tests/testthat/test-render-functions.R | 4 tests/testthat/test-stacks.R | 6 tests/testthat/test-tabPanel.R | 4 tests/testthat/test-test-runTests.R | 2 tests/testthat/test-test-server-app.R | 4 tests/testthat/test-update-input.R | 23 tests/testthat/test-utils.R | 2 86 files changed, 8137 insertions(+), 25783 deletions(-)
Title: Facilitate Analysis of Proteomic Data from Olink
Description: A collection of functions to facilitate analysis of proteomic
data from Olink, primarily NPX data that has been exported from Olink
Software. The functions also work on QUANT data from
Olink by log- transforming the QUANT data. The functions are focused
on reading data, facilitating data wrangling and quality control
analysis, performing statistical analysis and generating figures to
visualize the results of the statistical analysis. The goal of this
package is to help users extract biological insights from proteomic
data run on the Olink platform.
Author: Kathleen Nevola [aut, cre] ,
Marianne Sandin [aut] ,
Jamey Guess [aut] ,
Simon Forsberg [aut] ,
Christoffer Cambronero [aut] ,
Pascal Pucholt [aut] ,
Boxi Zhang [aut] ,
Masoumeh Sheikhi [aut] ,
Klev Diamanti [aut] ,
Amrita Kar [aut] ,
Lei Conze [aut] [...truncated...]
Maintainer: Kathleen Nevola <biostattools@olink.com>
Diff between OlinkAnalyze versions 4.2.0 dated 2025-02-24 and 4.3.0 dated 2025-06-24
OlinkAnalyze-4.2.0/OlinkAnalyze/tests/testthat/_snaps/olink_Pathway_Heatmap |only OlinkAnalyze-4.2.0/OlinkAnalyze/tests/testthat/_snaps/olink_Pathway_Visualization |only OlinkAnalyze-4.3.0/OlinkAnalyze/DESCRIPTION | 50 OlinkAnalyze-4.3.0/OlinkAnalyze/MD5 | 127 -- OlinkAnalyze-4.3.0/OlinkAnalyze/NEWS.md | 14 OlinkAnalyze-4.3.0/OlinkAnalyze/R/Olink_anova.R | 2 OlinkAnalyze-4.3.0/OlinkAnalyze/R/Olink_boxplot.R | 16 OlinkAnalyze-4.3.0/OlinkAnalyze/R/Olink_bridgeselector.R | 4 OlinkAnalyze-4.3.0/OlinkAnalyze/R/Olink_heatmap.R | 3 OlinkAnalyze-4.3.0/OlinkAnalyze/R/Olink_one_non_parametric.R | 5 OlinkAnalyze-4.3.0/OlinkAnalyze/R/Olink_ordinalRegression.R | 6 OlinkAnalyze-4.3.0/OlinkAnalyze/R/Olink_ttest.R | 3 OlinkAnalyze-4.3.0/OlinkAnalyze/R/Olink_wilcox.R | 3 OlinkAnalyze-4.3.0/OlinkAnalyze/R/dist_plot.R | 9 OlinkAnalyze-4.3.0/OlinkAnalyze/R/globals.R | 2 OlinkAnalyze-4.3.0/OlinkAnalyze/R/linear_mixed_model.R | 8 OlinkAnalyze-4.3.0/OlinkAnalyze/R/npxCheck.R | 5 OlinkAnalyze-4.3.0/OlinkAnalyze/R/npx_check_uniprot_dups.R |only OlinkAnalyze-4.3.0/OlinkAnalyze/R/olink_Pathway_Enrichment.R | 59 OlinkAnalyze-4.3.0/OlinkAnalyze/R/olink_bridgeability_plot.R | 631 ++++++---- OlinkAnalyze-4.3.0/OlinkAnalyze/R/olink_lod.R | 101 - OlinkAnalyze-4.3.0/OlinkAnalyze/R/olink_normalization.R | 46 OlinkAnalyze-4.3.0/OlinkAnalyze/R/olink_normalization_product.R | 251 ++- OlinkAnalyze-4.3.0/OlinkAnalyze/R/olink_normalization_utils.R | 237 ++- OlinkAnalyze-4.3.0/OlinkAnalyze/R/olink_qc_plot.R | 8 OlinkAnalyze-4.3.0/OlinkAnalyze/R/pca_plot.R | 2 OlinkAnalyze-4.3.0/OlinkAnalyze/R/read_npx_parquet.R | 6 OlinkAnalyze-4.3.0/OlinkAnalyze/R/umap_plot.R | 3 OlinkAnalyze-4.3.0/OlinkAnalyze/inst/doc/LOD.html | 2 OlinkAnalyze-4.3.0/OlinkAnalyze/inst/doc/OutlierExclusion.html | 4 OlinkAnalyze-4.3.0/OlinkAnalyze/inst/doc/Vignett.html | 4 OlinkAnalyze-4.3.0/OlinkAnalyze/inst/doc/bridging_crossproduct.R | 2 OlinkAnalyze-4.3.0/OlinkAnalyze/inst/doc/bridging_crossproduct.Rmd | 2 OlinkAnalyze-4.3.0/OlinkAnalyze/inst/doc/bridging_crossproduct.html | 10 OlinkAnalyze-4.3.0/OlinkAnalyze/inst/doc/bridging_introduction.R | 2 OlinkAnalyze-4.3.0/OlinkAnalyze/inst/doc/bridging_introduction.Rmd | 2 OlinkAnalyze-4.3.0/OlinkAnalyze/inst/doc/bridging_introduction.html | 98 - OlinkAnalyze-4.3.0/OlinkAnalyze/inst/doc/plate_randomizer.html | 4 OlinkAnalyze-4.3.0/OlinkAnalyze/man/olink_bridgeability_plot.Rd | 94 - OlinkAnalyze-4.3.0/OlinkAnalyze/man/olink_norm_input_assay_overlap.Rd | 2 OlinkAnalyze-4.3.0/OlinkAnalyze/man/olink_norm_input_check_samples.Rd | 2 OlinkAnalyze-4.3.0/OlinkAnalyze/man/olink_norm_input_clean_assays.Rd | 2 OlinkAnalyze-4.3.0/OlinkAnalyze/man/olink_norm_input_cross_product.Rd | 2 OlinkAnalyze-4.3.0/OlinkAnalyze/man/olink_normalization_product_format.Rd | 52 OlinkAnalyze-4.3.0/OlinkAnalyze/man/olink_normalization_qs.Rd | 4 OlinkAnalyze-4.3.0/OlinkAnalyze/tests/testthat.R | 3 OlinkAnalyze-4.3.0/OlinkAnalyze/tests/testthat/Rplots.pdf |only OlinkAnalyze-4.3.0/OlinkAnalyze/tests/testthat/_snaps/Read_NPX_data.md | 24 OlinkAnalyze-4.3.0/OlinkAnalyze/tests/testthat/_snaps/olink_bridgeability_plot |only OlinkAnalyze-4.3.0/OlinkAnalyze/tests/testthat/data/example_3k_data.R | 2 OlinkAnalyze-4.3.0/OlinkAnalyze/tests/testthat/data/ref_results_norm.R | 7 OlinkAnalyze-4.3.0/OlinkAnalyze/tests/testthat/helper-get_example_olink_data.R | 5 OlinkAnalyze-4.3.0/OlinkAnalyze/tests/testthat/test-Olink_anova.R | 3 OlinkAnalyze-4.3.0/OlinkAnalyze/tests/testthat/test-Olink_bridgeselector.R | 22 OlinkAnalyze-4.3.0/OlinkAnalyze/tests/testthat/test-npxProcessing.R | 29 OlinkAnalyze-4.3.0/OlinkAnalyze/tests/testthat/test-olink_Pathway_Enrichment.R | 491 ++++++- OlinkAnalyze-4.3.0/OlinkAnalyze/tests/testthat/test-olink_Pathway_Heatmap.R | 2 OlinkAnalyze-4.3.0/OlinkAnalyze/tests/testthat/test-olink_Pathway_Visualization.R | 2 OlinkAnalyze-4.3.0/OlinkAnalyze/tests/testthat/test-olink_bridgeability_plot.R |only OlinkAnalyze-4.3.0/OlinkAnalyze/tests/testthat/test-olink_normalization.R | 68 - OlinkAnalyze-4.3.0/OlinkAnalyze/tests/testthat/test-olink_normalization_n.R | 12 OlinkAnalyze-4.3.0/OlinkAnalyze/tests/testthat/test-olink_normalization_product.R | 585 ++++++--- OlinkAnalyze-4.3.0/OlinkAnalyze/tests/testthat/test-olink_normalization_utils.R | 242 +++ OlinkAnalyze-4.3.0/OlinkAnalyze/vignettes/bridging_crossproduct.Rmd | 2 OlinkAnalyze-4.3.0/OlinkAnalyze/vignettes/bridging_introduction.Rmd | 2 65 files changed, 2261 insertions(+), 1129 deletions(-)
Title: Cyclic Coordinate Descent for Logistic, Poisson and Survival
Analysis
Description: This model fitting tool incorporates cyclic coordinate descent and
majorization-minimization approaches to fit a variety of regression models
found in large-scale observational healthcare data. Implementations focus
on computational optimization and fine-scale parallelization to yield
efficient inference in massive datasets. Please see:
Suchard, Simpson, Zorych, Ryan and Madigan (2013) <doi:10.1145/2414416.2414791>.
Author: Marc A. Suchard [aut, cre],
Martijn J. Schuemie [aut],
Trevor R. Shaddox [aut],
Yuxi Tian [aut],
Jianxiao Yang [aut],
Eric Kawaguchi [aut],
Sushil Mittal [ctb],
Observational Health Data Sciences and Informatics [cph],
Marcus Geelnard [cph, ctb] ,
Ru [...truncated...]
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Diff between Cyclops versions 3.5.1 dated 2025-04-11 and 3.5.2 dated 2025-06-24
Cyclops-3.5.1/Cyclops/tests/testthat/test-largeProfileLikelihood.R |only Cyclops-3.5.2/Cyclops/DESCRIPTION | 6 +++--- Cyclops-3.5.2/Cyclops/MD5 | 5 ++--- Cyclops-3.5.2/Cyclops/NEWS.md | 5 +++++ 4 files changed, 10 insertions(+), 6 deletions(-)
Title: Stochastic Search Inconsistency Factor Selection
Description: Evaluating the consistency assumption of Network Meta-Analysis both globally and locally in the Bayesian framework. Inconsistencies are located by applying Bayesian variable selection to the inconsistency factors. The implementation of the method is described by Seitidis et al. (2023) <doi:10.1002/sim.9891>.
