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 0.3-17 dated 2025-05-15 and 0.3-18 dated 2025-07-03
ChangeLog | 9 ++ DESCRIPTION | 10 +-- MD5 | 22 +++--- data/stomata.rda |binary inst/doc/testStat.pdf |binary inst/preVignettes/kanova.bib | 11 +++ inst/preVignettes/testStat.aux | 17 +++-- inst/preVignettes/testStat.bbl | 9 ++ inst/preVignettes/testStat.blg | 58 ++++++++--------- inst/preVignettes/testStat.log | 32 +++++---- inst/preVignettes/testStat.pdf |binary inst/preVignettes/testStat.tex | 136 +++++++++++++++++++++++++---------------- 12 files changed, 187 insertions(+), 117 deletions(-)
Title: Partial Profile Score Feature Selection in High-Dimensional
Generalized Linear Interaction Models
Description: This is an implementation of the partial profile score feature
selection (PPSFS) approach to generalized linear (interaction) models.
The PPSFS is highly scalable even for ultra-high-dimensional feature space.
See the paper by Xu, Luo and Chen (2022, <doi:10.4310/21-SII706>).
Author: Zengchao Xu [aut, cre],
Shan Luo [aut],
Zehua Chen [aut]
Maintainer: Zengchao Xu <zengc.xu@aliyun.com>
Diff between PPSFS versions 0.1.0 dated 2022-03-21 and 0.1.1 dated 2025-07-03
DESCRIPTION | 12 ++++++------ MD5 | 20 ++++++++++---------- NEWS.md | 7 +++++++ R/RcppExports.R | 20 ++++++++++---------- R/ppsfs.R | 2 +- README.md | 2 +- build/partial.rdb |binary man/PPS-method.Rd | 2 +- man/PPSFS-package.Rd | 2 +- src/Makevars | 3 ++- src/Makevars.win | 3 ++- 11 files changed, 41 insertions(+), 32 deletions(-)
Title: Collecting Social Media Data and Generating Networks for
Analysis
Description: A suite of easy to use functions for collecting social media
data and generating networks for analysis. Supports Mastodon, YouTube,
Reddit and Web 1.0 data sources.
Author: Bryan Gertzel [aut, cre],
Robert Ackland [aut] ,
Timothy Graham [aut] ,
Francisca Borquez [ctb]
Maintainer: Bryan Gertzel <bryan.gertzel@anu.edu.au>
Diff between vosonSML versions 0.32.7 dated 2022-08-16 and 0.35.1 dated 2025-07-03
vosonSML-0.32.7/vosonSML/R/AddText.twitter.R |only vosonSML-0.32.7/vosonSML/R/AddUserData.R |only vosonSML-0.32.7/vosonSML/R/Authenticate.twitter.R |only vosonSML-0.32.7/vosonSML/R/Collect.reddit.R |only vosonSML-0.32.7/vosonSML/R/Collect.search.twitter.R |only vosonSML-0.32.7/vosonSML/R/Collect.timeline.twitter.R |only vosonSML-0.32.7/vosonSML/R/Create.activity.twitter.R |only vosonSML-0.32.7/vosonSML/R/Create.actor.twitter.R |only vosonSML-0.32.7/vosonSML/R/Create.semantic.twitter.R |only vosonSML-0.32.7/vosonSML/R/Create.twomode.twitter.R |only vosonSML-0.32.7/vosonSML/R/Utils.R |only vosonSML-0.32.7/vosonSML/R/import_rtweet.R |only vosonSML-0.32.7/vosonSML/R/tokens_twitter.R |only vosonSML-0.32.7/vosonSML/R/utils_twitter.R |only vosonSML-0.32.7/vosonSML/R/wrappers.R |only vosonSML-0.32.7/vosonSML/man/AddText.activity.twitter.Rd |only vosonSML-0.32.7/vosonSML/man/AddText.actor.twitter.Rd |only vosonSML-0.32.7/vosonSML/man/AddText.semantic.twitter.Rd |only vosonSML-0.32.7/vosonSML/man/AddText.twomode.twitter.Rd |only vosonSML-0.32.7/vosonSML/man/AddUserData.Rd |only vosonSML-0.32.7/vosonSML/man/AddUserData.actor.twitter.Rd |only vosonSML-0.32.7/vosonSML/man/AddUserData.twomode.twitter.Rd |only vosonSML-0.32.7/vosonSML/man/Authenticate.twitter.Rd |only vosonSML-0.32.7/vosonSML/man/Collect.reddit.Rd |only vosonSML-0.32.7/vosonSML/man/Collect.search.twitter.Rd |only vosonSML-0.32.7/vosonSML/man/Collect.timeline.twitter.Rd |only vosonSML-0.32.7/vosonSML/man/Create.activity.twitter.Rd |only vosonSML-0.32.7/vosonSML/man/Create.actor.twitter.Rd |only vosonSML-0.32.7/vosonSML/man/Create.semantic.twitter.Rd |only vosonSML-0.32.7/vosonSML/man/Create.twomode.twitter.Rd |only vosonSML-0.32.7/vosonSML/man/ImportRtweet.Rd |only vosonSML-0.32.7/vosonSML/man/auth_twitter_app.Rd |only vosonSML-0.32.7/vosonSML/man/auth_twitter_dev.Rd |only vosonSML-0.32.7/vosonSML/man/auth_twitter_user.Rd |only vosonSML-0.35.1/vosonSML/DESCRIPTION | 32 vosonSML-0.35.1/vosonSML/MD5 | 166 - vosonSML-0.35.1/vosonSML/NAMESPACE | 73 vosonSML-0.35.1/vosonSML/NEWS.md | 103 vosonSML-0.35.1/vosonSML/R/AddText.R | 89 vosonSML-0.35.1/vosonSML/R/AddText.mastodon.R |only vosonSML-0.35.1/vosonSML/R/AddVideoData.R | 78 vosonSML-0.35.1/vosonSML/R/Authenticate.R | 18 vosonSML-0.35.1/vosonSML/R/Authenticate.mastodon.R |only vosonSML-0.35.1/vosonSML/R/Authenticate.reddit.R | 5 vosonSML-0.35.1/vosonSML/R/Authenticate.web.R | 5 vosonSML-0.35.1/vosonSML/R/Authenticate.youtube.R | 10 vosonSML-0.35.1/vosonSML/R/Collect.R | 85 vosonSML-0.35.1/vosonSML/R/Collect.listing.reddit.R |only vosonSML-0.35.1/vosonSML/R/Collect.search.mastodon.R |only vosonSML-0.35.1/vosonSML/R/Collect.thread.mastodon.R |only vosonSML-0.35.1/vosonSML/R/Collect.thread.reddit.R |only vosonSML-0.35.1/vosonSML/R/Collect.web.R | 43 vosonSML-0.35.1/vosonSML/R/Collect.youtube.R | 115 vosonSML-0.35.1/vosonSML/R/Create.R | 69 vosonSML-0.35.1/vosonSML/R/Create.activity.mastodon.R |only vosonSML-0.35.1/vosonSML/R/Create.activity.reddit.R | 9 vosonSML-0.35.1/vosonSML/R/Create.activity.web.R | 8 vosonSML-0.35.1/vosonSML/R/Create.activity.youtube.R | 10 vosonSML-0.35.1/vosonSML/R/Create.actor.mastodon.R |only vosonSML-0.35.1/vosonSML/R/Create.actor.reddit.R | 7 vosonSML-0.35.1/vosonSML/R/Create.actor.web.R | 11 vosonSML-0.35.1/vosonSML/R/Create.actor.youtube.R | 19 vosonSML-0.35.1/vosonSML/R/Graph.R | 306 -- vosonSML-0.35.1/vosonSML/R/Merge.R | 161 - vosonSML-0.35.1/vosonSML/R/import_rtoot.R |only vosonSML-0.35.1/vosonSML/R/utils.R |only vosonSML-0.35.1/vosonSML/R/utils_mastodon.R |only vosonSML-0.35.1/vosonSML/R/utils_reddit.R | 122 - vosonSML-0.35.1/vosonSML/R/utils_web.R | 8 vosonSML-0.35.1/vosonSML/R/vosonSML-package.R | 4 vosonSML-0.35.1/vosonSML/R/zzz.R |only vosonSML-0.35.1/vosonSML/README.md | 956 +++---- vosonSML-0.35.1/vosonSML/build/vignette.rds |binary vosonSML-0.35.1/vosonSML/inst/CITATION | 31 vosonSML-0.35.1/vosonSML/inst/doc/Intro-to-vosonSML.R | 1141 +++------ vosonSML-0.35.1/vosonSML/inst/doc/Intro-to-vosonSML.Rmd | 642 ----- vosonSML-0.35.1/vosonSML/inst/doc/Intro-to-vosonSML.html | 1452 +++--------- vosonSML-0.35.1/vosonSML/man/AddText.Rd | 10 vosonSML-0.35.1/vosonSML/man/AddText.activity.mastodon.Rd |only vosonSML-0.35.1/vosonSML/man/AddText.activity.reddit.Rd | 6 vosonSML-0.35.1/vosonSML/man/AddText.actor.mastodon.Rd |only vosonSML-0.35.1/vosonSML/man/AddText.actor.reddit.Rd | 6 vosonSML-0.35.1/vosonSML/man/AddText.actor.youtube.Rd | 16 vosonSML-0.35.1/vosonSML/man/AddVideoData.Rd | 10 vosonSML-0.35.1/vosonSML/man/AddVideoData.actor.youtube.Rd | 8 vosonSML-0.35.1/vosonSML/man/Authenticate.Rd | 10 vosonSML-0.35.1/vosonSML/man/Authenticate.mastodon.Rd |only vosonSML-0.35.1/vosonSML/man/Authenticate.reddit.Rd | 4 vosonSML-0.35.1/vosonSML/man/Authenticate.web.Rd | 4 vosonSML-0.35.1/vosonSML/man/Authenticate.youtube.Rd | 4 vosonSML-0.35.1/vosonSML/man/Collect.Rd | 9 vosonSML-0.35.1/vosonSML/man/Collect.listing.reddit.Rd |only vosonSML-0.35.1/vosonSML/man/Collect.search.mastodon.Rd |only vosonSML-0.35.1/vosonSML/man/Collect.thread.mastodon.Rd |only vosonSML-0.35.1/vosonSML/man/Collect.thread.reddit.Rd |only vosonSML-0.35.1/vosonSML/man/Collect.web.Rd | 12 vosonSML-0.35.1/vosonSML/man/Collect.youtube.Rd | 18 vosonSML-0.35.1/vosonSML/man/Create.Rd | 18 vosonSML-0.35.1/vosonSML/man/Create.activity.mastodon.Rd |only vosonSML-0.35.1/vosonSML/man/Create.activity.reddit.Rd | 8 vosonSML-0.35.1/vosonSML/man/Create.activity.web.Rd | 15 vosonSML-0.35.1/vosonSML/man/Create.activity.youtube.Rd | 8 vosonSML-0.35.1/vosonSML/man/Create.actor.mastodon.Rd |only vosonSML-0.35.1/vosonSML/man/Create.actor.reddit.Rd | 6 vosonSML-0.35.1/vosonSML/man/Create.actor.web.Rd | 8 vosonSML-0.35.1/vosonSML/man/Create.actor.youtube.Rd | 6 vosonSML-0.35.1/vosonSML/man/Graph.Rd | 8 vosonSML-0.35.1/vosonSML/man/ImportRtoot.Rd |only vosonSML-0.35.1/vosonSML/man/Merge.Rd | 14 vosonSML-0.35.1/vosonSML/man/MergeFiles.Rd | 8 vosonSML-0.35.1/vosonSML/man/vosonSML-package.Rd | 7 vosonSML-0.35.1/vosonSML/vignettes/Intro-to-vosonSML.Rmd | 642 ----- 112 files changed, 2153 insertions(+), 4490 deletions(-)
Title: Prediction Intervals for Synthetic Control Methods with Multiple
Treated Units and Staggered Adoption
Description: Implementation of prediction and inference procedures for Synthetic Control methods using least square, lasso, ridge, or simplex-type constraints. Uncertainty is quantified with prediction intervals as developed in Cattaneo, Feng, and Titiunik (2021) <doi:10.1080/01621459.2021.1979561> for a single treated unit and in Cattaneo, Feng, Palomba, and Titiunik (2025) <doi:10.1162/rest_a_01588> for multiple treated units and staggered adoption. More details about the software implementation can be found in Cattaneo, Feng, Palomba, and Titiunik (2025) <doi:10.18637/jss.v113.i01>.