Author: Georgios Seitidis [aut, cre] ,
Stavros Nikolakopoulos [aut] ,
Ioannis Ntzoufras [aut] ,
Dimitris Mavridis [aut]
Maintainer: Georgios Seitidis <g.seitidis@uoi.gr>
Diff between ssifs versions 1.0.4 dated 2025-02-04 and 1.0.5 dated 2025-06-24
DESCRIPTION | 21 +++++++++++--------- MD5 | 16 +++++++-------- NEWS.md | 2 + R/subnet.R | 21 +++++++------------- README.md | 4 +-- build/vignette.rds |binary inst/doc/An_introduction_to_ssifs.Rmd | 2 - inst/doc/An_introduction_to_ssifs.html | 34 ++++++++++++++++----------------- vignettes/An_introduction_to_ssifs.Rmd | 2 - 9 files changed, 51 insertions(+), 51 deletions(-)
Title: 'Rcpp' Bindings for 'Redis' using the 'hiredis' Library
Description: Connection to the 'Redis' (or 'Valkey') key/value store
using the C-language client library 'hiredis' (included as a fallback)
with 'MsgPack' encoding provided via 'RcppMsgPack' headers. It now
also includes the pub/sub functions from the 'rredis' package.
Author: Dirk Eddelbuettel [aut, cre] ,
Bryan Lewis [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppRedis versions 0.2.5 dated 2025-03-26 and 0.2.6 dated 2025-06-24
ChangeLog | 39 +++++ DESCRIPTION | 19 +- MD5 | 33 ++--- README.md | 10 + build/vignette.rds |binary configure | 18 +- configure.ac | 2 inst/NEWS.Rd | 9 + inst/demos/queueDemo.R |only inst/doc/market-monitoring.pdf |binary inst/doc/redis-introduction.pdf |binary inst/tinytest/test_basics.R | 3 inst/tinytest/test_exec.R | 3 inst/tinytest/test_exists.R | 3 inst/tinytest/test_expire.R | 2 inst/tinytest/test_list.R | 40 +++++- inst/tinytest/test_set.R | 3 src/Redis.cpp | 262 ++++++++++++++++++---------------------- 18 files changed, 255 insertions(+), 191 deletions(-)
Title: Data Quality Reporting for Temporal Datasets
Description: Generate reports that enable quick visual review of
temporal shifts in record-level data. Time series plots showing aggregated
values are automatically created for each data field (column) depending on its
contents (e.g. min/max/mean values for numeric data, no. of distinct
values for categorical data), as well as overviews for missing values,
non-conformant values, and duplicated rows. The resulting reports are shareable
and can contribute to forming a transparent record of the entire analysis process.
It is designed with Electronic Health Records in mind, but can be used for
any type of record-level temporal data (i.e. tabular data where each row represents
a single "event", one column contains the "event date", and other columns
contain any associated values for the event).
Author: T. Phuong Quan [aut, cre] ,
Jack Cregan [ctb],
University of Oxford [cph],
National Institute for Health Research [fnd],
Brad Cannell [rev]
Maintainer: T. Phuong Quan <phuong.quan@ndm.ox.ac.uk>
Diff between daiquiri versions 1.1.1 dated 2023-07-18 and 1.2.0 dated 2025-06-24
DESCRIPTION | 11 MD5 | 36 +- NAMESPACE | 1 NEWS.md | 12 R/field_types.R | 272 +++++++++++++----- R/reports.R | 15 - R/source_data.R | 36 ++ README.md | 2 build/vignette.rds |binary inst/doc/daiquiri.R | 136 ++++----- inst/doc/daiquiri.Rmd | 2 inst/doc/daiquiri.html | 19 - inst/rmd/logo.png |only inst/rmd/report_htmldoc.Rmd | 24 + man/field_types_advanced.Rd |only tests/testthat/_snaps/field_types.md | 50 +-- tests/testthat/_snaps/source_data.md | 509 +++++++++++++++++------------------ tests/testthat/test-field_types.R | 60 ++++ tests/testthat/test-source_data.R | 62 ++++ vignettes/daiquiri.Rmd | 2 20 files changed, 779 insertions(+), 470 deletions(-)
Title: Utility Functions and Development Tools for the Admiral Package
Family
Description: Utility functions to check data, variables and conditions for
functions used in 'admiral' and 'admiral' extension packages.
Additional utility helper functions to assist developers with
maintaining documentation, testing and general upkeep of 'admiral' and
'admiral' extension packages.
Author: Ben Straub [aut, cre],
Stefan Bundfuss [aut] ,
Jeffrey Dickinson [aut],
Ross Farrugia [aut],
Fanny Gautier [aut],
Edoardo Mancini [aut] ,
Gordon Miller [aut],
Daniel Sjoberg [aut] ,
Stefan Thoma [aut] ,
F. Hoffmann-La Roche AG [cph, fnd],
GlaxoSmithK [...truncated...]
Maintainer: Ben Straub <ben.x.straub@gsk.com>
Diff between admiraldev versions 1.2.0 dated 2025-01-15 and 1.3.0 dated 2025-06-24
DESCRIPTION | 26 +--- MD5 | 183 +++++++++++++++-------------- NAMESPACE | 39 ++++-- NEWS.md | 30 ++++ R/admiraldev-package.R | 24 ++- R/assertions.R | 16 +- R/dataset_vignette.R | 8 - R/demo_fun.R |only R/expect_dfs_equal.R | 3 R/get.R | 4 R/process_set_values_to.R | 4 R/quo.R | 31 +++- R/roclet_rdx.R |only README.md | 18 +- build/vignette.rds |binary inst/WORDLIST | 6 inst/doc/admiraldev.Rmd | 19 ++- inst/doc/admiraldev.html | 18 ++ inst/doc/package_extensions.html | 2 inst/doc/rcmd_issues.Rmd | 3 inst/doc/rcmd_issues.html | 2 man/add_suffix_to_vars.Rd | 17 ++ man/admiraldev-package.Rd | 3 man/arg_name.Rd | 6 man/assert_atomic_vector.Rd | 24 +++ man/assert_character_scalar.Rd | 36 ++++- man/assert_character_vector.Rd | 36 ++++- man/assert_data_frame.Rd | 36 ++++- man/assert_date_var.Rd | 30 +++- man/assert_date_vector.Rd | 24 +++ man/assert_expr.Rd | 24 +++ man/assert_expr_list.Rd | 36 ++++- man/assert_filter_cond.Rd | 24 +++ man/assert_function.Rd | 30 +++- man/assert_integer_scalar.Rd | 32 ++++- man/assert_list_element.Rd | 42 +++++- man/assert_list_of.Rd | 36 ++++- man/assert_logical_scalar.Rd | 24 +++ man/assert_named.Rd | 24 +++ man/assert_numeric_vector.Rd | 30 +++- man/assert_one_to_one.Rd | 29 +++- man/assert_param_does_not_exist.Rd | 24 +++ man/assert_s3_class.Rd | 30 +++- man/assert_same_type.Rd | 28 +++- man/assert_symbol.Rd | 24 +++ man/assert_unit.Rd | 39 ++++-- man/assert_vars.Rd | 30 +++- man/assert_varval_list.Rd | 42 +++++- man/backquote.Rd | 6 man/capture_message.Rd |only man/capture_output.Rd |only man/contains_vars.Rd | 6 man/convert_dtm_to_dtc.Rd | 6 man/dataset_vignette.Rd | 22 ++- man/demo_fun.Rd |only man/dquote.Rd | 6 man/enumerate.Rd | 18 ++ man/execute_example.Rd |only man/expect_dfs_equal.Rd | 25 +++ man/expr_c.Rd | 6 man/extract_vars.Rd | 12 + man/filter_if.Rd | 12 + man/friendly_type_of.Rd | 18 ++ man/get_constant_vars.Rd | 19 ++- man/get_dataset.Rd | 6 man/get_duplicates.Rd | 6 man/get_new_tmp_var.Rd | 12 + man/get_param_tag.Rd |only man/get_source_vars.Rd | 6 man/grapes-notin-grapes.Rd | 12 + man/grapes-or-grapes.Rd | 12 + man/is_auto.Rd | 6 man/is_order_vars.Rd | 6 man/is_valid_dtc.Rd | 6 man/joins.Rd | 36 ++++- man/parse_code.Rd |only man/process_set_values_to.Rd | 18 ++ man/rdx_roclet.Rd |only man/remove_tmp_vars.Rd | 6 man/replace_symbol_in_expr.Rd | 23 +++ man/replace_values_by_names.Rd | 6 man/roxygen/rdx_meta.R |only man/squote.Rd | 6 man/suppress_warning.Rd | 12 + man/transform_examplesx.Rd |only man/transform_param.Rd |only man/vars2chr.Rd | 6 man/warn_if_incomplete_dtc.Rd | 12 + man/warn_if_inconsistent_list.Rd | 24 +++ man/warn_if_invalid_dtc.Rd | 12 + man/warn_if_vars_exist.Rd | 12 + man/what_is_it.Rd | 6 tests/testthat/_snaps/roclet_rdx |only tests/testthat/fixtures |only tests/testthat/test-compat_friendly_type.R | 2 tests/testthat/test-quo.R | 20 ++- tests/testthat/test-roclet_rdx.R |only tests/testthat/test-what.R | 2 vignettes/admiraldev.Rmd | 19 ++- vignettes/rcmd_issues.Rmd | 3 100 files changed, 1272 insertions(+), 377 deletions(-)
Title: Single Trial Analysis (STA) of Field Trials
Description: Phenotypic analysis of field trials using mixed models with and
without spatial components. One of a series of statistical genetic packages
for streamlining the analysis of typical plant breeding experiments developed
by Biometris.
Some functions have been created to be used in conjunction with the R
package 'asreml' for the 'ASReml' software, which can be obtained upon
purchase from 'VSN' international (<https://vsni.co.uk/software/asreml-r/>).
Author: Bart-Jan van Rossum [aut, cre] ,
Fred van Eeuwijk [ctb] ,
Martin Boer [ctb] ,
Marcos Malosetti [ctb] ,
Daniela Bustos-Korts [ctb] ,
Emilie J. Millet [ctb] ,
Joao Paulo [ctb] ,
Maikel Verouden [ctb] ,
Willem Kruijer [ctb] ,
Ron Wehrens [ctb] ,
Choazhi [...truncated...]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenSTA versions 1.0.14 dated 2024-10-14 and 1.0.15 dated 2025-06-24
DESCRIPTION | 33 +++++++++++++++-------------- MD5 | 28 ++++++++++++------------ NEWS.md | 5 ++++ R/createSTA.R | 12 +++++++--- R/createTD.R | 4 +-- R/extractSTA.R | 2 - R/fitTD.R | 2 - R/layoutPlot.R | 6 ++--- R/outliers.R | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/statgenSTA.R | 44 +++++++++++++++++++-------------------- inst/doc/statgenSTA.html | 26 +++++++++++------------ tests/testthat/Rplots.pdf |binary tests/testthat/test-layoutPlot.R | 2 - 15 files changed, 88 insertions(+), 78 deletions(-)
Title: Genotype by Environment (GxE) Analysis
Description: Analysis of multi environment data of plant breeding experiments
following the analyses described in Malosetti, Ribaut,
and van Eeuwijk (2013), <doi:10.3389/fphys.2013.00044>.
One of a series of statistical genetic packages for streamlining the analysis of
typical plant breeding experiments developed by Biometris.
Some functions have been created to be used in conjunction with the R
package 'asreml' for the 'ASReml' software, which can be obtained upon
purchase from 'VSN' international (<https://vsni.co.uk/software/asreml-r/>).
Author: Bart-Jan van Rossum [aut, cre],
Fred van Eeuwijk [ctb] ,
Martin Boer [ctb],
Marcos Malosetti [ctb] ,
Daniela Bustos-Korts [ctb] ,
Emilie J Millet [ctb] ,
Joao Paulo [ctb] ,
Maikel Verouden [ctb] ,
Willem Kruijer [ctb] ,
Ron Wehrens [ctb] ,
Choazhi Zh [...truncated...]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenGxE versions 1.0.9 dated 2024-09-18 and 1.0.10 dated 2025-06-24
DESCRIPTION | 27 +++--- MD5 | 56 ++++++------ NEWS.md | 5 + R/createAMMI.R | 8 - R/createFW.R | 8 - R/createMegaEnv.R | 2 R/createStability.R | 4 R/createVarComp.R | 66 +++++++++------ R/createVarCov.R | 6 - R/gxeAmmi.R | 2 R/gxeFw.R | 2 R/gxeMegaEnv.R | 2 R/gxeStability.R | 2 R/gxeVarComp.R | 8 + R/gxeVarCov.R | 2 R/multmissing.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/statgenGxE.R | 46 +++++----- inst/doc/statgenGxE.Rmd | 8 - inst/doc/statgenGxE.html | 16 +-- man/createVarComp.Rd | 1 tests/testthat/Rplots.pdf |binary tests/testthat/test-gxeAmmi.R | 16 +++ tests/testthat/test-gxeFW.R | 18 ++++ tests/testthat/test-gxeVarComp.R | 170 ++++++++++++++++++++++++--------------- tests/testthat/test-gxeVarCov.R | 17 +++ tests/testthat/test-plots.R | 27 ++++-- vignettes/statgenGxE.Rmd | 8 - 29 files changed, 331 insertions(+), 198 deletions(-)
Title: Simulate Data from a DAG and Associated Node Information
Description: Simulate complex data from a given directed acyclic graph and information about each individual node.
Root nodes are simply sampled from the specified distribution. Child Nodes are simulated according to
one of many implemented regressions, such as logistic regression, linear
regression, poisson regression and more. Also includes a comprehensive framework for discrete-time
simulation, which can generate even more complex longitudinal data. For more details, see
Robin Denz, Nina Timmesfeld (2025) <doi:10.48550/arXiv.2506.01498>.
Author: Robin Denz [aut, cre],
Katharina Meiszl [aut]
Maintainer: Robin Denz <robin.denz@rub.de>
Diff between simDAG versions 0.3.1 dated 2025-05-28 and 0.3.2 dated 2025-06-24
DESCRIPTION | 11 ++++++----- MD5 | 36 ++++++++++++++++++++++-------------- NEWS.md | 7 +++++++ README.md | 18 ++++++++---------- build/vignette.rds |binary inst/CITATION | 10 +++++----- inst/doc/simDAG.R |only inst/doc/simDAG.Rmd |only inst/doc/simDAG.html |only inst/doc/v_sim_discrete_time.Rmd | 4 +++- inst/doc/v_sim_discrete_time.html | 5 ++++- inst/doc/v_sim_from_dag.Rmd | 6 +++--- inst/doc/v_sim_from_dag.html | 15 +++++++++------ man/simDAG.Rd | 4 +++- man/sim_discrete_time.Rd | 6 ++++-- man/sim_from_dag.Rd | 7 +++++-- vignettes/images_v_joss |only vignettes/simDAG.Rmd |only vignettes/v_sim_discrete_time.Rmd | 4 +++- vignettes/v_sim_from_dag.Rmd | 6 +++--- 20 files changed, 85 insertions(+), 54 deletions(-)
Title: Data Wrangling for Antimicrobial Resistance Studies
Description: Designed for analyzing the Medical Information Mart for Intensive Care(MIMIC) dataset,
a repository of freely accessible electronic health records. MIMER(MIMIC-enabled Research) package, offers
a suite of data wrangling functions tailored specifically for preparing the dataset for research purposes,
particularly in antimicrobial resistance(AMR) studies. It simplifies complex data manipulation tasks, allowing
researchers to focus on their primary inquiries without being bogged down by wrangling complexities.
Author: Anoop Velluva [aut, cre] ,
Alessandro Gerada [ctb] ,
Alexander Howard [ctb]
Maintainer: Anoop Velluva <anoop.velluva@liverpool.ac.uk>
Diff between MIMER versions 1.0.3 dated 2024-06-16 and 1.0.4 dated 2025-06-24
DESCRIPTION | 15 MD5 | 14 NEWS.md | 2 R/common_utils.R | 2 R/convert_antibiotics.R | 5 inst/extdata/combined_key.csv |19178 +++++++++++++++--------------- man/ndc_is_antimicrobial.Rd | 4 tests/testthat/test-convert_antibiotics.R | 2 8 files changed, 9697 insertions(+), 9525 deletions(-)
Title: Simplifies Exploratory Data Analysis
Description: Interactive data exploration with one line of code, automated
reporting or use an easy to remember set of tidy functions for low
code exploratory data analysis.
Author: Roland Krasser [aut, cre]
Maintainer: Roland Krasser <roland.krasser@gmail.com>
Diff between explore versions 1.3.4 dated 2025-03-30 and 1.3.5 dated 2025-06-24
DESCRIPTION | 6 MD5 | 96 +++---- R/tools.R | 30 ++ R/use-data.R | 14 - build/vignette.rds |binary inst/doc/abtest.html | 41 +-- inst/doc/clean-drop.html | 39 +- inst/doc/data.R | 4 inst/doc/data.Rmd | 5 inst/doc/data.html | 545 ++++++++++++++++++++--------------------- inst/doc/describe.html | 49 +-- inst/doc/explain.html | 95 +++---- inst/doc/explore-mtcars.html | 49 +-- inst/doc/explore-penguins.html | 29 -- inst/doc/explore-titanic.html | 41 +-- inst/doc/explore.R | 26 - inst/doc/explore.html | 89 +++--- inst/doc/predict.html | 105 +++---- inst/doc/report-target.R | 2 inst/doc/report-target.html | 27 -- inst/doc/report-targetpct.R | 2 inst/doc/report-targetpct.html | 27 -- inst/doc/report.R | 2 inst/doc/report.html | 25 - inst/doc/tips-tricks.R | 18 - inst/doc/tips-tricks.Rmd | 1 inst/doc/tips-tricks.html | 67 ++--- man/check_vec_low_variance.Rd | 50 +-- man/create_data_abtest.Rd | 90 +++--- man/create_data_esoteric.Rd | 72 ++--- man/cut_vec_num_avg.Rd | 38 +- man/drop_obs_if.Rd | 46 +-- man/drop_obs_with_na.Rd | 44 +-- man/drop_var_by_names.Rd | 46 +-- man/drop_var_low_variance.Rd | 46 +-- man/drop_var_no_variance.Rd | 42 +-- man/drop_var_not_numeric.Rd | 42 +-- man/drop_var_with_na.Rd | 42 +-- man/explore-package.Rd | 1 man/explore_col.Rd | 106 +++---- man/get_color.Rd | 72 ++--- man/interact.Rd | 54 ++-- man/log_info_if.Rd | 38 +- man/show_color.Rd | 42 +-- man/use_data_penguins.Rd | 6 man/use_data_wordle.Rd | 42 +-- man/yyyymm_calc.Rd | 54 ++-- vignettes/data.Rmd | 5 vignettes/tips-tricks.Rmd | 1 49 files changed, 1192 insertions(+), 1221 deletions(-)
Title: Handling and Analysing EQ-5d Data
Description: The EQ-5D is a widely-used standarized instrument for measuring Health Related Quality Of Life (HRQOL),
developed by the EuroQol group <https://euroqol.org/>. It assesses five dimensions; mobility, self-care,
usual activities, pain/discomfort, and anxiety/depression, using either a three-level (EQ-5D-3L) or five-level (EQ-5D-5L) scale.
Scores from these dimensions are commonly converted into a single utility index using country-specific value sets,
which are critical in clinical and economic evaluations of healthcare and in population health surveys.
The eq5dsuite package enables users to calculate utility index values for the EQ-5D instruments,
including crosswalk utilities using the original crosswalk developed by van Hout et al. (2012) <doi:10.1016/j.jval.2012.02.008>
(mapping EQ-5D-5L responses to EQ-5D-3L index values), or the recently developed reverse crosswalk
by van Hout et al. (2021) <doi:10.1016/j.jval.2021.03.009> (mapping EQ-5D-3L responses
to EQ-5D-5L in [...truncated...]
Author: Kim Rand [aut, cre] ,
Iryna Schlackow [aut] ,
Anabel Estevez-Carrillo [aut]
Maintainer: Kim Rand <krand@mathsinhealth.com>
Diff between eq5dsuite versions 1.0.0 dated 2024-05-21 and 1.0.1 dated 2025-06-24
DESCRIPTION | 17 MD5 | 106 +-- NAMESPACE | 6 NEWS.md |only R/EQ_functions.R | 273 +++++--- R/data.R | 12 R/eq5d_aux.R | 37 - R/eq5d_devlin.R | 1359 ++++++++++++++++++++++++++++++++------------ R/eqxw.R | 96 +++ R/init.R | 11 R/sysdata.rda |binary R/utils.R | 44 + data/example_data.rda |binary man/dot-get_names.Rd | 1 man/dot-pchc_plot_by_dim.Rd | 12 man/dot-pchctab.Rd | 7 man/dot-prep_eq5d.Rd | 2 man/eq5d3l.Rd | 50 - man/eq5d5l.Rd | 50 - man/eq5dy3l.Rd | 54 - man/eqvs_add.Rd | 26 man/eqvs_drop.Rd | 13 man/eqvs_load.Rd | 34 - man/eqxw_UK.Rd |only man/example_data.Rd | 12 man/figure_1_2_1.Rd | 85 +- man/figure_1_2_2.Rd | 86 +- man/figure_1_2_3.Rd | 83 +- man/figure_1_2_4.Rd | 85 +- man/figure_1_2_5.Rd |only man/figure_1_3_1.Rd | 64 +- man/figure_1_3_2.Rd | 63 +- man/figure_1_4_1.Rd |only man/figure_2_1.Rd | 2 man/figure_2_2.Rd | 2 man/figure_3_1.Rd | 9 man/figure_3_2.Rd | 8 man/figure_3_3.Rd | 97 +-- man/figure_3_4.Rd | 63 +- man/figure_3_5.Rd | 80 +- man/table_1_1_1.Rd | 7 man/table_1_1_2.Rd | 8 man/table_1_1_3.Rd | 59 + man/table_1_2_1.Rd | 9 man/table_1_2_2.Rd | 83 +- man/table_1_2_3.Rd | 83 +- man/table_1_2_4.Rd | 64 +- man/table_1_3_1.Rd | 61 + man/table_1_3_2.Rd | 53 - man/table_1_3_3.Rd | 63 +- man/table_1_3_4.Rd | 60 + man/table_2_1.Rd | 57 + man/table_2_2.Rd | 52 - man/table_3_1.Rd | 11 man/table_3_2.Rd | 26 man/table_3_3.Rd | 105 +-- 56 files changed, 2417 insertions(+), 1333 deletions(-)
Title: Direct Labels for Multicolor Plots
Description: An extensible framework
for automatically placing direct labels onto multicolor 'lattice' or
'ggplot2' plots.