Author: Matias Cattaneo [aut],
Yingjie Feng [aut],
Filippo Palomba [aut, cre],
Rocio Titiunik [aut]
Maintainer: Filippo Palomba <fpalomba@princeton.edu>
Diff between scpi versions 3.0.0 dated 2025-01-31 and 3.0.1 dated 2025-07-03
DESCRIPTION | 27 +++++++++------- MD5 | 43 ++++++++++++++------------ NAMESPACE | 1 R/data.R | 34 ++++++++++----------- R/scdata.R | 32 +++++++------------ R/scdataMulti.R | 35 ++++++++------------- R/scdataMulti_methods.R | 76 +++++++++++++++++++++++------------------------ R/scest.R | 30 ++++++------------ R/scpi-package.R | 18 +++-------- R/scpi.R | 35 +++++++++------------ R/scplot.R | 20 +++--------- R/scplotMulti.R | 26 ++++++---------- R/supporting_functions.R | 1 build |only inst |only man/scdata.Rd | 19 +++-------- man/scdataMulti.Rd | 34 ++++++++------------- man/scest.Rd | 20 +++--------- man/scpi-package.Rd | 17 ++-------- man/scpi.Rd | 25 ++++++--------- man/scpi_germany.Rd | 2 - man/scplot.Rd | 20 +++--------- man/scplotMulti.Rd | 22 ++++--------- 23 files changed, 223 insertions(+), 314 deletions(-)
Title: Water Quality Models for Drinking Water Treatment Processes
Description: Provides multiple water chemistry-based models and published empirical models in one standard format.
As many models have been included as possible, however, users should be aware that models have varying degrees of accuracy and applicability.
To learn more, read the references provided below for the models implemented.
Functions can be chained together to model a complete treatment process and are designed to work in a 'tidyverse' workflow.
Models are primarily based on these sources:
Benjamin, M. M. (2002, ISBN:147862308X),
Crittenden, J. C., Trussell, R., Hand, D., Howe, J. K., & Tchobanoglous, G., Borchardt, J. H. (2012, ISBN:9781118131473),
USEPA. (2001) <https://www.epa.gov/sites/default/files/2017-03/documents/wtp_model_v._2.0_manual_508.pdf>.
Author: Sierra Johnson [aut, cre],
Libby McKenna [aut],
Riley Mulhern [aut] ,
Chris Corwin [aut] ,
Rachel Merrifield [ctb],
Mayuri Namasivayam [ctb],
Phoebe Chen [ctb],
Jiaming Yuan [ctb],
USEPA [cph] ),
Brown and Caldwell [fnd, cph]
Maintainer: Sierra Johnson <sjohnson2@brwncald.com>
Diff between tidywater versions 0.8.2 dated 2025-05-17 and 0.9.0 dated 2025-07-03
tidywater-0.8.2/tidywater/man/calculate_dic.Rd |only tidywater-0.9.0/tidywater/DESCRIPTION | 14 tidywater-0.9.0/tidywater/MD5 | 165 +++-- tidywater-0.9.0/tidywater/NAMESPACE | 13 tidywater-0.9.0/tidywater/NEWS.md | 27 tidywater-0.9.0/tidywater/R/balance_ions.R | 6 tidywater-0.9.0/tidywater/R/biofilter_toc.R | 20 tidywater-0.9.0/tidywater/R/blend_waters.R | 21 tidywater-0.9.0/tidywater/R/calculate_corrosion.R | 164 +++-- tidywater-0.9.0/tidywater/R/chemdose_chloramine.R | 11 tidywater-0.9.0/tidywater/R/chemdose_chlordecay.R | 4 tidywater-0.9.0/tidywater/R/chemdose_dbp.R | 151 +++-- tidywater-0.9.0/tidywater/R/chemdose_ph.R | 231 ++++++-- tidywater-0.9.0/tidywater/R/chemdose_toc.R | 120 ++-- tidywater-0.9.0/tidywater/R/convert_pluck_water.R | 8 tidywater-0.9.0/tidywater/R/decarbonate_ph.R |only tidywater-0.9.0/tidywater/R/define_water.R | 88 ++- tidywater-0.9.0/tidywater/R/dissolve_cu.R |only tidywater-0.9.0/tidywater/R/dissolve_pb.R | 4 tidywater-0.9.0/tidywater/R/general.R | 203 +++---- tidywater-0.9.0/tidywater/R/modify_water.R |only tidywater-0.9.0/tidywater/R/ozonate_bromate.R | 4 tidywater-0.9.0/tidywater/R/pac_toc.R | 13 tidywater-0.9.0/tidywater/R/solve_ph.R | 8 tidywater-0.9.0/tidywater/R/solvect_chlorine.R | 14 tidywater-0.9.0/tidywater/R/solvect_o3.R | 19 tidywater-0.9.0/tidywater/R/solvedose_ph_alk.R | 24 tidywater-0.9.0/tidywater/R/solveresid_o3.R | 8 tidywater-0.9.0/tidywater/R/waterclass.R | 22 tidywater-0.9.0/tidywater/README.md | 2 tidywater-0.9.0/tidywater/build/vignette.rds |binary tidywater-0.9.0/tidywater/data/mweights.rda |binary tidywater-0.9.0/tidywater/inst/doc/help_functions_blend_waters.R | 13 tidywater-0.9.0/tidywater/inst/doc/help_functions_blend_waters.Rmd | 49 - tidywater-0.9.0/tidywater/inst/doc/help_functions_blend_waters.html | 107 +-- tidywater-0.9.0/tidywater/inst/doc/help_functions_chemdose_ph.R | 27 tidywater-0.9.0/tidywater/inst/doc/help_functions_chemdose_ph.Rmd | 71 +- tidywater-0.9.0/tidywater/inst/doc/help_functions_chemdose_ph.html | 286 ++++++--- tidywater-0.9.0/tidywater/inst/doc/intro.Rmd | 18 tidywater-0.9.0/tidywater/inst/doc/intro.html | 46 + tidywater-0.9.0/tidywater/inst/doc/tidywater.R | 8 tidywater-0.9.0/tidywater/inst/doc/tidywater.Rmd | 31 - tidywater-0.9.0/tidywater/inst/doc/tidywater.html | 113 ++- tidywater-0.9.0/tidywater/man/balance_ions.Rd | 4 tidywater-0.9.0/tidywater/man/biofilter_toc.Rd | 6 tidywater-0.9.0/tidywater/man/blend_waters.Rd | 4 tidywater-0.9.0/tidywater/man/calculate_activity.Rd |only tidywater-0.9.0/tidywater/man/calculate_corrosion.Rd | 44 - tidywater-0.9.0/tidywater/man/chemdose_chloramine.Rd | 6 tidywater-0.9.0/tidywater/man/chemdose_chlordecay.Rd | 4 tidywater-0.9.0/tidywater/man/chemdose_dbp.Rd | 46 + tidywater-0.9.0/tidywater/man/chemdose_ph.Rd | 104 ++- tidywater-0.9.0/tidywater/man/chemdose_toc.Rd | 62 +- tidywater-0.9.0/tidywater/man/correct_k.Rd |only tidywater-0.9.0/tidywater/man/decarbonate_ph.Rd |only tidywater-0.9.0/tidywater/man/define_water.Rd | 72 ++ tidywater-0.9.0/tidywater/man/define_water_chain.Rd | 4 tidywater-0.9.0/tidywater/man/dissolve_cu.Rd |only tidywater-0.9.0/tidywater/man/dissolve_cu_once.Rd |only tidywater-0.9.0/tidywater/man/dissolve_pb.Rd | 4 tidywater-0.9.0/tidywater/man/modify_water.Rd |only tidywater-0.9.0/tidywater/man/ozonate_bromate.Rd | 4 tidywater-0.9.0/tidywater/man/pac_toc.Rd | 7 tidywater-0.9.0/tidywater/man/pluck_water.Rd | 4 tidywater-0.9.0/tidywater/man/solvect_chlorine.Rd | 7 tidywater-0.9.0/tidywater/man/solvect_o3.Rd | 3 tidywater-0.9.0/tidywater/man/solvedose_alk.Rd | 4 tidywater-0.9.0/tidywater/man/solvedose_ph.Rd | 4 tidywater-0.9.0/tidywater/man/summarize_wq.Rd | 4 tidywater-0.9.0/tidywater/man/tidywater-package.Rd | 3 tidywater-0.9.0/tidywater/tests/testthat/test-balance_ions.R | 1 tidywater-0.9.0/tidywater/tests/testthat/test-biofilter_toc.R | 33 - tidywater-0.9.0/tidywater/tests/testthat/test-blend_waters.R | 7 tidywater-0.9.0/tidywater/tests/testthat/test-calculate_corrosion.R | 287 ++++------ tidywater-0.9.0/tidywater/tests/testthat/test-chemdose_dbp.R | 143 +++- tidywater-0.9.0/tidywater/tests/testthat/test-chemdose_ph.R | 116 +++- tidywater-0.9.0/tidywater/tests/testthat/test-chemdose_toc.R | 77 ++ tidywater-0.9.0/tidywater/tests/testthat/test-decarbonate_ph.R |only tidywater-0.9.0/tidywater/tests/testthat/test-define_water.R | 9 tidywater-0.9.0/tidywater/tests/testthat/test-dissolve_cu.R |only tidywater-0.9.0/tidywater/tests/testthat/test-general.R | 23 tidywater-0.9.0/tidywater/tests/testthat/test-modify_water.R |only tidywater-0.9.0/tidywater/tests/testthat/test-solvect_chlorine.R | 11 tidywater-0.9.0/tidywater/tests/testthat/test-solvect_o3.R | 18 tidywater-0.9.0/tidywater/tests/testthat/test-solvedose_ph_alk.R | 8 tidywater-0.9.0/tidywater/tests/testthat/test-solveresid_o3.R | 4 tidywater-0.9.0/tidywater/vignettes/help_functions_blend_waters.Rmd | 49 - tidywater-0.9.0/tidywater/vignettes/help_functions_chemdose_ph.Rmd | 71 +- tidywater-0.9.0/tidywater/vignettes/intro.Rmd | 18 tidywater-0.9.0/tidywater/vignettes/tidywater.Rmd | 31 - 90 files changed, 2175 insertions(+), 1264 deletions(-)
Title: Interactive Analytic Networks
Description: Create interactive analytic networks. It joins the data analysis power of R to obtain coincidences, co-occurrences and correlations, and the visualization libraries of 'JavaScript' in one package.
Author: Modesto Escobar [cre, aut, cph] ,
David Barrios [aut],
Carlos Prieto [aut] ,
Luis Martinez-Uribe [aut] ,
Pablo Cabrera-Alvarez [aut] ,
Cristina Calvo-Lopez [aut]
Maintainer: Modesto Escobar <modesto@usal.es>
Diff between netCoin versions 2.1.0 dated 2025-01-15 and 2.1.9 dated 2025-07-03
DESCRIPTION | 31 ++-- MD5 | 52 +++---- R/coex.R | 84 +++++------ R/exports.R | 24 +-- R/get_templates.R | 17 ++ R/multigraph.R | 68 ++++----- R/pie.R | 74 +++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/netCoin.R | 54 +++---- inst/doc/netCoin.html | 4 inst/doc/surCoin.R | 80 +++++----- inst/doc/surCoin.Rmd | 336 +++++++++++++++++++++++----------------------- man/addDescription.Rd | 78 +++++----- man/addImage.Rd | 78 +++++----- man/cobCoin.Rd | 90 ++++++------ man/coexist.Rd | 108 +++++++------- man/d_netCorr.Rd | 114 +++++++-------- man/dyncohort.Rd | 106 +++++++------- man/exhibit.Rd | 12 + man/get_panel_template.Rd | 74 +++++----- man/get_template.Rd | 122 ++++++++-------- man/logCoin.Rd | 102 ++++++------- man/renderLinks.Rd | 78 +++++----- man/saveGhml.Rd | 62 ++++---- man/works.Rd | 68 ++++----- vignettes/surCoin.Rmd | 336 +++++++++++++++++++++++----------------------- 27 files changed, 1140 insertions(+), 1112 deletions(-)
Title: Statistical Methods for the Analysis of Excess Lifetimes
Description: A collection of parametric and nonparametric methods for the analysis of survival data. Parametric families implemented include Gompertz-Makeham, exponential and generalized Pareto models and extended models. The package includes an implementation of the nonparametric maximum likelihood estimator for arbitrary truncation and censoring pattern based on Turnbull (1976) <doi:10.1111/j.2517-6161.1976.tb01597.x>, along with graphical goodness-of-fit diagnostics. Parametric models for positive random variables and peaks over threshold models based on extreme value theory are described in Rootzén and Zholud (2017) <doi:10.1007/s10687-017-0305-5>; Belzile et al. (2021) <doi:10.1098/rsos.202097> and Belzile et al. (2022) <doi:10.1146/annurev-statistics-040120-025426>.