Label positions are described using Positioning Methods
which can be re-used across several different plots.
There are heuristics for examining "trellis" and "ggplot" objects
and inferring an appropriate Positioning Method.
Author: Toby Dylan Hocking [aut, cre]
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Diff between directlabels versions 2025.5.20 dated 2025-05-20 and 2025.6.24 dated 2025-06-24
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS | 4 ++++ R/ggplot2.R | 6 +++--- build/vignette.rds |binary inst/doc/examples.R | 10 ++++------ inst/doc/examples.Rmd | 10 ++++------ inst/doc/examples.html | 27 +++++++++++---------------- vignettes/examples.Rmd | 10 ++++------ 9 files changed, 41 insertions(+), 48 deletions(-)
Title: Visualization of BART and BARP using SHAP
Description: Complex machine learning models are often difficult to interpret. Shapley values serve as a powerful tool to understand and explain why a model makes a particular prediction. This package computes variable contributions using permutation-based Shapley values for Bayesian Additive Regression Trees (BART) and its extension with Post-Stratification (BARP). The permutation-based SHAP method proposed by Strumbel and Kononenko (2014) <doi:10.1007/s10115-013-0679-x> is grounded in data obtained via MCMC sampling. Similar to the BART model introduced by Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>, this package leverages Bayesian posterior samples generated during model estimation, allowing variable contributions to be computed without requiring additional sampling. For XGBoost and baseline adjustments, the approach by Lundberg et al. (2020) <doi:10.1038/s42256-019-0138-9> is also considered.The BARP model proposed by Bisbee (2019) <doi:10.1017/S000305541 [...truncated...]
Author: Dong-eun Lee [aut, cre],
Eun-Kyung Lee [aut]
Maintainer: Dong-eun Lee <ldongeun.leel@gmail.com>
Diff between bartXViz versions 1.0.3 dated 2025-04-28 and 1.0.5 dated 2025-06-24
DESCRIPTION | 10 ++--- MD5 | 54 +++++++++++++-------------- R/BARP_barp.R | 14 ++++--- R/decision_plot.R | 8 ++-- R/explain.barp.R | 16 ++++---- R/explain.dbart.R | 55 ++++++++++++++++++++------- R/explain_bartMachine.R | 65 +++++++++++++++------------------ R/explain_wbart.R | 20 +++++----- R/fastshap_explain_fastshap_modified.R | 58 ++++++++++++++--------------- R/plot.explainbarp.R | 32 ++++++++-------- R/plot_default.R | 32 ++++++++-------- R/plot_explainBART.R | 47 ++++++++++++----------- R/plot_explainbartMachine.R | 34 ++++++++--------- R/waterfall_plot.R | 40 ++++++++++++-------- man/Explain.barp.Rd | 16 ++++---- man/Explain.bart.Rd | 18 ++++----- man/Explain.bartMachine.Rd | 20 +++++----- man/Explain.default.Rd | 58 ++++++++++++++--------------- man/Explain.wbart.Rd | 20 +++++----- man/barps.Rd | 12 +++--- man/census06.Rd | 2 - man/decision_plot.Rd | 8 ++-- man/plot.Explain.Rd | 32 ++++++++-------- man/plot.ExplainBART.Rd | 34 ++++++++--------- man/plot.Explainbarp.Rd | 32 ++++++++-------- man/plot.ExplainbartMachine.Rd | 34 ++++++++--------- man/svy.Rd | 2 - man/waterfall_plot.Rd | 15 ++++++- 28 files changed, 417 insertions(+), 371 deletions(-)
Title: Fairness Auditing and Debiasing for 'mlr3'
Description: Integrates fairness auditing and bias mitigation methods for
the 'mlr3' ecosystem. This includes fairness metrics, reporting
tools, visualizations and bias mitigation techniques such as
"Reweighing" described in 'Kamiran, Calders' (2012)
<doi:10.1007/s10115-011-0463-8> and "Equalized Odds" described in
'Hardt et al.' (2016)
<https://papers.nips.cc/paper/2016/file/9d2682367c3935defcb1f9e247a97c0d-Paper.pdf>.
Integration with 'mlr3' allows for auditing of ML models as well as
convenient joint tuning of machine learning algorithms and debiasing
methods.
Author: Florian Pfisterer [cre, aut] ,
Wei Siyi [aut],
Michel Lang [aut]
Maintainer: Florian Pfisterer <pfistererf@googlemail.com>
Diff between mlr3fairness versions 0.3.2 dated 2023-05-04 and 0.4.0 dated 2025-06-24
DESCRIPTION | 75 +++--- MD5 | 155 +++++++------- NEWS.md | 12 - R/MeasureFairness.R | 10 R/MeasureFairnessComposite.R | 6 R/MeasureFairnessConstraint.R | 8 R/MeasurePositiveProbability.R | 2 R/MeasureSubgroup.R | 14 - R/PipeOpEOd.R | 32 +- R/PipeOpExplicitPta.R | 19 - R/PipeOpReweighing.R | 37 +-- R/adult.R | 12 - R/compare_metrics.R | 20 - R/compas.R | 10 R/compute_metrics.R | 2 R/fairness_accuracy_tradeoff.R | 21 - R/fairness_prediction_density.R | 8 R/fairness_tensor.R | 10 R/helpers.R | 30 +- R/learner_fairml_classif_fairzlrm.R | 8 R/learner_fairml_regr_fairzlm.R | 6 R/measure_operations.R | 2 R/mlr_learners_fairness.R | 8 R/mlr_measures_fairness.R | 6 R/mlr_pipeops_equalized_odds.R |only R/mlr_pipeops_explicit_pta.R |only R/mlr_pipeops_reweighing.R |only R/reports.R | 8 README.md | 20 - inst/doc/debiasing-vignette.R | 2 inst/doc/debiasing-vignette.Rmd | 2 inst/doc/debiasing-vignette.html | 40 +-- inst/doc/measures-vignette.R | 6 inst/doc/measures-vignette.html | 140 +++++++----- inst/doc/reports-vignette.R | 2 inst/doc/reports-vignette.Rmd | 2 inst/doc/reports-vignette.html | 2 inst/doc/visualization-vignette.R | 2 inst/doc/visualization-vignette.html | 62 +++-- inst/rmarkdown/templates/datasheets/skeleton/skeleton.Rmd | 2 inst/rmarkdown/templates/modelcards/skeleton/skeleton.Rmd | 2 man/MeasureFairness.Rd | 14 - man/MeasureFairnessComposite.Rd | 2 man/MeasureFairnessConstraint.Rd | 4 man/MeasureSubgroup.Rd | 6 man/compas.Rd | 9 man/compute_metrics.Rd | 4 man/fairness_accuracy_tradeoff.Rd | 23 +- man/fairness_compare_metrics.Rd | 22 + man/fairness_prediction_density.Rd | 10 man/fairness_tensor.Rd | 12 - man/figures/unnamed-chunk-6-1.png |binary man/groupdiff_tau.Rd | 4 man/groupwise_metrics.Rd | 4 man/mlr_learners_classif.fairfgrrm.Rd | 11 man/mlr_learners_classif.fairzlrm.Rd | 13 - man/mlr_learners_fairness.Rd | 8 man/mlr_learners_regr.fairfrrm.Rd | 11 man/mlr_learners_regr.fairnclm.Rd | 13 - man/mlr_learners_regr.fairzlm.Rd | 13 - man/mlr_measures_fairness.Rd | 2 man/mlr_measures_positive_probability.Rd | 2 man/mlr_pipeops_equalized_odds.Rd | 30 +- man/mlr_pipeops_explicit_pta.Rd | 16 - man/mlr_pipeops_reweighing.Rd | 26 +- man/report_datasheet.Rd | 2 man/report_fairness.Rd | 4 man/report_modelcard.Rd | 2 man/task_summary.Rd | 2 tests/testthat/helper_data.R | 19 + tests/testthat/helper_test.R | 6 tests/testthat/setup.R |only tests/testthat/teardown.R |only tests/testthat/test_datasets.R | 10 tests/testthat/test_learners_fairml.R | 18 - tests/testthat/test_learners_fairml_ptas.R | 2 tests/testthat/test_measures.R | 1 tests/testthat/test_pipeop_reweighing.R | 22 - tests/testthat/test_report_modelcard_datasheet.R | 6 vignettes/debiasing-vignette.Rmd | 2 vignettes/reports-vignette.Rmd | 2 81 files changed, 635 insertions(+), 527 deletions(-)
Title: Import Data from EDC Software
Description: A convenient toolbox to import data exported from Electronic Data Capture (EDC) software 'TrialMaster'.
Author: Dan Chaltiel [aut, cre]
Maintainer: Dan Chaltiel <dan.chaltiel@gmail.com>
Diff between EDCimport versions 0.5.2 dated 2024-11-14 and 0.6.0 dated 2025-06-24
EDCimport-0.5.2/EDCimport/R/crf_status.R |only EDCimport-0.5.2/EDCimport/man/build_lookup.Rd |only EDCimport-0.5.2/EDCimport/man/crf_status_plot.Rd |only EDCimport-0.5.2/EDCimport/man/data_example.Rd |only EDCimport-0.5.2/EDCimport/man/extend_lookup.Rd |only EDCimport-0.5.2/EDCimport/man/find_keyword.Rd |only EDCimport-0.5.2/EDCimport/man/get_key_cols.Rd |only EDCimport-0.5.2/EDCimport/man/get_meta_cols.Rd |only EDCimport-0.5.2/EDCimport/man/harmonize_subjid.Rd |only EDCimport-0.5.2/EDCimport/man/load_as_list.Rd |only EDCimport-0.5.2/EDCimport/man/load_list.Rd |only EDCimport-0.5.2/EDCimport/man/save_list.Rd |only EDCimport-0.5.2/EDCimport/man/split_mixed_datasets.Rd |only EDCimport-0.5.2/EDCimport/tests/testthat/_snaps/local.md |only EDCimport-0.5.2/EDCimport/tests/testthat/_snaps/utils.md |only EDCimport-0.5.2/EDCimport/tests/testthat/csv |only EDCimport-0.5.2/EDCimport/tests/testthat/debug_buildpane.R |only EDCimport-0.5.2/EDCimport/tests/testthat/helper-local.R |only EDCimport-0.5.2/EDCimport/tests/testthat/test-local.R |only EDCimport-0.5.2/EDCimport/tests/testthat/test-plot.R |only EDCimport-0.5.2/EDCimport/tests/testthat/test-quicktest.R |only EDCimport-0.6.0/EDCimport/DESCRIPTION | 31 EDCimport-0.6.0/EDCimport/MD5 | 228 ++-- EDCimport-0.6.0/EDCimport/NAMESPACE | 56 - EDCimport-0.6.0/EDCimport/NEWS.md | 50 - EDCimport-0.6.0/EDCimport/R/7zip.R | 11 EDCimport-0.6.0/EDCimport/R/EDCimport-package.R | 21 EDCimport-0.6.0/EDCimport/R/aaa.R |only EDCimport-0.6.0/EDCimport/R/assertions.R | 24 EDCimport-0.6.0/EDCimport/R/burgled.R | 5 EDCimport-0.6.0/EDCimport/R/clean_names.R |only EDCimport-0.6.0/EDCimport/R/crf_plot.R |only EDCimport-0.6.0/EDCimport/R/data.R | 216 ++-- EDCimport-0.6.0/EDCimport/R/edc_unify_subjid.R |only EDCimport-0.6.0/EDCimport/R/find.R |only EDCimport-0.6.0/EDCimport/R/helpers.R | 482 ++++------ EDCimport-0.6.0/EDCimport/R/lastnews_table.R |only EDCimport-0.6.0/EDCimport/R/lookup.R | 113 +- EDCimport-0.6.0/EDCimport/R/options.R | 8 EDCimport-0.6.0/EDCimport/R/patient_gridplot.R |only EDCimport-0.6.0/EDCimport/R/population_plot.R | 20 EDCimport-0.6.0/EDCimport/R/read_all_csv.R | 78 + EDCimport-0.6.0/EDCimport/R/read_all_sas.R | 56 - EDCimport-0.6.0/EDCimport/R/read_all_xpt.R | 99 -- EDCimport-0.6.0/EDCimport/R/read_trialmaster.R | 59 - EDCimport-0.6.0/EDCimport/R/sanity_checks.R | 220 +++- EDCimport-0.6.0/EDCimport/R/sas_format.R | 6 EDCimport-0.6.0/EDCimport/R/save_to_excel.R | 4 EDCimport-0.6.0/EDCimport/R/split_mixed.R | 149 ++- EDCimport-0.6.0/EDCimport/R/swimmerplot.R | 353 ++++--- EDCimport-0.6.0/EDCimport/R/utils.R | 160 ++- EDCimport-0.6.0/EDCimport/R/utils_read.R | 53 - EDCimport-0.6.0/EDCimport/R/viewer.R |only EDCimport-0.6.0/EDCimport/R/viewer_server.R |only EDCimport-0.6.0/EDCimport/R/viewer_ui.R |only EDCimport-0.6.0/EDCimport/README.md | 106 -- EDCimport-0.6.0/EDCimport/build |only EDCimport-0.6.0/EDCimport/inst/IMPORTLIST | 82 - EDCimport-0.6.0/EDCimport/inst/WORDLIST | 17 EDCimport-0.6.0/EDCimport/inst/autoimport_cache.rds |only EDCimport-0.6.0/EDCimport/inst/doc |only EDCimport-0.6.0/EDCimport/inst/edc_viewer |only EDCimport-0.6.0/EDCimport/inst/figures |only EDCimport-0.6.0/EDCimport/inst/hex.R |only EDCimport-0.6.0/EDCimport/man/EDCimport-package.Rd | 2 EDCimport-0.6.0/EDCimport/man/edc_clean_names.Rd |only EDCimport-0.6.0/EDCimport/man/edc_crf_plot.Rd |only EDCimport-0.6.0/EDCimport/man/edc_data_warn.Rd | 32 EDCimport-0.6.0/EDCimport/man/edc_database.Rd |only EDCimport-0.6.0/EDCimport/man/edc_db_to_excel.Rd | 4 EDCimport-0.6.0/EDCimport/man/edc_example.Rd |only EDCimport-0.6.0/EDCimport/man/edc_find_value.Rd |only EDCimport-0.6.0/EDCimport/man/edc_left_join.Rd |only EDCimport-0.6.0/EDCimport/man/edc_lookup.Rd | 11 EDCimport-0.6.0/EDCimport/man/edc_options.Rd | 4 EDCimport-0.6.0/EDCimport/man/edc_patient_gridplot.Rd |only EDCimport-0.6.0/EDCimport/man/edc_peek_options.Rd | 4 EDCimport-0.6.0/EDCimport/man/edc_population_plot.Rd | 2 EDCimport-0.6.0/EDCimport/man/edc_reset_options.Rd | 4 EDCimport-0.6.0/EDCimport/man/edc_split_mixed.Rd |only EDCimport-0.6.0/EDCimport/man/edc_swimmerplot.Rd | 61 - 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EDCimport-0.6.0/EDCimport/tests/testthat/test-swimmerplot.R |only EDCimport-0.6.0/EDCimport/tests/testthat/test-trialmaster-simple.R | 2 EDCimport-0.6.0/EDCimport/tests/testthat/test-trialmaster.R | 56 - EDCimport-0.6.0/EDCimport/tests/testthat/test-utils.R | 128 +- EDCimport-0.6.0/EDCimport/vignettes |only 125 files changed, 2418 insertions(+), 1646 deletions(-)
Title: High Dimensional Categorical Data Visualization
Description: Easy visualization for datasets with more than two categorical variables and additional continuous variables. 'diceplot' is particularly useful for exploring complex categorical data in the context of pathway analysis across multiple conditions. For a detailed documentation please visit <https://dice-and-domino-plot.readthedocs.io/en/latest/>.
Author: Matthias Flotho [aut, cre]
Maintainer: Matthias Flotho <matthias.flotho@ccb.uni-saarland.de>
Diff between diceplot versions 0.1.7 dated 2025-04-14 and 0.2.0 dated 2025-06-24
DESCRIPTION | 9 MD5 | 19 NAMESPACE | 2 R/dice_facet.R |only R/dominoplot.R | 61 +- R/utils.R | 592 ++++++++++++++++++------ inst/CITATION | 14 man/create_custom_domino_legends.Rd | 35 - man/create_custom_domino_legends_categorical.Rd |only man/dice_facet_plot.Rd |only man/domino_plot.Rd | 3 man/geom_dice_sf.Rd | 35 + 12 files changed, 576 insertions(+), 194 deletions(-)
Title: Simulation of Ecological (and Other) Dynamic Systems
Description: An object oriented framework to simulate
ecological (and other) dynamic systems. It can be used for
differential equations, individual-based (or agent-based) and other
models as well. It supports structuring of simulation scenarios (to avoid copy
and paste) and aims to improve readability and re-usability of code.
Author: Thomas Petzoldt [aut, cre]
Maintainer: Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>
Diff between simecol versions 0.9-2 dated 2025-05-19 and 0.9-3 dated 2025-06-24
simecol-0.9-2/simecol/inst/doc/examples |only simecol-0.9-3/simecol/DESCRIPTION | 6 +- simecol-0.9-3/simecol/MD5 | 36 +++----------- simecol-0.9-3/simecol/R/iteration.R | 2 simecol-0.9-3/simecol/build/partial.rdb |binary simecol-0.9-3/simecol/demo/jss.R | 2 simecol-0.9-3/simecol/inst/doc/a-simecol-introduction.pdf |binary simecol-0.9-3/simecol/inst/doc/b-simecol-howtos.Rnw | 6 +- simecol-0.9-3/simecol/inst/doc/b-simecol-howtos.pdf |binary simecol-0.9-3/simecol/vignettes/b-simecol-howtos.Rnw | 6 +- 10 files changed, 19 insertions(+), 39 deletions(-)
Title: Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup
Description: Processes the raw data from closed loop flux chamber (or tent)
setups into ecosystem gas fluxes usable for analysis. It goes from a
data frame of gas concentration over time (which can contain several
measurements) and a meta data file indicating which measurement was done
when, to a data frame of ecosystem gas fluxes including quality diagnostics.
Functions provided include different models (exponential as described in
Zhao et al (2018) <doi:10.1016/j.agrformet.2018.08.022>, quadratic and
linear) to estimate the fluxes from the raw data, quality assessment,
plotting for visual check and calculation of fluxes based on the setup
specific parameters (chamber size, plot area, ...).
Author: Joseph Gaudard [aut, cre] ,
Richard James Telford [aut]
Maintainer: Joseph Gaudard <joseph.gaudard@pm.me>
Diff between fluxible versions 1.2.2 dated 2025-06-05 and 1.2.6 dated 2025-06-24
DESCRIPTION | 10 +-- MD5 | 53 +++++++++++------- NAMESPACE | 6 ++ NEWS.md | 17 ++++++ R/data-co2_fluxes_lrc.R |only R/flux_calc.R | 96 ++++++++++++++++------------------ R/flux_lrc.R |only R/flux_match.R | 6 -- R/flux_units.R |only README.md | 2 build/partial.rdb |binary build/vignette.rds |binary data/co2_fluxes_lrc.rda |only inst/CITATION |only inst/doc/fluxible.R | 4 - inst/doc/fluxible.Rmd | 4 - inst/doc/fluxible.html | 2 inst/doc/two-gases.R | 4 - inst/doc/two-gases.Rmd | 4 - inst/doc/two-gases.html | 4 - man/co2_fluxes_lrc.Rd |only man/flux_calc.Rd | 21 +++---- man/flux_lrc.Rd |only man/flux_match.Rd | 6 -- man/flux_units.Rd |only tests/testthat/_snaps/flux_calc.md | 23 ++++---- tests/testthat/_snaps/flux_lrc.md |only tests/testthat/test-flux_calc.R | 46 ++++++++-------- tests/testthat/test-flux_flag_count.R | 2 tests/testthat/test-flux_lrc.R |only tests/testthat/test-flux_units.R |only vignettes/fluxible.Rmd | 4 - vignettes/two-gases.Rmd | 4 - 33 files changed, 171 insertions(+), 147 deletions(-)
Title: Easily Install and Load PACTA for Banks Packages
Description: PACTA (Paris Agreement Capital Transition Assessment) for Banks is
a tool that allows banks to calculate the climate alignment of their corporate
lending portfolios. This package is designed to make it easy to install and
load multiple PACTA for Banks packages in a single step. It also provides
thorough documentation - the PACTA for Banks cookbook at
<https://rmi-pacta.github.io/pacta.loanbook/articles/cookbook_overview.html> -
on how to run a PACTA for Banks analysis. This covers prerequisites for the
analysis, the separate steps of running the analysis, the interpretation of
PACTA for Banks results, and advanced use cases.