Author: Leo Belzile [aut, cre]
Maintainer: Leo Belzile <belzilel@gmail.com>
Diff between longevity versions 1.2 dated 2025-05-11 and 1.2.1 dated 2025-07-03
DESCRIPTION | 6 MD5 | 24 - NAMESPACE | 1 NEWS.md | 7 R/endpoint.R | 9 R/northrop.R | 712 ++++++++++++++++++------------- R/plots.R | 12 R/tests.R | 745 ++++++++++++++++++-------------- R/threshstab.R | 996 ++++++++++++++++++++++++++------------------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/introduction.html | 4 inst/doc/nonparametric.html | 6 13 files changed, 1492 insertions(+), 1030 deletions(-)
Title: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
Description: Provides the 'Molecular Signatures Database' (MSigDB) gene
sets typically used with the 'Gene Set Enrichment Analysis' (GSEA)
software (Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>,
Liberzon et al. 2015 <doi:10.1016/j.cels.2015.12.004>, Castanza et al.
2023 <doi:10.1038/s41592-023-02014-7>) as an R data frame. The package
includes the human genes as listed in MSigDB as well as the
corresponding symbols and IDs for frequently studied model organisms
such as mouse, rat, pig, fly, and yeast.
Author: Igor Dolgalev [aut, cre]
Maintainer: Igor Dolgalev <igor.dolgalev@nyumc.org>
Diff between msigdbr versions 24.1.0 dated 2025-05-13 and 25.1.0 dated 2025-07-03
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/msigdbr-package.R | 2 +- R/msigdbr.R | 34 +++++++++++++++++++++------------- R/utils.R | 12 ++++++++---- README.md | 30 +++++------------------------- man/msigdbr.Rd | 8 +++----- tests/testthat/test-msigdbr.R | 8 ++++---- 10 files changed, 59 insertions(+), 64 deletions(-)
Title: A Tool for Semi-Automating the Statistical Disclosure Control of
Research Outputs
Description: A Tool for Semi-Automating the Statistical Disclosure Control of Research Outputs.
Author: Jim Smith [cre, ctb] ,
Maha Albashir [aut, ctb],
Richard John Preen [aut, ctb]
Maintainer: Jim Smith <James.Smith@uwe.ac.uk>
Diff between acro versions 0.1.4 dated 2025-01-29 and 0.1.5 dated 2025-07-03
DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- NEWS.md | 4 ++++ R/create_virtualenv.R | 4 ++-- README.md | 3 +++ 5 files changed, 20 insertions(+), 12 deletions(-)
Title: Interface to the 'nanoarrow' 'C' Library
Description: Provides an 'R' interface to the 'nanoarrow' 'C' library and the
'Apache Arrow' application binary interface. Functions to import and
export 'ArrowArray', 'ArrowSchema', and 'ArrowArrayStream' 'C' structures
to and from 'R' objects are provided alongside helpers to facilitate zero-copy
data transfer among 'R' bindings to libraries implementing the 'Arrow' 'C'
data interface.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between nanoarrow versions 0.6.0-1 dated 2025-04-16 and 0.7.0 dated 2025-07-03
nanoarrow-0.6.0-1/nanoarrow/src/Makevars |only nanoarrow-0.7.0/nanoarrow/DESCRIPTION | 14 nanoarrow-0.7.0/nanoarrow/MD5 | 101 +- nanoarrow-0.7.0/nanoarrow/NAMESPACE | 8 nanoarrow-0.7.0/nanoarrow/NEWS.md | 9 nanoarrow-0.7.0/nanoarrow/R/as-array.R | 70 + nanoarrow-0.7.0/nanoarrow/R/buffer.R | 18 nanoarrow-0.7.0/nanoarrow/R/convert-array.R | 22 nanoarrow-0.7.0/nanoarrow/R/extension-vctrs.R | 6 nanoarrow-0.7.0/nanoarrow/R/extension.R | 2 nanoarrow-0.7.0/nanoarrow/R/ipc.R | 63 + nanoarrow-0.7.0/nanoarrow/R/nanoarrow-package.R | 8 nanoarrow-0.7.0/nanoarrow/R/schema.R | 8 nanoarrow-0.7.0/nanoarrow/R/type.R | 62 + nanoarrow-0.7.0/nanoarrow/configure |only nanoarrow-0.7.0/nanoarrow/man/convert_array.Rd | 2 nanoarrow-0.7.0/nanoarrow/man/example_ipc_stream.Rd |only nanoarrow-0.7.0/nanoarrow/man/na_type.Rd | 24 nanoarrow-0.7.0/nanoarrow/man/nanoarrow_extension_array.Rd | 2 nanoarrow-0.7.0/nanoarrow/man/nanoarrow_extension_spec.Rd | 2 nanoarrow-0.7.0/nanoarrow/man/nanoarrow_version.Rd | 5 nanoarrow-0.7.0/nanoarrow/man/read_nanoarrow.Rd | 3 nanoarrow-0.7.0/nanoarrow/src/Makevars.in |only nanoarrow-0.7.0/nanoarrow/src/Makevars.ucrt |only nanoarrow-0.7.0/nanoarrow/src/Makevars.win |only nanoarrow-0.7.0/nanoarrow/src/as_array.c | 121 ++ nanoarrow-0.7.0/nanoarrow/src/convert.c | 45 - nanoarrow-0.7.0/nanoarrow/src/convert.h | 4 nanoarrow-0.7.0/nanoarrow/src/convert_array.c | 1 nanoarrow-0.7.0/nanoarrow/src/convert_array_stream.c | 4 nanoarrow-0.7.0/nanoarrow/src/infer_ptype.c | 5 nanoarrow-0.7.0/nanoarrow/src/init.c | 2 nanoarrow-0.7.0/nanoarrow/src/materialize.c | 88 + nanoarrow-0.7.0/nanoarrow/src/materialize_chr.h | 35 nanoarrow-0.7.0/nanoarrow/src/materialize_common.h | 1 nanoarrow-0.7.0/nanoarrow/src/materialize_dbl.h | 39 nanoarrow-0.7.0/nanoarrow/src/nanoarrow.c | 251 +++++ nanoarrow-0.7.0/nanoarrow/src/nanoarrow.h | 447 ++++++---- nanoarrow-0.7.0/nanoarrow/src/nanoarrow_ipc.c | 327 ++++++- nanoarrow-0.7.0/nanoarrow/src/nanoarrow_ipc.h | 248 +++-- nanoarrow-0.7.0/nanoarrow/src/schema.c | 4 nanoarrow-0.7.0/nanoarrow/src/version.c | 8 nanoarrow-0.7.0/nanoarrow/tests/testthat/_snaps/buffer.md | 28 nanoarrow-0.7.0/nanoarrow/tests/testthat/test-altrep.R | 1 nanoarrow-0.7.0/nanoarrow/tests/testthat/test-array.R | 2 nanoarrow-0.7.0/nanoarrow/tests/testthat/test-as-array.R | 139 +++ nanoarrow-0.7.0/nanoarrow/tests/testthat/test-buffer.R | 37 nanoarrow-0.7.0/nanoarrow/tests/testthat/test-convert-array-stream.R | 115 ++ nanoarrow-0.7.0/nanoarrow/tests/testthat/test-convert-array.R | 114 ++ nanoarrow-0.7.0/nanoarrow/tests/testthat/test-extension-vctrs.R | 1 nanoarrow-0.7.0/nanoarrow/tests/testthat/test-infer-ptype.R | 13 nanoarrow-0.7.0/nanoarrow/tests/testthat/test-ipc.R | 25 nanoarrow-0.7.0/nanoarrow/tests/testthat/test-schema.R | 4 nanoarrow-0.7.0/nanoarrow/tests/testthat/test-type.R | 23 nanoarrow-0.7.0/nanoarrow/tools/test_zstd.c |only 55 files changed, 2111 insertions(+), 450 deletions(-)
Title: Interactive Maps with 'Mapbox GL JS' and 'MapLibre GL JS'
Description: Provides an interface to the 'Mapbox GL JS' (<https://docs.mapbox.com/mapbox-gl-js/guides>)
and the 'MapLibre GL JS' (<https://maplibre.org/maplibre-gl-js/docs/>) interactive mapping libraries to help users
create custom interactive maps in R. Users can create interactive globe visualizations; layer 'sf' objects to create
filled maps, circle maps, 'heatmaps', and three-dimensional graphics; and customize map styles and views. The package
also includes utilities to use 'Mapbox' and 'MapLibre' maps in 'Shiny' web applications.
Author: Kyle Walker [aut, cre]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between mapgl versions 0.3 dated 2025-06-16 and 0.3.1 dated 2025-07-03
DESCRIPTION | 8 MD5 | 50 NAMESPACE | 4 NEWS.md | 8 R/controls.R | 38 R/hover.R | 28 R/legends.R | 1330 +++-- R/query_rendered_features.R |only R/quickview.R | 1328 +++++ R/shiny.R | 1032 ++-- R/sources.R | 107 R/utils.R |only inst/htmlwidgets/lib/mapbox-pmtiles |only inst/htmlwidgets/mapboxgl.js | 184 inst/htmlwidgets/mapboxgl.yaml | 10 inst/htmlwidgets/mapboxgl_compare.js | 107 inst/htmlwidgets/mapboxgl_compare.yaml | 82 inst/htmlwidgets/maplibregl.js | 7330 +++++++++++++++++---------------- inst/htmlwidgets/maplibregl_compare.js | 97 man/add_layers_control.Rd | 22 man/add_pmtiles_source.Rd |only man/add_view.Rd |only man/clear_legend.Rd |only man/enable_shiny_hover.Rd | 6 man/get_queried_features.Rd |only man/legend_style.Rd |only man/map_legends.Rd | 188 man/mapboxgl_view.Rd | 13 man/maplibre_view.Rd | 13 man/query_rendered_features.Rd |only 30 files changed, 6869 insertions(+), 5116 deletions(-)
Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data sets,
regression models, and more. The code to create the tables is concise
and highly customizable. Data frames can be summarized with any
function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers.