Author: Jacob Kastl [aut, cre, ctr] ,
Jackson Hoffart [aut, ctr] ,
CJ Yetman [aut, ctr] ,
RMI [cph, fnd]
Maintainer: Jacob Kastl <jacob.kastl@gmail.com>
Diff between pacta.loanbook versions 0.1.0 dated 2025-03-17 and 0.1.1 dated 2025-06-24
pacta.loanbook-0.1.0/pacta.loanbook/man/market_share.Rd |only pacta.loanbook-0.1.0/pacta.loanbook/man/sda.Rd |only pacta.loanbook-0.1.1/pacta.loanbook/DESCRIPTION | 29 pacta.loanbook-0.1.1/pacta.loanbook/MD5 | 80 pacta.loanbook-0.1.1/pacta.loanbook/NAMESPACE | 4 pacta.loanbook-0.1.1/pacta.loanbook/NEWS.md | 10 pacta.loanbook-0.1.1/pacta.loanbook/R/r2dii.match.R | 54 pacta.loanbook-0.1.1/pacta.loanbook/R/r2dii.plot.R | 47 pacta.loanbook-0.1.1/pacta.loanbook/R/update.R | 2 pacta.loanbook-0.1.1/pacta.loanbook/build/vignette.rds |binary pacta.loanbook-0.1.1/pacta.loanbook/inst/doc/data_abcd.html | 119 - pacta.loanbook-0.1.1/pacta.loanbook/inst/doc/data_classification.html | 803 ++++----- pacta.loanbook-0.1.1/pacta.loanbook/inst/doc/data_loanbook.html | 119 - pacta.loanbook-0.1.1/pacta.loanbook/inst/doc/data_outputs.R | 4 pacta.loanbook-0.1.1/pacta.loanbook/inst/doc/data_outputs.Rmd | 8 pacta.loanbook-0.1.1/pacta.loanbook/inst/doc/data_outputs.html | 811 +++++----- pacta.loanbook-0.1.1/pacta.loanbook/inst/doc/data_scenario.html | 233 +- pacta.loanbook-0.1.1/pacta.loanbook/man/abcd_demo.Rd | 4 pacta.loanbook-0.1.1/pacta.loanbook/man/co2_intensity_scenario_demo.Rd | 16 pacta.loanbook-0.1.1/pacta.loanbook/man/loanbook_demo.Rd | 4 pacta.loanbook-0.1.1/pacta.loanbook/man/market_share_demo.Rd |only pacta.loanbook-0.1.1/pacta.loanbook/man/overwrite_demo.Rd | 4 pacta.loanbook-0.1.1/pacta.loanbook/man/pacta.loanbook-package.Rd | 2 pacta.loanbook-0.1.1/pacta.loanbook/man/plot_emission_intensity.Rd | 2 pacta.loanbook-0.1.1/pacta.loanbook/man/plot_techmix.Rd | 2 pacta.loanbook-0.1.1/pacta.loanbook/man/plot_trajectory.Rd | 2 pacta.loanbook-0.1.1/pacta.loanbook/man/prep_emission_intensity.Rd | 10 pacta.loanbook-0.1.1/pacta.loanbook/man/prep_techmix.Rd | 10 pacta.loanbook-0.1.1/pacta.loanbook/man/prep_trajectory.Rd | 10 pacta.loanbook-0.1.1/pacta.loanbook/man/qplot_emission_intensity.Rd | 2 pacta.loanbook-0.1.1/pacta.loanbook/man/qplot_techmix.Rd | 2 pacta.loanbook-0.1.1/pacta.loanbook/man/qplot_trajectory.Rd | 2 pacta.loanbook-0.1.1/pacta.loanbook/man/region_isos_demo.Rd | 4 pacta.loanbook-0.1.1/pacta.loanbook/man/scale_colour_r2dii.Rd | 4 pacta.loanbook-0.1.1/pacta.loanbook/man/scale_colour_r2dii_sector.Rd | 4 pacta.loanbook-0.1.1/pacta.loanbook/man/scale_colour_r2dii_tech.Rd | 4 pacta.loanbook-0.1.1/pacta.loanbook/man/scale_fill_r2dii.Rd | 4 pacta.loanbook-0.1.1/pacta.loanbook/man/scale_fill_r2dii_sector.Rd | 4 pacta.loanbook-0.1.1/pacta.loanbook/man/scale_fill_r2dii_tech.Rd | 4 pacta.loanbook-0.1.1/pacta.loanbook/man/scenario_demo_2020.Rd | 4 pacta.loanbook-0.1.1/pacta.loanbook/man/sda_demo.Rd |only pacta.loanbook-0.1.1/pacta.loanbook/man/theme_2dii.Rd | 2 pacta.loanbook-0.1.1/pacta.loanbook/vignettes/data_outputs.Rmd | 8 43 files changed, 1179 insertions(+), 1258 deletions(-)
More information about pacta.loanbook at CRAN
Permanent link
Title: Distributed Online Goodness-of-Fit Tests for Distributed
Datasets
Description: Distributed Online Goodness-of-Fit Test can process the distributed datasets. The philosophy of the package is described in Guo G.(2024) <doi:10.1016/j.apm.2024.115709>.
Author: Guangbao Guo [aut, cre] ,
Di Chang [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between Dogoftest versions 0.1 dated 2025-02-18 and 0.2 dated 2025-06-24
DESCRIPTION | 11 ++++++----- MD5 | 28 ++++++++++++++++++++++------ NAMESPACE | 37 ++++++++++++++++++++++++++++--------- R/AD2gof.R |only R/ADgof.R |only R/CVM2gof.R |only R/CVMgof2.R |only R/KS2gof.R |only R/KSgof2.R |only R/Kuiper2gof.R |only R/Wgof.R |only R/cvmgof.R | 14 +++++++------- R/ksgof.R | 15 +++++++-------- R/qCvMgof.R | 10 +++++----- R/simpleCvMgof.R | 14 +++++++------- man/AD2gof.Rd |only man/ADgof.Rd |only man/CVM2gof.Rd |only man/CVMgof2.Rd |only man/KS2gof.Rd |only man/KSgof2.Rd |only man/Kuiper2gof.Rd |only man/Wgof.Rd |only 23 files changed, 82 insertions(+), 47 deletions(-)
More information about fastpolicytree at CRAN
Permanent link
Title: Calculate Metrics for Trauma System Performance
Description: Hospitals, hospital systems, and even trauma systems that
provide care to injured patients may not be aware of robust metrics
that can help gauge the efficacy of their programs in saving the lives
of injured patients. 'traumar' provides robust functions driven by
the academic literature to automate the calculation of relevant
metrics to individuals desiring to measure the performance of their
trauma center or even a trauma system. 'traumar' also provides some
helper functions for the data analysis journey. Users can refer to the
following publications for descriptions of the methods used in
'traumar'. TRISS methodology, including probability of survival, and
the W, M, and Z Scores - Flora (1978)
<doi:10.1097/00005373-197810000-00003>, Boyd et al. (1987,
PMID:3106646), Llullaku et al. (2009) <doi:10.1186/1749-7922-4-2>,
Singh et al. (2011) <doi:10.4103/0974-2700.86626>, Baker et al. (1974,
PMID:4814394), and Champion et al. (1989)
<doi:10.1097/00005373-198905000- [...truncated...]
Author: Nicolas Foss [aut, cre],
Iowa Department of Health and Human Services [cph]
Maintainer: Nicolas Foss <nicolas.foss@hhs.iowa.gov>
Diff between traumar versions 1.2.0 dated 2025-05-22 and 1.2.1 dated 2025-06-24
DESCRIPTION | 10 - MD5 | 14 +- NEWS.md | 12 + R/globalVariables.R | 2 R/trauma_performance.r | 11 - README.md | 1 build/partial.rdb |binary tests/testthat/test-relative_mortality.R | 202 +++++++++++++++++++++---------- 8 files changed, 173 insertions(+), 79 deletions(-)
Title: Additional Matrix Functionality
Description: Additional matrix functionality for R including: (1) wrappers for
the base matrix function that allow matrices to be created from character
strings and lists (the former is especially useful for creating block
matrices), (2) better printing of large matrices via the generic "pretty"
print function, and (3) a number of convenience functions for users more
familiar with other scientific languages like 'Julia', 'Matlab'/'Octave', or
'Python'+'NumPy'.
Author: Brandon M. Greenwell [aut, cre]
Maintainer: Brandon M. Greenwell <greenwell.brandon@gmail.com>
Diff between ramify versions 0.3.3 dated 2016-12-17 and 0.4.0 dated 2025-06-24
ramify-0.3.3/ramify/NEWS |only ramify-0.3.3/ramify/inst/doc/introduction.R |only ramify-0.3.3/ramify/inst/doc/introduction.Rmd |only ramify-0.3.3/ramify/inst/doc/introduction.html |only ramify-0.3.3/ramify/man/ramify.Rd |only ramify-0.3.3/ramify/vignettes/introduction.Rmd |only ramify-0.4.0/ramify/DESCRIPTION | 25 ramify-0.4.0/ramify/MD5 | 101 +-- ramify-0.4.0/ramify/NEWS.md |only ramify-0.4.0/ramify/R/bmat.R | 44 - ramify-0.4.0/ramify/R/convenience.R | 592 +++++++++++------- ramify-0.4.0/ramify/R/dmat.R | 27 ramify-0.4.0/ramify/R/mat.R | 95 +- ramify-0.4.0/ramify/R/matrix_rank.R | 22 ramify-0.4.0/ramify/R/pprint.R | 143 ++-- ramify-0.4.0/ramify/R/ramify.R | 26 ramify-0.4.0/ramify/R/utils.R | 4 ramify-0.4.0/ramify/R/zzz.R | 6 ramify-0.4.0/ramify/README.md |only ramify-0.4.0/ramify/build/vignette.rds |binary ramify-0.4.0/ramify/inst/doc/ramify.R |only ramify-0.4.0/ramify/inst/doc/ramify.Rmd |only ramify-0.4.0/ramify/inst/doc/ramify.html |only ramify-0.4.0/ramify/man/argmax.Rd | 3 ramify-0.4.0/ramify/man/atleast_2d.Rd | 4 ramify-0.4.0/ramify/man/bmat.Rd | 19 ramify-0.4.0/ramify/man/clip.Rd | 17 ramify-0.4.0/ramify/man/dmat.Rd | 15 ramify-0.4.0/ramify/man/eye.Rd | 13 ramify-0.4.0/ramify/man/fill.Rd | 22 ramify-0.4.0/ramify/man/flatten.Rd | 7 ramify-0.4.0/ramify/man/hcat.Rd | 11 ramify-0.4.0/ramify/man/inv.Rd | 8 ramify-0.4.0/ramify/man/is.tril.Rd | 5 ramify-0.4.0/ramify/man/is.triu.Rd | 5 ramify-0.4.0/ramify/man/linspace.Rd | 7 ramify-0.4.0/ramify/man/logspace.Rd | 9 ramify-0.4.0/ramify/man/mat.Rd | 42 - ramify-0.4.0/ramify/man/matrix_rank.Rd | 10 ramify-0.4.0/ramify/man/meshgrid.Rd | 13 ramify-0.4.0/ramify/man/pprint.Rd | 32 ramify-0.4.0/ramify/man/ramify-package.Rd |only ramify-0.4.0/ramify/man/rand.Rd | 21 ramify-0.4.0/ramify/man/randi.Rd | 11 ramify-0.4.0/ramify/man/randn.Rd | 17 ramify-0.4.0/ramify/man/repmat.Rd | 8 ramify-0.4.0/ramify/man/resize.Rd | 18 ramify-0.4.0/ramify/man/size.Rd | 5 ramify-0.4.0/ramify/man/tr.Rd | 3 ramify-0.4.0/ramify/man/tri.Rd | 11 ramify-0.4.0/ramify/man/tril.Rd | 10 ramify-0.4.0/ramify/man/triu.Rd | 10 ramify-0.4.0/ramify/tests/testthat/test-bmat.R | 18 ramify-0.4.0/ramify/tests/testthat/test-convenience.R | 64 - ramify-0.4.0/ramify/tests/testthat/test-mat.R | 32 ramify-0.4.0/ramify/tests/testthat/test-matrix_rank.R | 4 ramify-0.4.0/ramify/tests/testthat/test-utils.R | 2 ramify-0.4.0/ramify/vignettes/ramify.Rmd |only 58 files changed, 853 insertions(+), 708 deletions(-)
Title: Daily Streamflow Trend and Change Point Screening
Description: Screens daily streamflow time series for temporal trends and
change-points. This package has been primarily developed for assessing the
quality of daily streamflow time series. It also contains tools for plotting
and calculating many different streamflow metrics. The package can be used to
produce summary screening plots showing change-points and significant temporal
trends for high flow, low flow, and/or baseflow statistics, or it can be used
to perform more detailed hydrological time series analyses. The package was
designed for screening daily streamflow time series from Water Survey Canada
and the United States Geological Survey but will also work with streamflow time
series from many other agencies.