Author: Daniel D. Sjoberg [aut, cre] ,
Joseph Larmarange [aut] ,
Michael Curry [aut] ,
Emily de la Rua [aut] ,
Jessica Lavery [aut] ,
Karissa Whiting [aut] ,
Emily C. Zabor [aut] ,
Xing Bai [ctb],
Esther Drill [ctb] ,
Jessica Flynn [ctb] ,
Margie Hannum [ctb [...truncated...]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between gtsummary versions 2.2.0 dated 2025-04-14 and 2.3.0 dated 2025-07-03
gtsummary-2.2.0/gtsummary/R/modify_column_indent.R |only gtsummary-2.2.0/gtsummary/man/modify_column_indent.Rd |only gtsummary-2.2.0/gtsummary/man/tbl_split.Rd |only gtsummary-2.2.0/gtsummary/tests/testthat/test-modify_column_indent.R |only gtsummary-2.2.0/gtsummary/vignettes/delete.docx |only gtsummary-2.3.0/gtsummary/DESCRIPTION | 41 gtsummary-2.3.0/gtsummary/MD5 | 305 +- gtsummary-2.3.0/gtsummary/NAMESPACE | 11 gtsummary-2.3.0/gtsummary/NEWS.md | 58 gtsummary-2.3.0/gtsummary/R/add_ci.R | 6 gtsummary-2.3.0/gtsummary/R/add_ci.tbl_svysummary.R | 6 gtsummary-2.3.0/gtsummary/R/add_difference.R | 2 gtsummary-2.3.0/gtsummary/R/add_difference.tbl_svysummary.R | 2 gtsummary-2.3.0/gtsummary/R/add_difference_row.R |only gtsummary-2.3.0/gtsummary/R/add_glance.R | 2 gtsummary-2.3.0/gtsummary/R/add_n.R | 8 gtsummary-2.3.0/gtsummary/R/add_overall.R | 80 gtsummary-2.3.0/gtsummary/R/add_p.R | 243 +- gtsummary-2.3.0/gtsummary/R/add_p.tbl_cross.R | 2 gtsummary-2.3.0/gtsummary/R/add_variable_group_header.R | 4 gtsummary-2.3.0/gtsummary/R/add_vif.R | 2 gtsummary-2.3.0/gtsummary/R/as_tibble.R | 1 gtsummary-2.3.0/gtsummary/R/assign_summary_digits.R | 12 gtsummary-2.3.0/gtsummary/R/brdg_hierarchical.R | 14 gtsummary-2.3.0/gtsummary/R/brdg_summary.R | 8 gtsummary-2.3.0/gtsummary/R/custom_tidiers.R | 2 gtsummary-2.3.0/gtsummary/R/deprecated.R | 23 gtsummary-2.3.0/gtsummary/R/filter_hierarchical.R | 37 gtsummary-2.3.0/gtsummary/R/gather_ard.R | 7 gtsummary-2.3.0/gtsummary/R/import-standalone-checks.R | 76 gtsummary-2.3.0/gtsummary/R/import-standalone-cli_call_env.R | 3 gtsummary-2.3.0/gtsummary/R/import-standalone-forcats.R | 5 gtsummary-2.3.0/gtsummary/R/inline_text.R | 10 gtsummary-2.3.0/gtsummary/R/inline_text.tbl_summary.R | 4 gtsummary-2.3.0/gtsummary/R/inline_text.tbl_survfit.R | 6 gtsummary-2.3.0/gtsummary/R/label_style.R | 17 gtsummary-2.3.0/gtsummary/R/modify_bold_italic.R | 2 gtsummary-2.3.0/gtsummary/R/modify_column_merge.R | 9 gtsummary-2.3.0/gtsummary/R/modify_fmt_fun.R | 2 gtsummary-2.3.0/gtsummary/R/modify_indent.R |only gtsummary-2.3.0/gtsummary/R/modify_post_fmt_fun.R | 10 gtsummary-2.3.0/gtsummary/R/modify_source_note.R | 2 gtsummary-2.3.0/gtsummary/R/modify_table_styling.R | 4 gtsummary-2.3.0/gtsummary/R/sort_hierarchical.R | 38 gtsummary-2.3.0/gtsummary/R/style_number.R | 8 gtsummary-2.3.0/gtsummary/R/style_percent.R | 10 gtsummary-2.3.0/gtsummary/R/style_pvalue.R | 35 gtsummary-2.3.0/gtsummary/R/style_ratio.R | 8 gtsummary-2.3.0/gtsummary/R/style_sigfig.R | 3 gtsummary-2.3.0/gtsummary/R/sysdata.rda |binary gtsummary-2.3.0/gtsummary/R/tbl_ard_hierarchical.R | 2 gtsummary-2.3.0/gtsummary/R/tbl_continuous.R | 4 gtsummary-2.3.0/gtsummary/R/tbl_custom_summary.R | 10 gtsummary-2.3.0/gtsummary/R/tbl_hierarchical.R | 78 gtsummary-2.3.0/gtsummary/R/tbl_likert.R | 4 gtsummary-2.3.0/gtsummary/R/tbl_merge.R | 40 gtsummary-2.3.0/gtsummary/R/tbl_regression.R | 48 gtsummary-2.3.0/gtsummary/R/tbl_regression_methods.R | 37 gtsummary-2.3.0/gtsummary/R/tbl_split.R | 352 ++- gtsummary-2.3.0/gtsummary/R/tbl_stack.R | 32 gtsummary-2.3.0/gtsummary/R/tbl_strata.R | 35 gtsummary-2.3.0/gtsummary/R/tbl_strata_nested_stack.R | 23 gtsummary-2.3.0/gtsummary/R/tbl_summary.R | 37 gtsummary-2.3.0/gtsummary/R/tbl_survfit.R | 8 gtsummary-2.3.0/gtsummary/R/tbl_svysummary.R | 41 gtsummary-2.3.0/gtsummary/R/tbl_uvregression.R | 1 gtsummary-2.3.0/gtsummary/R/tbl_wide_summary.R | 8 gtsummary-2.3.0/gtsummary/R/tests.R | 22 gtsummary-2.3.0/gtsummary/R/utils-add_p_tests.R | 2 gtsummary-2.3.0/gtsummary/R/utils-as.R | 2 gtsummary-2.3.0/gtsummary/build/vignette.rds |binary gtsummary-2.3.0/gtsummary/inst/WORDLIST | 1 gtsummary-2.3.0/gtsummary/inst/doc/gtsummary_definition.html | 1102 +++++----- gtsummary-2.3.0/gtsummary/man/add_difference.tbl_svysummary.Rd | 2 gtsummary-2.3.0/gtsummary/man/add_difference_row.Rd |only gtsummary-2.3.0/gtsummary/man/add_difference_row.tbl_summary.Rd |only gtsummary-2.3.0/gtsummary/man/add_variable_group_header.Rd | 2 gtsummary-2.3.0/gtsummary/man/add_vif.Rd | 2 gtsummary-2.3.0/gtsummary/man/brdg_summary.Rd | 4 gtsummary-2.3.0/gtsummary/man/deprecated.Rd | 10 gtsummary-2.3.0/gtsummary/man/filter_hierarchical.Rd | 10 gtsummary-2.3.0/gtsummary/man/label_style.Rd | 7 gtsummary-2.3.0/gtsummary/man/modify_bold_italic.Rd | 6 gtsummary-2.3.0/gtsummary/man/modify_column_merge.Rd | 10 gtsummary-2.3.0/gtsummary/man/modify_fmt_fun.Rd | 2 gtsummary-2.3.0/gtsummary/man/modify_indent.Rd |only gtsummary-2.3.0/gtsummary/man/modify_post_fmt_fun.Rd | 6 gtsummary-2.3.0/gtsummary/man/modify_source_note.Rd | 2 gtsummary-2.3.0/gtsummary/man/modify_table_styling.Rd | 6 gtsummary-2.3.0/gtsummary/man/sort_hierarchical.Rd | 10 gtsummary-2.3.0/gtsummary/man/style_number.Rd | 4 gtsummary-2.3.0/gtsummary/man/style_percent.Rd | 4 gtsummary-2.3.0/gtsummary/man/style_pvalue.Rd | 4 gtsummary-2.3.0/gtsummary/man/style_ratio.Rd | 4 gtsummary-2.3.0/gtsummary/man/style_sigfig.Rd | 4 gtsummary-2.3.0/gtsummary/man/tbl_ard_hierarchical.Rd | 6 gtsummary-2.3.0/gtsummary/man/tbl_custom_summary.Rd | 4 gtsummary-2.3.0/gtsummary/man/tbl_hierarchical.Rd | 8 gtsummary-2.3.0/gtsummary/man/tbl_merge.Rd | 14 gtsummary-2.3.0/gtsummary/man/tbl_regression_methods.Rd | 3 gtsummary-2.3.0/gtsummary/man/tbl_split_by.Rd |only gtsummary-2.3.0/gtsummary/man/tbl_stack.Rd | 22 gtsummary-2.3.0/gtsummary/man/tbl_strata.Rd | 11 gtsummary-2.3.0/gtsummary/man/tbl_summary.Rd | 10 gtsummary-2.3.0/gtsummary/man/tbl_svysummary.Rd | 4 gtsummary-2.3.0/gtsummary/man/tests.Rd | 7 gtsummary-2.3.0/gtsummary/tests/testthat/_snaps/add_difference.tbl_summary.md | 24 gtsummary-2.3.0/gtsummary/tests/testthat/_snaps/add_difference_row.tbl_summary.md |only gtsummary-2.3.0/gtsummary/tests/testthat/_snaps/add_overall.tbl_continuous.md | 10 gtsummary-2.3.0/gtsummary/tests/testthat/_snaps/add_overall.tbl_summary.md | 10 gtsummary-2.3.0/gtsummary/tests/testthat/_snaps/add_overall.tbl_svysummary.md | 10 gtsummary-2.3.0/gtsummary/tests/testthat/_snaps/add_p.tbl_summary.md | 18 gtsummary-2.3.0/gtsummary/tests/testthat/_snaps/tbl_hierarchical.md | 512 ++-- gtsummary-2.3.0/gtsummary/tests/testthat/_snaps/tbl_merge.md | 10 gtsummary-2.3.0/gtsummary/tests/testthat/_snaps/tbl_regression_methods.md | 18 gtsummary-2.3.0/gtsummary/tests/testthat/_snaps/tbl_split.md |only gtsummary-2.3.0/gtsummary/tests/testthat/_snaps/tbl_summary.md | 17 gtsummary-2.3.0/gtsummary/tests/testthat/_snaps/tbl_svysummary.md | 9 gtsummary-2.3.0/gtsummary/tests/testthat/test-add_ci.tbl_summary.R | 180 - gtsummary-2.3.0/gtsummary/tests/testthat/test-add_ci.tbl_svysummary.R | 162 - gtsummary-2.3.0/gtsummary/tests/testthat/test-add_difference.tbl_summary.R | 65 gtsummary-2.3.0/gtsummary/tests/testthat/test-add_difference_row.tbl_summary.R |only gtsummary-2.3.0/gtsummary/tests/testthat/test-add_glance.R | 4 gtsummary-2.3.0/gtsummary/tests/testthat/test-add_overall.tbl_continuous.R | 16 gtsummary-2.3.0/gtsummary/tests/testthat/test-add_overall.tbl_summary.R | 7 gtsummary-2.3.0/gtsummary/tests/testthat/test-add_overall.tbl_svysummary.R | 7 gtsummary-2.3.0/gtsummary/tests/testthat/test-add_p.tbl_continuous.R | 6 gtsummary-2.3.0/gtsummary/tests/testthat/test-add_p.tbl_cross.R | 4 gtsummary-2.3.0/gtsummary/tests/testthat/test-add_p.tbl_summary.R | 7 gtsummary-2.3.0/gtsummary/tests/testthat/test-add_q.R | 3 gtsummary-2.3.0/gtsummary/tests/testthat/test-add_stat.R | 3 gtsummary-2.3.0/gtsummary/tests/testthat/test-as_flex_table.R | 2 gtsummary-2.3.0/gtsummary/tests/testthat/test-as_gt.R | 2 gtsummary-2.3.0/gtsummary/tests/testthat/test-as_hux_table.R | 4 gtsummary-2.3.0/gtsummary/tests/testthat/test-as_kable_extra.R | 2 gtsummary-2.3.0/gtsummary/tests/testthat/test-filter_hierarchical.R | 38 gtsummary-2.3.0/gtsummary/tests/testthat/test-gather_ard.R | 109 gtsummary-2.3.0/gtsummary/tests/testthat/test-label_style.R | 11 gtsummary-2.3.0/gtsummary/tests/testthat/test-modify_caption.R | 3 gtsummary-2.3.0/gtsummary/tests/testthat/test-modify_indent.R |only gtsummary-2.3.0/gtsummary/tests/testthat/test-modify_post_fmt_fun.R | 16 gtsummary-2.3.0/gtsummary/tests/testthat/test-modify_spanning_header.R | 3 gtsummary-2.3.0/gtsummary/tests/testthat/test-sort_hierarchical.R | 13 gtsummary-2.3.0/gtsummary/tests/testthat/test-style_number.R | 5 gtsummary-2.3.0/gtsummary/tests/testthat/test-style_percent.R | 8 gtsummary-2.3.0/gtsummary/tests/testthat/test-style_pvalue.R | 12 gtsummary-2.3.0/gtsummary/tests/testthat/test-style_ratio.R | 5 gtsummary-2.3.0/gtsummary/tests/testthat/test-style_sigfig.R | 10 gtsummary-2.3.0/gtsummary/tests/testthat/test-tbl_ard_summary.R | 2 gtsummary-2.3.0/gtsummary/tests/testthat/test-tbl_custom_summary.R | 4 gtsummary-2.3.0/gtsummary/tests/testthat/test-tbl_hierarchical.R | 21 gtsummary-2.3.0/gtsummary/tests/testthat/test-tbl_merge.R | 7 gtsummary-2.3.0/gtsummary/tests/testthat/test-tbl_regression_methods.R | 11 gtsummary-2.3.0/gtsummary/tests/testthat/test-tbl_split.R | 270 ++ gtsummary-2.3.0/gtsummary/tests/testthat/test-tbl_stack.R | 14 gtsummary-2.3.0/gtsummary/tests/testthat/test-tbl_strata.R | 6 gtsummary-2.3.0/gtsummary/tests/testthat/test-tbl_strata_nested_stack.R | 17 gtsummary-2.3.0/gtsummary/tests/testthat/test-tbl_summary.R | 37 gtsummary-2.3.0/gtsummary/tests/testthat/test-tbl_svysummary.R | 63 gtsummary-2.3.0/gtsummary/tests/testthat/test-tbl_wide_summary.R | 2 gtsummary-2.3.0/gtsummary/tests/testthat/test-theme_elements_gtsummary.R | 64 161 files changed, 3301 insertions(+), 1767 deletions(-)
Title: Help to Fit of a Parametric Distribution to Non-Censored or
Censored Data
Description: Extends the fitdistr() function (of the MASS package) with several functions
to help the fit of a parametric distribution to non-censored or censored data.
Censored data may contain left censored, right censored and interval censored values,
with several lower and upper bounds. In addition to maximum likelihood estimation (MLE),
the package provides moment matching (MME), quantile matching (QME), maximum goodness-of-fit
estimation (MGE) and maximum spacing estimation (MSE) methods (available only for
non-censored data). Weighted versions of MLE, MME, QME and MSE are available. See e.g.
Casella & Berger (2002), Statistical inference, Pacific Grove, for a general introduction
to parametric estimation.
Author: Marie-Laure Delignette-Muller [aut] ,
Christophe Dutang [aut] ,
Regis Pouillot [ctb],
Jean-Baptiste Denis [ctb],
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between fitdistrplus versions 1.2-3 dated 2025-07-01 and 1.2-4 dated 2025-07-03
DESCRIPTION | 6 +- MD5 | 18 +++--- NEWS.md | 9 ++- inst/doc/FAQ.R | 4 - inst/doc/FAQ.Rmd | 4 - inst/doc/FAQ.html | 108 ++++++++++++++++++------------------ inst/doc/Optimalgo.html | 82 +++++++++++++-------------- inst/doc/fitdistrplus_vignette.html | 31 +++++----- inst/doc/starting-values.html | 4 - vignettes/FAQ.Rmd | 4 - 10 files changed, 139 insertions(+), 131 deletions(-)
Title: Interpreting Regression Effects
Description: The purpose of this package is to provide methods to interpret multiple
linear regression and canonical correlation results including beta weights,structure coefficients,
validity coefficients, product measures, relative weights, all-possible-subsets regression,
dominance analysis, commonality analysis, and adjusted effect sizes.
Author: Kim Nimon [aut, cre],
Fred Oswald [aut],
J. Kyle Roberts [aut]
Maintainer: Kim Nimon <kim.nimon@gmail.com>
Diff between yhat versions 2.0-4 dated 2023-10-10 and 2.0-5 dated 2025-07-03
DESCRIPTION | 13 ++++++++----- MD5 | 20 ++++++++++---------- R/calc.yhat.r | 9 +++++---- R/regr.R | 7 ++++--- man/boot.yhat.Rd | 8 ++++---- man/booteval.yhat.rd | 6 +++--- man/combCI.rd | 2 +- man/commonality.rd | 2 +- man/dombin.rd | 2 +- man/dominance.rd | 2 +- man/plotCI.yhat.rd | 8 ++++---- 11 files changed, 42 insertions(+), 37 deletions(-)
Title: Integrating Data Exchange and Analysis for Networks ('ideanet')
Description: A suite of convenient tools for social network analysis geared toward students, entry-level users, and non-expert practitioners. ‘ideanet’ features unique functions for the processing and measurement of sociocentric and egocentric network data. These functions automatically generate node- and system-level measures commonly used in the analysis of these types of networks. Outputs from these functions maximize the ability of novice users to employ network measurements in further analyses while making all users less prone to common data analytic errors. Additionally, ‘ideanet’ features an R Shiny graphic user interface that allows novices to explore network data with minimal need for coding.
Author: Tom Wolff [aut, cre] ,
Jonathan Howard Morgan [aut] ,
Gabriel Varela [aut] ,
Kieran Lele [aut],
Ethan Bhojani [aut],
Emily Heraty [aut],
Dana Pasquale [aut] ,
Peter Mucha [aut] ,
James Moody [aut]
Maintainer: Tom Wolff <tom.wolff@northwestern.edu>
Diff between ideanet versions 1.1.0 dated 2025-05-08 and 1.1.1 dated 2025-07-03
DESCRIPTION | 13 +-- MD5 | 56 ++++++------- NAMESPACE | 1 R/community_detection.R | 70 ++-------------- R/data.R | 6 - R/get_egograph.R |only R/netwrite.R | 183 +++++++++++++++++++++---------------------- R/role_analysis.R | 7 + build/partial.rdb |binary build/vignette.rds |binary inst/apps/ideanetViz/app.R | 9 -- inst/doc/CHAMP.R | 10 +- inst/doc/CHAMP.Rmd | 24 ++--- inst/doc/CHAMP.html | 79 +++++++++--------- inst/doc/CHAMP_football.Rmd | 4 inst/doc/CHAMP_football.html | 26 +++--- inst/doc/CHAMP_karate.Rmd | 2 inst/doc/CHAMP_karate.html | 10 +- inst/doc/ego_netwrite.html | 12 +- inst/doc/mrqap.html | 2 inst/doc/nc_read.html | 12 +- inst/doc/netwrite.html | 139 +++++++++++--------------------- inst/doc/roles.html | 26 +++--- man/florentine_edges.Rd | 2 man/florentine_nodes.Rd | 2 man/get_egograph.Rd |only man/hightech.Rd | 2 vignettes/CHAMP.Rmd | 24 ++--- vignettes/CHAMP_football.Rmd | 4 vignettes/CHAMP_karate.Rmd | 2 30 files changed, 324 insertions(+), 403 deletions(-)
Title: EcoPhyloMapper
Description: Facilitates the aggregation of species' geographic ranges from vector or raster spatial data, and that enables the calculation of various morphological and phylogenetic community metrics across geography. Citation: Title, PO, DL Swiderski and ML Zelditch (2022) <doi:10.1111/2041-210X.13914>.
Author: Pascal Title [aut, cre] ,
Donald Swiderski [aut],
Miriam Zelditch [aut]
Maintainer: Pascal Title <pascal.title@stonybrook.edu>
Diff between epm versions 1.1.4 dated 2025-02-14 and 1.1.5 dated 2025-07-03
DESCRIPTION | 9 +++++---- MD5 | 6 +++--- R/createEPMgrid.R | 6 +++++- build/partial.rdb |binary 4 files changed, 13 insertions(+), 8 deletions(-)
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 1.0.3 dated 2025-06-24 and 1.0.4 dated 2025-07-03
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 7 +++++++ data/troopdata_rebuild_long.rda |binary data/troopdata_rebuild_reports.rda |binary 5 files changed, 14 insertions(+), 7 deletions(-)
Title: Interactive Networks, Timelines, Barplots, Galleries with
'D3.js'
Description: Creates interactive analytic graphs with 'R'. It joins the data analysis power of R and the visualization libraries of JavaScript in one package. The package provides interactive networks, timelines, barplots, image galleries and evolving networks. Graphs are represented as 'D3.js' graphs embedded in a web page ready for its interactive analysis and exploration.
Author: Modesto Escobar [aut, cph, cre] ,
Carlos Prieto [aut] ,
David Barrios [aut]
Maintainer: Modesto Escobar <modesto@usal.es>
Diff between rD3plot versions 1.1.26 dated 2025-01-15 and 1.1.37 dated 2025-07-03
DESCRIPTION | 18 MD5 | 79 R/gallery.R | 53 R/layouts.R | 518 R/pie.R | 310 README.md | 26 inst/www/barplot.js | 1752 +-- inst/www/bootstrap.scrolling.nav.css |20398 +++++++++++++++++------------------ inst/www/ca.js | 1 inst/www/colorScales.js | 136 inst/www/d3.layout.cloud.js | 998 - inst/www/d3.min.js | 4 inst/www/en.js | 1 inst/www/es.js | 1 inst/www/functions.js | 61 inst/www/gallery.js | 3 inst/www/gallery2.js | 503 inst/www/help_es.html | 190 inst/www/html2canvas.min.js | 38 inst/www/iro.min.js | 14 inst/www/jspdf.min.js | 570 inst/www/jszip.min.js | 28 inst/www/multigraph.js | 212 inst/www/multipages.css | 264 inst/www/multipages.js | 370 inst/www/pie.js | 1298 +- inst/www/reset.css | 90 inst/www/styles.css | 3 inst/www/styles2.css | 276 inst/www/template.html | 24 inst/www/timeline.js | 2364 ++-- inst/www/tutorial.css | 254 inst/www/tutorial2.css |only inst/www/tutorial2.js |only inst/www/tutorial2_ca.js |only inst/www/tutorial2_en.js |only inst/www/tutorial2_es.js |only inst/www/tutorial_ca.js | 84 inst/www/tutorial_en.js | 84 inst/www/tutorial_es.js | 84 man/gallery2_rd3.Rd | 14 man/rd3_addDescription.Rd | 64 man/rd3_addImage.Rd | 64 43 files changed, 15992 insertions(+), 15259 deletions(-)
Title: G-Formula for Causal Inference via Multiple Imputation
Description: Implements the G-Formula method for causal inference with time-varying treatments and
confounders using Bayesian multiple imputation methods, as described by
Bartlett et al (2025) <doi:10.1177/09622802251316971>. It creates multiple synthetic imputed
datasets under treatment regimes of interest using the 'mice' package. These can then be analysed
using rules developed for analysing multiple synthetic datasets.
Author: Jonathan Bartlett [aut, cre] ,
Camila Olarte Parra [ctb] ,
Erik van Zwet [ctb]
Maintainer: Jonathan Bartlett <jonathan.bartlett1@lshtm.ac.uk>
Diff between gFormulaMI versions 1.0.1 dated 2025-05-13 and 1.0.2 dated 2025-07-03
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/gFormulaImpute.R | 8 +++++--- build/partial.rdb |binary build/vignette.rds |binary man/gFormulaImpute.Rd | 4 +++- tests/testthat/test-gFormulaMI.R | 12 +++++++++--- 8 files changed, 31 insertions(+), 17 deletions(-)
Title: Estimation and Visualization of Linear Panel Event Studies
Description: Estimates linear panel event study models. Plots coefficients following the recommendations in Freyaldenhoven et al. (2021) <doi:10.3386/w29170>. Includes sup-t bands, testing for key hypotheses, least wiggly path through the Wald region. Allows instrumental variables estimation following Freyaldenhoven et al. (2019) <doi:10.1257/aer.20180609>.
Author: Simon Freyaldenhoven [aut],
Christian Hansen [aut],
Jorge Perez Perez [aut],
Jesse Shapiro [aut],
Veli Andirin [aut],
Richard Calvo [aut],
Santiago Hermo [aut, cre],
Nathan Schor [aut],
Emily Wang [aut],
JMSLab [cph],
Ryan Kessler [cph]
Maintainer: Santiago Hermo <santiago.hermo@monash.edu>
Diff between eventstudyr versions 1.1.3 dated 2024-03-04 and 1.1.4 dated 2025-07-03
DESCRIPTION | 8 MD5 | 26 NAMESPACE | 58 - R/ComputeShifts.R | 202 +++--- R/EventStudy.R | 734 ++++++++++++------------ README.md | 3 build/vignette.rds |binary inst/doc/documentation.Rmd | 278 ++++----- inst/doc/documentation.html | 266 ++++---- man/figures/README-example-1.png |binary tests/testthat/test-ComputeShifts.R | 220 +++---- tests/testthat/test-EventStudy.R | 1038 +++++++++++++++++------------------ tests/testthat/test-EventStudyPlot.R | 80 +- vignettes/documentation.Rmd | 278 ++++----- 14 files changed, 1599 insertions(+), 1592 deletions(-)
Title: Extra Analysis Results Data Utilities
Description: Create extra Analysis Results Data (ARD) summary objects.
The package supplements the simple ARD functions from the 'cards'
package, exporting functions to put statistical results in the ARD
format. These objects are used and re-used to construct summary
tables, visualizations, and written reports.