Package update to version 2.0 made updates to read.flows function to allow
loading of GRDC and ROBIN streamflow record formats.
This package uses the `changepoint` package for change point detection.
For more information on change point methods, see the changepoint
package at <https [...truncated...]
Author: Jennifer Dierauer [aut, cre],
Paul Whitfield [aut]
Maintainer: Jennifer Dierauer <jen.r.brand@gmail.com>
Diff between FlowScreen versions 1.2.6 dated 2019-04-05 and 2.0 dated 2025-06-24
FlowScreen-1.2.6/FlowScreen/R/NA.sum.r |only FlowScreen-1.2.6/FlowScreen/R/sysdata.rda |only FlowScreen-1.2.6/FlowScreen/man/NA.sum.Rd |only FlowScreen-2.0/FlowScreen/DESCRIPTION | 22 FlowScreen-2.0/FlowScreen/MD5 | 188 ++-- FlowScreen-2.0/FlowScreen/NAMESPACE | 86 +- FlowScreen-2.0/FlowScreen/NEWS.md |only FlowScreen-2.0/FlowScreen/R/FDC.R | 388 ++++++--- FlowScreen-2.0/FlowScreen/R/MAMn.R | 157 ++- FlowScreen-2.0/FlowScreen/R/NA.count.runs.R |only FlowScreen-2.0/FlowScreen/R/NA.runs.r | 135 ++- FlowScreen-2.0/FlowScreen/R/Qn.R | 139 ++- FlowScreen-2.0/FlowScreen/R/YMD.internal.r | 24 FlowScreen-2.0/FlowScreen/R/add.station.metadata.R |only FlowScreen-2.0/FlowScreen/R/axis_doy.internal.r | 33 FlowScreen-2.0/FlowScreen/R/bf.seas.R | 119 +- FlowScreen-2.0/FlowScreen/R/bf.stats.R | 162 ++- FlowScreen-2.0/FlowScreen/R/bf_boughton.r | 66 - FlowScreen-2.0/FlowScreen/R/bf_eckhardt.r | 66 - FlowScreen-2.0/FlowScreen/R/bf_oneparam.r | 61 - FlowScreen-2.0/FlowScreen/R/cania.sub.ts.R | 73 - FlowScreen-2.0/FlowScreen/R/check_completeness.R |only FlowScreen-2.0/FlowScreen/R/create.ts.r | 129 ++- FlowScreen-2.0/FlowScreen/R/dr.events.R | 320 ++++--- FlowScreen-2.0/FlowScreen/R/dr.pds.R | 133 +-- FlowScreen-2.0/FlowScreen/R/dr.seas.R | 222 ++--- FlowScreen-2.0/FlowScreen/R/drop.years.R |only FlowScreen-2.0/FlowScreen/R/get.station.internal.r | 73 + FlowScreen-2.0/FlowScreen/R/get.titles.internal.R | 244 +++-- FlowScreen-2.0/FlowScreen/R/hyear.internal.r | 121 +- FlowScreen-2.0/FlowScreen/R/metrics.all.R | 632 +++++++-------- FlowScreen-2.0/FlowScreen/R/missingness.R |only FlowScreen-2.0/FlowScreen/R/mqt.r | 147 +-- FlowScreen-2.0/FlowScreen/R/pk.bf.stats.R | 209 ++-- FlowScreen-2.0/FlowScreen/R/pk.cov.R | 201 ++-- FlowScreen-2.0/FlowScreen/R/pk.max.R | 77 + FlowScreen-2.0/FlowScreen/R/pk.max.doy.R | 98 +- FlowScreen-2.0/FlowScreen/R/pks.R | 130 ++- FlowScreen-2.0/FlowScreen/R/pks.dur.R | 100 +- FlowScreen-2.0/FlowScreen/R/read.flows.R | 596 +++++++++----- FlowScreen-2.0/FlowScreen/R/regime.R | 266 +++--- FlowScreen-2.0/FlowScreen/R/regime.internal.R | 95 +- FlowScreen-2.0/FlowScreen/R/remove.station.metadata.R |only FlowScreen-2.0/FlowScreen/R/screen.cpts.R | 490 ++++++----- FlowScreen-2.0/FlowScreen/R/screen.frames.R | 403 ++++----- FlowScreen-2.0/FlowScreen/R/screen.frames.internal.R | 364 ++++---- FlowScreen-2.0/FlowScreen/R/screen.metric.R | 423 +++++----- FlowScreen-2.0/FlowScreen/R/screen.series.R | 202 ++-- FlowScreen-2.0/FlowScreen/R/screen.summary.R | 376 ++++---- FlowScreen-2.0/FlowScreen/R/screen.summary.internal.R | 394 ++++----- FlowScreen-2.0/FlowScreen/R/set.plot.titles.R |only FlowScreen-2.0/FlowScreen/R/station.info.R | 358 +++----- FlowScreen-2.0/FlowScreen/R/zzz.R |only FlowScreen-2.0/FlowScreen/data/cania.sub.ts.rda |binary FlowScreen-2.0/FlowScreen/data/caniapiscau.rda |binary FlowScreen-2.0/FlowScreen/data/caniapiscau.res.rda |binary FlowScreen-2.0/FlowScreen/inst |only FlowScreen-2.0/FlowScreen/man/FDC.Rd | 44 - FlowScreen-2.0/FlowScreen/man/MAMn.Rd | 40 FlowScreen-2.0/FlowScreen/man/NA.count.runs.Rd |only FlowScreen-2.0/FlowScreen/man/NA.runs.Rd | 19 FlowScreen-2.0/FlowScreen/man/Qn.Rd | 18 FlowScreen-2.0/FlowScreen/man/YMD.internal.Rd | 3 FlowScreen-2.0/FlowScreen/man/add.station.metadata.Rd |only FlowScreen-2.0/FlowScreen/man/axis_doy.internal.Rd | 5 FlowScreen-2.0/FlowScreen/man/bf.seas.Rd | 13 FlowScreen-2.0/FlowScreen/man/bf.stats.Rd | 7 FlowScreen-2.0/FlowScreen/man/bf_boughton.Rd | 7 FlowScreen-2.0/FlowScreen/man/bf_eckhardt.Rd | 7 FlowScreen-2.0/FlowScreen/man/bf_oneparam.Rd | 7 FlowScreen-2.0/FlowScreen/man/cania.sub.ts.Rd | 12 FlowScreen-2.0/FlowScreen/man/caniapiscau.Rd | 7 FlowScreen-2.0/FlowScreen/man/caniapiscau.res.Rd | 5 FlowScreen-2.0/FlowScreen/man/check_completeness.Rd |only FlowScreen-2.0/FlowScreen/man/create.ts.Rd | 14 FlowScreen-2.0/FlowScreen/man/dr.events.Rd | 14 FlowScreen-2.0/FlowScreen/man/dr.pds.Rd | 10 FlowScreen-2.0/FlowScreen/man/dr.seas.Rd | 20 FlowScreen-2.0/FlowScreen/man/drop.years.Rd |only FlowScreen-2.0/FlowScreen/man/get.station.internal.Rd | 13 FlowScreen-2.0/FlowScreen/man/get.titles.internal.Rd | 6 FlowScreen-2.0/FlowScreen/man/hyear.internal.Rd | 3 FlowScreen-2.0/FlowScreen/man/metrics.all.Rd | 30 FlowScreen-2.0/FlowScreen/man/missingness.Rd |only FlowScreen-2.0/FlowScreen/man/mqt.Rd | 14 FlowScreen-2.0/FlowScreen/man/pk.bf.stats.Rd | 14 FlowScreen-2.0/FlowScreen/man/pk.cov.Rd | 13 FlowScreen-2.0/FlowScreen/man/pk.max.Rd | 21 FlowScreen-2.0/FlowScreen/man/pk.max.doy.Rd | 21 FlowScreen-2.0/FlowScreen/man/pks.Rd | 15 FlowScreen-2.0/FlowScreen/man/pks.dur.Rd | 12 FlowScreen-2.0/FlowScreen/man/read.flows.Rd | 67 + FlowScreen-2.0/FlowScreen/man/regime.Rd | 59 - FlowScreen-2.0/FlowScreen/man/remove.station.metadata.Rd |only FlowScreen-2.0/FlowScreen/man/screen.cpts.Rd | 26 FlowScreen-2.0/FlowScreen/man/screen.frames.Rd | 45 - FlowScreen-2.0/FlowScreen/man/screen.frames.internal.Rd | 18 FlowScreen-2.0/FlowScreen/man/screen.metric.Rd | 40 FlowScreen-2.0/FlowScreen/man/screen.series.Rd | 23 FlowScreen-2.0/FlowScreen/man/screen.summary.Rd | 21 FlowScreen-2.0/FlowScreen/man/screen.summary.internal.Rd | 15 FlowScreen-2.0/FlowScreen/man/set.plot.titles.Rd |only FlowScreen-2.0/FlowScreen/man/station.info.Rd | 39 103 files changed, 5254 insertions(+), 4035 deletions(-)
Title: Extract Data from FAERS Database
Description: Provides functions to extract and process data from the FDA Adverse Event Reporting System (FAERS). It facilitates the conversion of raw FAERS data published after 2014Q3 into structured formats for analysis. See Yang et al. (2022) <doi:10.3389/fphar.2021.772768> for related information.