Author: Daniel D. Sjoberg [aut, cre] ,
Abinaya Yogasekaram [aut],
Emily de la Rua [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between cardx versions 0.2.4 dated 2025-04-11 and 0.2.5 dated 2025-07-03
DESCRIPTION | 11 MD5 | 126 +++++----- NAMESPACE | 2 NEWS.md | 16 + R/add_total_n.survey.design.R | 4 R/ard_aod_wald_test.R | 2 R/ard_car_anova.R | 2 R/ard_car_vif.R | 2 R/ard_categorical.survey.design.R | 42 ++- R/ard_categorical_ci.R | 7 R/ard_categorical_ci.survey.design.R | 2 R/ard_categorical_max.R | 29 +- R/ard_continuous.survey.design.R | 35 ++ R/ard_continuous_ci.survey.design.R | 2 R/ard_dichotomous.survey.design.R | 15 + R/ard_incidence_rate.R |only R/ard_missing.survey.design.R | 25 +- R/ard_regression.R | 2 R/ard_stats_anova.R | 2 R/ard_stats_aov.R | 2 R/ard_survival_survdiff.R | 2 R/ard_survival_survfit.R | 2 R/ard_survival_survfit_diff.R | 4 R/cardx-package.R | 1 R/import-standalone-forcats.R | 5 README.md | 16 - inst/WORDLIST | 1 man/ard_categorical.survey.design.Rd | 7 man/ard_categorical_max.Rd | 24 +- man/ard_continuous.survey.design.Rd | 7 man/ard_dichotomous.survey.design.Rd | 7 man/ard_incidence_rate.Rd |only man/ard_missing.survey.design.Rd | 7 man/cardx-package.Rd | 2 man/construction_helpers.Rd | 4 tests/testthat/_snaps/ard_aod_wald_test.md | 14 - tests/testthat/_snaps/ard_attributes.survey.design.md | 2 tests/testthat/_snaps/ard_car_anova.md | 14 - tests/testthat/_snaps/ard_car_vif.md | 20 - tests/testthat/_snaps/ard_categorical_ci.survey.design.md | 2 tests/testthat/_snaps/ard_categorical_max.md | 165 ++++++++------ tests/testthat/_snaps/ard_continuous.survey.design.md | 46 +-- tests/testthat/_snaps/ard_continuous_ci.survey.design.md | 26 +- tests/testthat/_snaps/ard_emmeans_mean_difference.md | 36 +-- tests/testthat/_snaps/ard_incidence_rate.md |only tests/testthat/_snaps/ard_proportion_ci.md | 4 tests/testthat/_snaps/ard_regression.md | 6 tests/testthat/_snaps/ard_regression_basic.md | 2 tests/testthat/_snaps/ard_stats_aov.md | 33 -- tests/testthat/_snaps/ard_stats_kruskal_test.md | 10 tests/testthat/_snaps/ard_stats_mantelhaen_test.md | 36 +-- tests/testthat/_snaps/ard_stats_mood_test.md | 10 tests/testthat/_snaps/ard_survival_survfit.md | 18 - tests/testthat/_snaps/ard_total_n.survey.design.md | 6 tests/testthat/_snaps/construction_helpers.md | 10 tests/testthat/test-ard_categorical_ci.data.frame.R | 67 +++++ tests/testthat/test-ard_categorical_ci.survey.design.R | 2 tests/testthat/test-ard_categorical_max.R | 38 ++- tests/testthat/test-ard_continuous.survey.design.R | 4 tests/testthat/test-ard_emmeans_mean_difference.R | 4 tests/testthat/test-ard_incidence_rate.R |only tests/testthat/test-ard_regression.R | 4 tests/testthat/test-ard_regression_basic.R | 2 tests/testthat/test-ard_stats_aov.R | 3 tests/testthat/test-ard_survival_survfit.R | 17 + tests/testthat/test-ard_total_n.survey.design.R | 22 + 66 files changed, 653 insertions(+), 387 deletions(-)
Title: Generalized Additive Latent and Mixed Models
Description: Estimates generalized additive latent and
mixed models using maximum marginal likelihood,
as defined in Sorensen et al. (2023)
<doi:10.1007/s11336-023-09910-z>, which is an extension of Rabe-Hesketh and
Skrondal (2004)'s unifying framework for multilevel latent variable
modeling <doi:10.1007/BF02295939>. Efficient computation is done using sparse
matrix methods, Laplace approximation, and automatic differentiation. The
framework includes generalized multilevel models with heteroscedastic
residuals, mixed response types, factor loadings, smoothing splines,
crossed random effects, and combinations thereof. Syntax for model
formulation is close to 'lme4' (Bates et al. (2015)
<doi:10.18637/jss.v067.i01>) and 'PLmixed' (Rockwood and Jeon (2019)
<doi:10.1080/00273171.2018.1516541>).
Author: Oeystein Soerensen [aut, cre] ,
Douglas Bates [ctb],
Ben Bolker [ctb],
Martin Maechler [ctb],
Allan Leal [ctb],
Fabian Scheipl [ctb],
Steven Walker [ctb],
Simon Wood [ctb]
Maintainer: Oeystein Soerensen <oystein.sorensen@psykologi.uio.no>
Diff between galamm versions 0.2.2 dated 2025-05-11 and 0.2.3 dated 2025-07-03
DESCRIPTION | 6 MD5 | 56 ++-- R/galamm.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/glmm_factor.Rmd | 5 inst/doc/glmm_factor.html | 15 - inst/doc/lmm_factor.Rmd | 39 -- inst/doc/lmm_factor.html | 93 +++---- inst/doc/scaling.html | 10 inst/doc/semiparametric.Rmd | 78 ++--- inst/doc/semiparametric.html | 196 +++++++-------- tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/galamm-heteroscedastic.md | 34 ++ tests/testthat/test-galamm-glmm.R | 3 tests/testthat/test-galamm-heteroscedastic.R | 56 ++++ vignettes/glmm_factor.Rmd | 5 vignettes/lmm_factor.Rmd | 39 -- vignettes/scaling-glmm-plot-1.png |binary vignettes/scaling-hsced-plot-1.png |binary vignettes/scaling-lmm-plot-1.png |binary vignettes/scaling-semiparametric-binomial-plot-1.png |binary vignettes/scaling-semiparametric-gaussian-plot-1.png |binary vignettes/semiparametric-gamm4-binomial-1.png |binary vignettes/semiparametric-gaussian-by-factor1-1.png |binary vignettes/semiparametric-gaussian-by-factor2-1.png |binary vignettes/semiparametric-gaussian-gamm-smooth2-1.png |binary vignettes/semiparametric-gaussian-gamm4-diagnostic-1.png |binary vignettes/semiparametric.Rmd | 78 ++--- 29 files changed, 383 insertions(+), 334 deletions(-)
Title: Adaptive Lasso Quantile Regression with Fixed Effects
Description: Quantile regression with fixed effects solves longitudinal data, considering the individual intercepts as fixed effects. The parametric set of this type of problem used to be huge. Thus penalized methods such as Lasso are currently applied. Adaptive Lasso presents oracle proprieties, which include Gaussianity and correct model selection. Bayesian information criteria (BIC) estimates the optimal tuning parameter lambda. Plot tools are also available.
Author: Ian Meneghel Danilevicz [aut, cre] ,
Pascal Bondon [aut],
Valderio A. Reisen [aut]
Maintainer: Ian Meneghel Danilevicz <iandanilevicz@gmail.com>
Diff between alqrfe versions 1.1 dated 2022-11-30 and 1.2 dated 2025-07-03
alqrfe-1.1/alqrfe/R/LQRFE_main_v2.R |only alqrfe-1.1/alqrfe/build |only alqrfe-1.1/alqrfe/man/alqrfe-package.Rd |only alqrfe-1.1/alqrfe/man/bic_hat.Rd |only alqrfe-1.1/alqrfe/man/df_hat.Rd |only alqrfe-1.1/alqrfe/man/f_den.Rd |only alqrfe-1.1/alqrfe/man/f_tab.Rd |only alqrfe-1.1/alqrfe/man/loss_alqr.Rd |only alqrfe-1.1/alqrfe/man/loss_lqr.Rd |only alqrfe-1.1/alqrfe/man/loss_qr.Rd |only alqrfe-1.1/alqrfe/man/loss_qrfe.Rd |only alqrfe-1.1/alqrfe/man/make_z.Rd |only alqrfe-1.1/alqrfe/man/optim_alqr.Rd |only alqrfe-1.1/alqrfe/man/optim_lqr.Rd |only alqrfe-1.1/alqrfe/man/optim_qr.Rd |only alqrfe-1.1/alqrfe/man/optim_qrfe.Rd |only alqrfe-1.1/alqrfe/man/print.ALQRFE.Rd |only alqrfe-1.1/alqrfe/man/q_cov.Rd |only alqrfe-1.1/alqrfe/man/rho_koenker.Rd |only alqrfe-1.1/alqrfe/man/sgf.Rd |only alqrfe-1.1/alqrfe/src/Makevars |only alqrfe-1.2/alqrfe/DESCRIPTION | 18 +-- alqrfe-1.2/alqrfe/MD5 | 44 ++------- alqrfe-1.2/alqrfe/NAMESPACE | 14 ++ alqrfe-1.2/alqrfe/R/LQRFE_main_v3.R |only alqrfe-1.2/alqrfe/R/RcppExports.R | 154 +++++++++++++++++--------------- alqrfe-1.2/alqrfe/man/clean_data.Rd | 6 - alqrfe-1.2/alqrfe/man/mqr.Rd | 2 alqrfe-1.2/alqrfe/man/mqr_alpha.Rd | 2 alqrfe-1.2/alqrfe/man/plot_alpha.Rd | 2 alqrfe-1.2/alqrfe/man/plot_taus.Rd | 2 alqrfe-1.2/alqrfe/man/qr.Rd | 4 alqrfe-1.2/alqrfe/src/LQRFE_arma.cpp | 120 ++++++++++++++---------- alqrfe-1.2/alqrfe/src/Makevars.win | 15 --- 34 files changed, 199 insertions(+), 184 deletions(-)
Title: Simple and Configurable Tables in 'HTML', 'LaTeX', 'Markdown',
'Word', 'PNG', 'PDF', and 'Typst' Formats
Description: Create highly customized tables with this simple and dependency-free package. Data frames can be converted to 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', or 'Typst' tables. The user interface is minimalist and easy to learn. The syntax is concise. 'HTML' tables can be customized using the flexible 'Bootstrap' framework, and 'LaTeX' code with the 'tabularray' package.
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinytable versions 0.9.0 dated 2025-05-04 and 0.10.0 dated 2025-07-03
tinytable-0.10.0/tinytable/DESCRIPTION | 6 tinytable-0.10.0/tinytable/MD5 | 128 +++---- tinytable-0.10.0/tinytable/NEWS.md | 18 tinytable-0.10.0/tinytable/R/class.R | 26 - tinytable-0.10.0/tinytable/R/finalize_typst.R | 6 tinytable-0.10.0/tinytable/R/group_bootstrap.R | 15 tinytable-0.10.0/tinytable/R/group_tt.R | 89 ++++ tinytable-0.10.0/tinytable/R/sanity.R | 21 - tinytable-0.10.0/tinytable/R/strip_tt.R | 174 ++++----- tinytable-0.10.0/tinytable/R/style_bootstrap.R | 10 tinytable-0.10.0/tinytable/R/style_tt.R | 11 tinytable-0.10.0/tinytable/R/theme_multipage.R | 28 - tinytable-0.10.0/tinytable/R/theme_revealjs.R | 72 +++ tinytable-0.10.0/tinytable/R/theme_zzz.R | 10 tinytable-0.10.0/tinytable/R/tt.R | 41 +- tinytable-0.10.0/tinytable/R/tt_bootstrap.R | 50 ++ tinytable-0.10.0/tinytable/R/tt_grid.R | 36 + tinytable-0.10.0/tinytable/README.md | 2 tinytable-0.10.0/tinytable/build/partial.rdb |binary tinytable-0.10.0/tinytable/inst/templates/bootstrap.html | 49 +- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/format_tt-vignette_html_markdown.html | 61 +-- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/group_tt-html_tutorial_01.html | 181 +++++----- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/group_tt-issue165_html_centering_style.html | 141 ++++--- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/group_tt-issue258_01_html.html | 149 ++++---- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/group_tt-issue258_02_html.html | 151 ++++---- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/group_tt_delim-all-delim.md |only tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/group_tt_delim-alt-delim.md |only tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/group_tt_delim-no-delim.md |only tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/group_tt_delim-some-delim.md |only tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/group_tt_style_tt_group.tex |only tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-alignment.html | 91 ++--- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-bootstrap_css.html | 109 +++--- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-borders.html | 101 ++--- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-caption.html | 77 ++-- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-conditional_styling.html | 121 +++--- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-font_size.html | 109 +++--- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-footnote.html | 77 ++-- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-formatting.html | 85 ++-- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-heatmap.html | 129 +++---- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-images.html | 65 +-- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-individual_cells.html | 95 ++--- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-issue297.html |only tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-issue355a.html |only tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-issue355b.html |only tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-issue58.html | 175 ++++----- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-issue88.html | 165 ++++----- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-issue92.html | 71 ++- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-line_break.html | 61 +-- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-merge_cells.html | 105 +++-- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-missing_value.html | 69 ++- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-omit_headers.html | 93 ++--- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-spanning_cells.html | 97 ++--- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-striped.html | 103 ++--- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-striped_orange.html | 105 +++-- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/html-vectorized_color_j.html | 115 +++--- tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/markdown-long_column_group.txt |only tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/markdown-long_mixed_groups.txt |only tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/markdown-long_row_group.txt |only tinytable-0.10.0/tinytable/inst/tinytest/_tinysnapshot/markdown-multiple_long_row_groups.txt |only tinytable-0.10.0/tinytable/inst/tinytest/test-bugfix.R |only tinytable-0.10.0/tinytable/inst/tinytest/test-group_tt.R | 76 +++- tinytable-0.10.0/tinytable/inst/tinytest/test-html.R | 36 + tinytable-0.10.0/tinytable/inst/tinytest/test-latex.R | 112 ++---- tinytable-0.10.0/tinytable/inst/tinytest/test-markdown.R | 27 + tinytable-0.10.0/tinytable/inst/tinytest/test-theme.R | 9 tinytable-0.10.0/tinytable/inst/tinytest/test-tt.R | 12 tinytable-0.10.0/tinytable/man/group_tt.Rd | 42 +- tinytable-0.10.0/tinytable/man/initialize-tinytable-method.Rd | 2 tinytable-0.10.0/tinytable/man/style_tt.Rd | 2 tinytable-0.10.0/tinytable/man/theme_tt.Rd | 17 tinytable-0.10.0/tinytable/man/tt.Rd | 6 tinytable-0.9.0/tinytable/inst/tinytest/_tinysnapshot/html-issue297.txt |only 72 files changed, 2287 insertions(+), 1747 deletions(-)
Title: High Throughput Phenotyping (HTP) Data Analysis
Description: Phenotypic analysis of data coming from high throughput
phenotyping (HTP) platforms, including different types of outlier detection,
spatial analysis, and parameter estimation. The package is being developed
within the EPPN2020 project (<https://cordis.europa.eu/project/id/731013>).