Author: Renjun Yang [ctb],
Renjun Yang [aut, cre]
Maintainer: Renjun Yang <rjyang@rcees.ac.cn>
Diff between extractFAERS versions 0.1.2 dated 2025-04-20 and 0.1.4 dated 2025-06-24
extractFAERS-0.1.2/extractFAERS/inst/extdata/DEMO |only extractFAERS-0.1.2/extractFAERS/inst/extdata/DEMO1PS |only extractFAERS-0.1.2/extractFAERS/inst/extdata/DRUG |only extractFAERS-0.1.2/extractFAERS/inst/extdata/F_COREDATA_1PS_PROF.RData |only extractFAERS-0.1.2/extractFAERS/inst/extdata/F_COREDATA_1PS_PROF_STU.RData |only extractFAERS-0.1.2/extractFAERS/inst/extdata/INDEX1PS |only extractFAERS-0.1.2/extractFAERS/inst/extdata/INDI |only extractFAERS-0.1.2/extractFAERS/inst/extdata/INDI1PS |only extractFAERS-0.1.2/extractFAERS/inst/extdata/REAC |only extractFAERS-0.1.2/extractFAERS/inst/extdata/REAC1PS |only extractFAERS-0.1.4/extractFAERS/DESCRIPTION | 9 extractFAERS-0.1.4/extractFAERS/MD5 | 45 - extractFAERS-0.1.4/extractFAERS/NEWS.md | 14 extractFAERS-0.1.4/extractFAERS/R/extract1PSFAERS.R | 2 extractFAERS-0.1.4/extractFAERS/R/filterbyoccpFAERS.R | 400 +++++----- extractFAERS-0.1.4/extractFAERS/R/timetodayFAERS.R | 1 extractFAERS-0.1.4/extractFAERS/R/zzz.R |only 17 files changed, 229 insertions(+), 242 deletions(-)
Title: Analysis of Data from a Crossover Design with GEE
Description: Analyze data from a crossover design using generalized estimation equations (GEE), including carryover effects and various correlation structures based on the Kronecker product. It contains functions for semiparametric estimates of carry-over effects in repeated measures and allows estimation of complex carry-over effects. Related work includes: a) Cruz N.A., Melo O.O., Martinez C.A. (2023). "CrossCarry: An R package for the analysis of data from a crossover design with GEE". <doi:10.48550/arXiv.2304.02440>. b) Cruz N.A., Melo O.O., Martinez C.A. (2023). "A correlation structure for the analysis of Gaussian and non-Gaussian responses in crossover experimental designs with repeated measures". <doi:10.1007/s00362-022-01391-z> and c) Cruz N.A., Melo O.O., Martinez C.A. (2023). "Semiparametric generalized estimating equations for repeated measurements in cross-over designs". <doi:10.1177/09622802231158736>.
Author: Nelson Alirio Cruz Gutierrez [aut, cre, cph],
Oscar Orlando Melo [aut],
Carlos Alberto Martinez [aut]
Maintainer: Nelson Alirio Cruz Gutierrez <nelson-alirio.cruz@uib.es>
Diff between CrossCarry versions 0.4.0 dated 2024-09-24 and 0.5.0 dated 2025-06-24
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/CrossGEESP.R | 11 ++++++----- 3 files changed, 11 insertions(+), 10 deletions(-)
Title: Parse and Deduplicate Author Names
Description: Utilities to parse authors fields from DESCRIPTION files and
general purpose functions to deduplicate names in database, beyond the
specific case of R package authors.
Author: Hugo Gruson [aut, cre, cph] ,
Chris Hartgerink [rev] ,
data.org [fnd]
Maintainer: Hugo Gruson <hugo.gruson+R@normalesup.org>
Diff between authoritative versions 0.1.0 dated 2025-02-03 and 0.2.0 dated 2025-06-24
DESCRIPTION | 25 ++++++++++++-------- MD5 | 45 +++++++++++++++++++------------------ NAMESPACE | 1 NEWS.md | 14 +++++++++-- R/dev-utils.R | 14 +++++------ R/expand_names.R | 3 -- R/invert_names.R |only R/parse_authors.R | 16 +++++++------ R/parse_authors_r.R | 13 +++++----- R/remove_brackets.R | 17 ++++++++----- README.md | 12 ++++----- build/vignette.rds |binary inst/WORDLIST | 9 +++++++ inst/doc/authoritative.R | 4 +-- inst/doc/authoritative.Rmd | 6 +++- inst/doc/authoritative.html | 2 - inst/doc/design-principles.R | 2 - inst/doc/design-principles.Rmd | 15 +++++------- inst/doc/design-principles.html | 30 ++++++++++-------------- man/authoritative-package.Rd | 13 ++++++++-- man/invert_names.Rd |only tests/testthat/test-expand_names.R | 3 -- tests/testthat/test-invert_names.R |only vignettes/authoritative.Rmd | 6 +++- vignettes/design-principles.Rmd | 15 +++++------- 25 files changed, 151 insertions(+), 114 deletions(-)
Title: Extensions to 'ggplot2' for Radiation Spectra
Description: Additional annotations, stats, geoms and scales for plotting
"light" spectra with 'ggplot2', together with specializations of ggplot()
and autoplot() methods for spectral data and waveband definitions
stored in objects of classes defined in package 'photobiology'. Part of the
'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggspectra versions 0.3.15 dated 2025-01-08 and 0.3.16 dated 2025-06-24
DESCRIPTION | 22 MD5 | 214 ++-- NAMESPACE | 8 NEWS.md | 28 R/autoplot-calibration-spct.R | 17 R/autoplot-cps-spct.r | 89 + R/autoplot-filter-spct.r | 93 +- R/autoplot-generic-spct.R | 8 R/autoplot-raw-spct.r | 109 +- R/autoplot-response-spct.r | 48 - R/autoplot-source-spct.r | 54 - R/autoplot-waveband.R | 5 R/axis-labels-texts.R | 56 - R/axis-utils-calibration-spct.R | 124 +- R/axis-utils-cps-spct.R | 22 R/axis-utils-filter-spct.R | 74 - R/axis-utils-raw-spct.R | 28 R/axis-utils-response-spct.R | 120 +- R/axis-utils-source-spct.R | 722 +++++++++++---- R/axis-utils-wlength.R | 438 ++++----- R/common-plot-utils.R | 43 R/decoration.R | 143 +-- R/set-options.R |only R/stat-color.R | 6 R/stat-find-wls.R | 8 R/stat-label-peaks.R | 101 -- R/stat-peaks.R | 182 +++ R/stat-spikes.R | 38 R/stat-wb-box.R | 187 ++-- R/stat-wb-hbar.R | 2 R/stat-wb-label.R | 168 ++- R/stat-wl-strip.R | 199 +++- R/utils-internal.R | 9 README.md | 8 build/partial.rdb |binary build/vignette.rds |binary inst/doc/userguide-0-r4p-introduction.Rmd | 158 +-- inst/doc/userguide-0-r4p-introduction.html | 158 +-- inst/doc/userguide1-grammar.R | 177 ++- inst/doc/userguide1-grammar.Rmd | 203 ++-- inst/doc/userguide1-grammar.html | 1345 ++++++++++++++--------------- inst/doc/userguide2-autoplot-methods.Rmd | 14 inst/doc/userguide2-autoplot-methods.html | 65 - man/A_plot.Rd | 5 man/Afr_label.Rd | 2 man/Afr_plot.Rd | 5 man/O_plot.Rd | 5 man/R_plot.Rd | 5 man/T_plot.Rd | 5 man/apply_normalization.Rd | 36 man/autoplot.calibration_spct.Rd | 25 man/autoplot.cps_spct.Rd | 30 man/autoplot.filter_spct.Rd | 25 man/autoplot.generic_spct.Rd | 17 man/autoplot.object_spct.Rd | 25 man/autoplot.raw_spct.Rd | 30 man/autoplot.reflector_spct.Rd | 25 man/autoplot.response_spct.Rd | 25 man/autoplot.source_spct.Rd | 32 man/autoplot.waveband.Rd | 20 man/axis_labels.Rd | 17 man/cal_plot.Rd | 5 man/check_idfactor_arg.Rd | 2 man/counts_label.Rd | 2 man/cps_label.Rd | 2 man/cps_plot.Rd | 5 man/decode_annotations.Rd | 12 man/decoration.Rd | 49 - man/duration2character.Rd | 3 man/e_plot.Rd | 5 man/e_rsp_plot.Rd | 5 man/fast_wb2rect_df.Rd |only man/figures/README-example2-1.png |binary man/find_idfactor.Rd | 14 man/generic_plot.Rd | 5 man/gg2spectra-ggproto.Rd | 8 man/multipliers_label.Rd | 2 man/q_plot.Rd | 5 man/q_rsp_plot.Rd | 1 man/raw_plot.Rd | 5 man/rename_idfactor.Rd | 5 man/s.e.irrad_label.Rd | 48 - man/s.e.response_label.Rd | 8 man/scale_x_energy_eV_continuous.Rd | 4 man/scale_x_frequency_continuous.Rd | 2 man/scale_x_wavenumber_continuous.Rd | 2 man/scale_x_wl_continuous.Rd | 2 man/scale_y_Afr_continuous.Rd | 2 man/scale_y_counts_continuous.Rd | 4 man/scale_y_cps_continuous.Rd | 2 man/scale_y_multipliers_continuous.Rd | 2 man/scale_y_s.e.irrad_continuous.Rd | 132 +- man/scale_y_s.e.response_continuous.Rd | 8 man/sec_axis_w_number.Rd | 10 man/set_annotations_default.Rd | 119 +- man/stat_color.Rd | 8 man/stat_find_qtys.Rd | 8 man/stat_find_wls.Rd | 8 man/stat_label_peaks.Rd | 116 +- man/stat_peaks.Rd | 163 ++- man/stat_spikes.Rd | 38 man/stat_wb_box.Rd | 29 man/stat_wb_hbar.Rd | 2 man/stat_wb_label.Rd | 29 man/stat_wl_strip.Rd | 31 man/w_length_label.Rd | 10 vignettes/userguide-0-r4p-introduction.Rmd | 158 +-- vignettes/userguide1-grammar.Rmd | 203 ++-- vignettes/userguide2-autoplot-methods.Rmd | 14 109 files changed, 4368 insertions(+), 2756 deletions(-)
Title: Distributed Linear Regression Models with Response Missing
Variables
Description: As a distributed imputation strategy, the Distributed full
information Multiple Imputation method is developed to impute
missing response variables in distributed linear regression.
The philosophy of the package is described in 'Guo' (2025)
<doi:10.1038/s41598-025-93333-6>.
Author: Guangbao Guo [aut, cre] ,
Limin Song [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between DLMRMV versions 0.1.0 dated 2025-04-08 and 0.2.0 dated 2025-06-24
DESCRIPTION | 17 +++++++++++------ MD5 | 18 ++++++++++++++++-- NAMESPACE | 34 ++++++++++++++++++++++------------ R/AVGM.R |only R/CSLMI.R |only R/DAVGMMI.R |only R/DCSLMI.R |only R/EMRE.R |only R/ERLS.R |only R/PMMMI.R |only man/AVGM.Rd |only man/CSLMI.Rd |only man/DAVGMMI.Rd |only man/DCSLMI.Rd |only man/EMRE.Rd |only man/ERLS.Rd |only man/PMMI.Rd |only 17 files changed, 49 insertions(+), 20 deletions(-)