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: Emilie J Millet [aut] ,
Maria Xose Rodriguez Alvarez [aut] ,
Diana Marcela Perez Valencia [aut] ,
Isabelle Sanchez [aut],
Nadine Hilgert [aut],
Bart-Jan van Rossum [aut, cre] ,
Fred van Eeuwijk [aut] ,
Martin Boer [aut]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenHTP versions 1.0.9 dated 2025-07-02 and 1.0.9.1 dated 2025-07-03
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 11 +++++++++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Overview_HTP.html | 10 +++++----- inst/tinytest/test_utils.R | 8 ++++---- 7 files changed, 28 insertions(+), 21 deletions(-)
Title: Machine Learning in R - Next Generation
Description: Efficient, object-oriented programming on the
building blocks of machine learning. Provides 'R6' objects for tasks,
learners, resamplings, and measures. The package is geared towards
scalability and larger datasets by supporting parallelization and
out-of-memory data-backends like databases. While 'mlr3' focuses on
the core computational operations, add-on packages provide additional
functionality.
Author: Michel Lang [aut] ,
Bernd Bischl [aut] ,
Jakob Richter [aut] ,
Patrick Schratz [aut] ,
Giuseppe Casalicchio [ctb] ,
Stefan Coors [ctb] ,
Quay Au [ctb] ,
Martin Binder [aut],
Florian Pfisterer [aut] ,
Raphael Sonabend [aut] ,
Lennart Schneider [ctb] , [...truncated...]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3 versions 1.0.0 dated 2025-06-18 and 1.0.1 dated 2025-07-03
DESCRIPTION | 20 +++++----- MD5 | 58 ++++++++++++++++--------------- NAMESPACE | 1 NEWS.md | 6 +++ R/BenchmarkResult.R | 2 - R/Learner.R | 5 ++ R/LearnerRegrDebug.R | 4 +- R/LearnerRegrFeatureless.R | 4 +- R/PredictionDataRegr.R | 2 - R/ResampleResult.R | 2 - R/Task.R | 14 +++---- R/TaskGeneratorPeak.R |only R/TaskRegr_california_housing.R | 2 - R/as_task_classif.R | 3 + R/as_task_regr.R | 3 + README.md | 9 ++-- man/TaskGenerator.Rd | 1 man/california_housing.Rd | 2 - man/mlr_task_generators.Rd | 1 man/mlr_task_generators_2dnormals.Rd | 1 man/mlr_task_generators_cassini.Rd | 1 man/mlr_task_generators_circle.Rd | 1 man/mlr_task_generators_friedman1.Rd | 1 man/mlr_task_generators_moons.Rd | 1 man/mlr_task_generators_peak.Rd |only man/mlr_task_generators_simplex.Rd | 1 man/mlr_task_generators_smiley.Rd | 1 man/mlr_task_generators_spirals.Rd | 1 man/mlr_task_generators_xor.Rd | 1 tests/testthat/test_PredictionDataRegr.R | 6 +-- tests/testthat/test_Task.R | 4 +- 31 files changed, 92 insertions(+), 66 deletions(-)
Title: Tools for Estimating, Measuring and Working with Migration Data
Description: Provides tools for estimating, measuring, and analyzing migration data. Designed to assist researchers and analysts in working effectively with migration data.
Author: Guy J. Abel [aut, cre]
Maintainer: Guy J. Abel <g.j.abel@gmail.com>
Diff between migest versions 2.0.4 dated 2023-11-18 and 2.0.5 dated 2025-07-03
migest-2.0.4/migest/R/sum_bilateral.R |only migest-2.0.5/migest/DESCRIPTION | 19 migest-2.0.5/migest/MD5 | 150 +++--- migest-2.0.5/migest/NAMESPACE | 13 migest-2.0.5/migest/NEWS.md | 98 ++-- migest-2.0.5/migest/R/alabama_1970.R | 4 migest-2.0.5/migest/R/dict_ims.R | 109 ++-- migest-2.0.5/migest/R/index_connectivity.R | 188 ++++---- migest-2.0.5/migest/R/index_distance.R | 172 ++++--- migest-2.0.5/migest/R/index_impact.R | 175 ++++--- migest-2.0.5/migest/R/ipumsi_age.R | 32 - migest-2.0.5/migest/R/korea_gravity.R | 66 +- migest-2.0.5/migest/R/mig_chord.R | 569 ++++++++++++------------- migest-2.0.5/migest/R/mig_matrix.R | 75 +-- migest-2.0.5/migest/R/mig_tibble.R | 73 +-- migest-2.0.5/migest/R/net_matrix_entropy.R |only migest-2.0.5/migest/R/net_matrix_ipf.R |only migest-2.0.5/migest/R/net_matrix_lp.R |only migest-2.0.5/migest/R/net_matrix_optim.R |only migest-2.0.5/migest/R/quadratic_eqn.R | 65 +- migest-2.0.5/migest/R/sum_bilat.R |only migest-2.0.5/migest/R/sum_expand.R | 362 ++++++++------- migest-2.0.5/migest/R/sum_lump.R | 341 +++++++------- migest-2.0.5/migest/R/sum_region.R | 281 ++++++------ migest-2.0.5/migest/README.md | 2 migest-2.0.5/migest/man/alabama_1970.Rd | 14 migest-2.0.5/migest/man/birth_mat.Rd | 46 +- migest-2.0.5/migest/man/block_matrix.Rd | 68 +- migest-2.0.5/migest/man/bombay_1951.Rd | 52 +- migest-2.0.5/migest/man/cm2.Rd | 158 +++--- migest-2.0.5/migest/man/cm3.Rd | 140 +++--- migest-2.0.5/migest/man/cm_net.Rd | 128 ++--- migest-2.0.5/migest/man/cm_net_tot.Rd | 146 +++--- migest-2.0.5/migest/man/death_mat.Rd | 62 +- migest-2.0.5/migest/man/dict_ims.Rd | 133 ++--- migest-2.0.5/migest/man/ffs_demo.Rd | 310 ++++++------- migest-2.0.5/migest/man/ffs_diff.Rd | 106 ++-- migest-2.0.5/migest/man/ffs_rates.Rd | 110 ++-- migest-2.0.5/migest/man/index_age.Rd | 144 +++--- migest-2.0.5/migest/man/index_age_rc.Rd | 58 +- migest-2.0.5/migest/man/index_connectivity.Rd | 134 ++--- migest-2.0.5/migest/man/index_distance.Rd | 132 ++--- migest-2.0.5/migest/man/index_impact.Rd | 162 +++---- migest-2.0.5/migest/man/index_intensity.Rd | 142 +++--- migest-2.0.5/migest/man/indian_sub.Rd | 58 +- migest-2.0.5/migest/man/ipf2.Rd | 166 +++---- migest-2.0.5/migest/man/ipf2_block.Rd | 132 ++--- migest-2.0.5/migest/man/ipf2_stripe.Rd | 136 ++--- migest-2.0.5/migest/man/ipf3.Rd | 184 ++++---- migest-2.0.5/migest/man/ipf3_qi.Rd | 194 ++++---- migest-2.0.5/migest/man/ipf_seed.Rd | 52 +- migest-2.0.5/migest/man/ipumsi_age.Rd | 56 +- migest-2.0.5/migest/man/italy_area.Rd | 56 +- migest-2.0.5/migest/man/korea_gravity.Rd | 43 + migest-2.0.5/migest/man/manila_1970.Rd | 60 +- migest-2.0.5/migest/man/mig_chord.Rd | 323 +++++++------- migest-2.0.5/migest/man/mig_matrix.Rd | 56 +- migest-2.0.5/migest/man/mig_tibble.Rd | 46 +- migest-2.0.5/migest/man/multi_comp.Rd | 72 +-- migest-2.0.5/migest/man/multi_comp2.Rd | 58 +- migest-2.0.5/migest/man/net_matrix_entropy.Rd |only migest-2.0.5/migest/man/net_matrix_ipf.Rd |only migest-2.0.5/migest/man/net_matrix_lp.Rd |only migest-2.0.5/migest/man/net_matrix_optim.Rd |only migest-2.0.5/migest/man/net_sr.Rd | 128 ++--- migest-2.0.5/migest/man/net_vs.Rd | 96 ++-- migest-2.0.5/migest/man/new_england_1960.Rd | 56 +- migest-2.0.5/migest/man/pipe.Rd | 40 - migest-2.0.5/migest/man/quadratic_eqn.Rd | 63 +- migest-2.0.5/migest/man/rc_model_fund.Rd | 46 +- migest-2.0.5/migest/man/rc_model_un.Rd | 52 +- migest-2.0.5/migest/man/rescale_integer_sum.Rd | 72 +-- migest-2.0.5/migest/man/stripe_matrix.Rd | 64 +- migest-2.0.5/migest/man/sum_bilat.Rd | 101 ++-- migest-2.0.5/migest/man/sum_expand.Rd | 190 ++++---- migest-2.0.5/migest/man/sum_lump.Rd | 174 +++---- migest-2.0.5/migest/man/sum_net.Rd | 58 +- migest-2.0.5/migest/man/sum_od.Rd | 54 +- migest-2.0.5/migest/man/sum_region.Rd | 184 ++++---- migest-2.0.5/migest/man/uar_1960.Rd | 50 +- migest-2.0.5/migest/man/usa_1960.Rd | 56 +- 81 files changed, 4191 insertions(+), 4024 deletions(-)
Title: Mapping Averaged Pairwise Information
Description: Mapping Averaged Pairwise Information (MAPI) is an
exploratory method providing graphical representations summarizing the
spatial variation of pairwise metrics (eg. distance, similarity
coefficient, ...) computed between georeferenced samples.
Author: Sylvain Piry [aut, cre] ,
Thomas Campolunghi [aut],
Florent Cestier [aut],
Karine Berthier [aut]
Maintainer: Sylvain Piry <sylvain.piry@inrae.fr>
Diff between mapi versions 1.1.3 dated 2025-06-27 and 1.1.4 dated 2025-07-03
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++-- R/MAPI_RunOnGrid.R | 2 +- tests/testthat/test-MAPI_RunOnGrid.R | 7 ++++++- tests/testthat/test-MAPI_Tails.R | 3 ++- 6 files changed, 20 insertions(+), 14 deletions(-)
Title: Analysis Results Data
Description: Construct CDISC (Clinical Data Interchange Standards
Consortium) compliant Analysis Results Data objects. These objects are
used and re-used to construct summary tables, visualizations, and
written reports. The package also exports utilities for working with
these objects and creating new Analysis Results Data objects.
Author: Daniel D. Sjoberg [aut, cre] ,
Becca Krouse [aut],
Emily de la Rua [aut],
F. Hoffmann-La Roche AG [cph, fnd],
GlaxoSmithKline Research & Development Limited [cph]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between cards versions 0.6.0 dated 2025-04-11 and 0.6.1 dated 2025-07-03
cards-0.6.0/cards/R/apply_fmt_fn.R |only cards-0.6.0/cards/man/alias_as_fmt_fn.Rd |only cards-0.6.0/cards/man/apply_fmt_fn.Rd |only cards-0.6.0/cards/man/dot-default_fmt_fn.Rd |only cards-0.6.0/cards/tests/testthat/_snaps/apply_fmt_fn.md |only cards-0.6.0/cards/tests/testthat/test-apply_fmt_fn.R |only cards-0.6.1/cards/DESCRIPTION | 13 cards-0.6.1/cards/MD5 | 206 ++-- cards-0.6.1/cards/NAMESPACE | 5 cards-0.6.1/cards/NEWS.md | 24 cards-0.6.1/cards/R/add_calculated_row.R | 20 cards-0.6.1/cards/R/apply_fmt_fun.R |only cards-0.6.1/cards/R/ard_attributes.R | 2 cards-0.6.1/cards/R/ard_categorical.R | 25 cards-0.6.1/cards/R/ard_complex.R | 16 cards-0.6.1/cards/R/ard_continuous.R | 44 - cards-0.6.1/cards/R/ard_dichotomous.R | 15 cards-0.6.1/cards/R/ard_hierarchical.R | 52 - cards-0.6.1/cards/R/ard_identity.R |only cards-0.6.1/cards/R/ard_missing.R | 15 cards-0.6.1/cards/R/ard_stack_hierarchical.R | 166 ++- cards-0.6.1/cards/R/as_nested_list.R | 4 cards-0.6.1/cards/R/cards-package.R | 1 cards-0.6.1/cards/R/check_ard_structure.R | 4 cards-0.6.1/cards/R/deprecated.R | 35 cards-0.6.1/cards/R/filter_ard_hierarchical.R | 33 cards-0.6.1/cards/R/import-standalone-checks.R | 31 cards-0.6.1/cards/R/import-standalone-cli_call_env.R | 3 cards-0.6.1/cards/R/import-standalone-forcats.R | 5 cards-0.6.1/cards/R/mock.R | 12 cards-0.6.1/cards/R/options.R | 7 cards-0.6.1/cards/R/print.R | 14 cards-0.6.1/cards/R/rename_ard_columns.R | 4 cards-0.6.1/cards/R/shuffle_ard.R | 91 +- cards-0.6.1/cards/R/sort_ard_hierarchical.R | 133 ++- cards-0.6.1/cards/R/tidy_ard_order.R | 2 cards-0.6.1/cards/R/tidy_as_ard.R | 2 cards-0.6.1/cards/R/unlist_ard_columns.R | 8 cards-0.6.1/cards/R/update_ard.R | 31 cards-0.6.1/cards/README.md | 2 cards-0.6.1/cards/data/ADAE.rda |binary cards-0.6.1/cards/data/ADSL.rda |binary cards-0.6.1/cards/data/ADTTE.rda |binary cards-0.6.1/cards/inst/WORDLIST | 3 cards-0.6.1/cards/man/adam.Rd | 4 cards-0.6.1/cards/man/add_calculated_row.Rd | 9 cards-0.6.1/cards/man/alias_as_fmt_fun.Rd |only cards-0.6.1/cards/man/apply_fmt_fun.Rd |only cards-0.6.1/cards/man/ard_categorical.Rd | 13 cards-0.6.1/cards/man/ard_complex.Rd | 12 cards-0.6.1/cards/man/ard_continuous.Rd | 7 cards-0.6.1/cards/man/ard_dichotomous.Rd | 9 cards-0.6.1/cards/man/ard_hierarchical.Rd | 12 cards-0.6.1/cards/man/ard_identity.Rd |only cards-0.6.1/cards/man/ard_missing.Rd | 7 cards-0.6.1/cards/man/ard_stack_hierarchical.Rd | 10 cards-0.6.1/cards/man/cards.options.Rd | 7 cards-0.6.1/cards/man/deprecated.Rd | 9 cards-0.6.1/cards/man/dot-check_fmt_string.Rd | 2 cards-0.6.1/cards/man/dot-check_var_nms.Rd | 2 cards-0.6.1/cards/man/dot-default_fmt_fun.Rd |only cards-0.6.1/cards/man/dot-fill_overall_grp_values.Rd | 6 cards-0.6.1/cards/man/dot-one_row_ard_to_nested_list.Rd | 2 cards-0.6.1/cards/man/filter_ard_hierarchical.Rd | 4 cards-0.6.1/cards/man/label_round.Rd | 2 cards-0.6.1/cards/man/mock.Rd | 6 cards-0.6.1/cards/man/print.card.Rd | 2 cards-0.6.1/cards/man/rename_ard_columns.Rd | 4 cards-0.6.1/cards/man/shuffle_ard.Rd | 2 cards-0.6.1/cards/man/sort_ard_hierarchical.Rd | 4 cards-0.6.1/cards/man/unlist_ard_columns.Rd | 8 cards-0.6.1/cards/man/update_ard.Rd | 23 cards-0.6.1/cards/tests/testthat/_snaps/add_calculated_row.md | 8 cards-0.6.1/cards/tests/testthat/_snaps/apply_fmt_fun.md |only cards-0.6.1/cards/tests/testthat/_snaps/ard_attributes.md | 2 cards-0.6.1/cards/tests/testthat/_snaps/ard_categorical.md | 12 cards-0.6.1/cards/tests/testthat/_snaps/ard_continuous.md | 24 cards-0.6.1/cards/tests/testthat/_snaps/ard_dichotomous.md | 2 cards-0.6.1/cards/tests/testthat/_snaps/ard_hierarchical.md | 9 cards-0.6.1/cards/tests/testthat/_snaps/ard_identity.md |only cards-0.6.1/cards/tests/testthat/_snaps/ard_missing.md | 2 cards-0.6.1/cards/tests/testthat/_snaps/ard_pairwise.md | 2 cards-0.6.1/cards/tests/testthat/_snaps/ard_stack.md | 8 cards-0.6.1/cards/tests/testthat/_snaps/ard_stack_hierarchical.md | 53 - cards-0.6.1/cards/tests/testthat/_snaps/ard_strata.md | 4 cards-0.6.1/cards/tests/testthat/_snaps/ard_total_n.md | 4 cards-0.6.1/cards/tests/testthat/_snaps/bind_ard.md | 22 cards-0.6.1/cards/tests/testthat/_snaps/filter_ard_hierarchical.md | 2 cards-0.6.1/cards/tests/testthat/_snaps/mock.md | 32 cards-0.6.1/cards/tests/testthat/_snaps/options.md | 2 cards-0.6.1/cards/tests/testthat/_snaps/print.md | 38 cards-0.6.1/cards/tests/testthat/_snaps/shuffle_ard.md | 45 - cards-0.6.1/cards/tests/testthat/_snaps/tidy_as_ard.md | 58 - cards-0.6.1/cards/tests/testthat/_snaps/update_ard.md | 36 cards-0.6.1/cards/tests/testthat/test-add_calculated_row.R | 4 cards-0.6.1/cards/tests/testthat/test-apply_fmt_fun.R |only cards-0.6.1/cards/tests/testthat/test-ard_categorical.R | 432 ++++++++-- cards-0.6.1/cards/tests/testthat/test-ard_continuous.R | 16 cards-0.6.1/cards/tests/testthat/test-ard_dichotomous.R | 2 cards-0.6.1/cards/tests/testthat/test-ard_hierarchical.R | 146 ++- cards-0.6.1/cards/tests/testthat/test-ard_identity.R |only cards-0.6.1/cards/tests/testthat/test-ard_missing.R | 2 cards-0.6.1/cards/tests/testthat/test-ard_stack_hierarchical.R | 189 +++- cards-0.6.1/cards/tests/testthat/test-bind_ard.R | 4 cards-0.6.1/cards/tests/testthat/test-filter_ard_hierarchical.R | 38 cards-0.6.1/cards/tests/testthat/test-mock.R | 10 cards-0.6.1/cards/tests/testthat/test-options.R | 8 cards-0.6.1/cards/tests/testthat/test-print.R | 4 cards-0.6.1/cards/tests/testthat/test-print_ard_conditions.R | 2 cards-0.6.1/cards/tests/testthat/test-shuffle_ard.R | 23 cards-0.6.1/cards/tests/testthat/test-sort_ard_hierarchical.R | 159 ++- cards-0.6.1/cards/tests/testthat/test-update_ard.R | 22 112 files changed, 1791 insertions(+), 829 deletions(-)
Title: Flexible, Extensible, & Reproducible Pupillometry Preprocessing
Description: Pupillometry offers a non-invasive window into the mind and has been used extensively as a psychophysiological readout of arousal signals linked with cognitive processes like attention, stress, and emotional states [Clewett et al. (2020) <doi:10.1038/s41467-020-17851-9>; Kret & Sjak-Shie (2018) <doi:10.3758/s13428-018-1075-y>; Strauch (2024) <doi:10.1016/j.tins.2024.06.002>]. Yet, despite decades of pupillometry research, many established packages and workflows to date lack design patterns based on Findability, Accessibility, Interoperability, and Reusability (FAIR) principles [see Wilkinson et al. (2016) <doi:10.1038/sdata.2016.18>]. 'eyeris' provides a modular, performant, and extensible preprocessing framework for pupillometry data with BIDS-like organization and interactive output reports [Esteban et al. (2019) <doi:10.1038/s41592-018-0235-4>; Gorgolewski et al. (2016) <doi:10.1038/sdata.2016.44>]. Development was supported, in part, by the S [...truncated...]
Author: Shawn Schwartz [aut, cre] ,
Mingjian He [ctb],
Haopei Yang [ctb],
Alice Xue [ctb],
Gustavo Santiago-Reyes [ctb]
Maintainer: Shawn Schwartz <shawn.t.schwartz@gmail.com>
Diff between eyeris versions 1.2.1 dated 2025-06-13 and 2.0.0 dated 2025-07-03
DESCRIPTION | 85 MD5 | 234 +- NAMESPACE | 12 NEWS.md | 360 ++- R/constants.R | 44 R/eyeris-package.R | 7 R/pipeline-bidsify.R | 1916 +++++++++++++++--- R/pipeline-bin.R |only R/pipeline-confounds.R |only R/pipeline-deblink.R | 62 R/pipeline-detransient.R | 76 R/pipeline-detrend.R | 36 R/pipeline-downsample.R |only R/pipeline-epoch.R | 288 ++ R/pipeline-glassbox.R | 703 +++++- R/pipeline-handler.R | 208 + R/pipeline-interpolate.R | 42 R/pipeline-loadasc.R | 79 R/pipeline-lpfilt.R | 76 R/pipeline-zscore.R | 54 R/plot.eyeris.R | 485 +++- R/utils-alert.R | 14 R/utils-baseline.R | 113 - R/utils-checks.R | 222 +- R/utils-epoch.R | 158 + R/utils-error_handler.R | 12 R/utils-eyelogger.R | 8 R/utils-gallery.R | 23 R/utils-parsers.R | 153 + R/utils-progress_bar.R | 36 R/utils-render_report.R | 417 +++ R/zzz.R | 18 README.md | 104 build/partial.rdb |binary build/vignette.rds |binary inst/doc/anatomy.R | 5 inst/doc/anatomy.Rmd | 6 inst/doc/anatomy.html | 10 inst/doc/complete-pipeline.R | 4 inst/doc/complete-pipeline.Rmd | 4 inst/doc/complete-pipeline.html | 54 inst/doc/custom-extensions.R | 43 inst/doc/custom-extensions.Rmd | 87 inst/doc/custom-extensions.html | 152 + inst/doc/epoching-bids-reports.html | 141 - inst/doc/reports.R | 9 inst/doc/reports.Rmd | 38 inst/doc/reports.html | 87 man/add_unique_event_identifiers.Rd |only man/add_unique_identifiers_to_df.Rd |only man/alert.Rd |only man/bidsify.Rd | 115 - man/bin.Rd |only man/bin_pupil.Rd |only man/calc_euclidean_dist.Rd |only man/calculate_epoched_confounds.Rd |only man/check_and_create_dir.Rd |only man/check_baseline_epoch_counts.Rd |only man/check_baseline_inputs.Rd |only man/check_baseline_mean.Rd |only man/check_column.Rd |only man/check_data.Rd |only man/check_epoch_input.Rd |only man/check_epoch_manual_input_data.Rd |only man/check_epoch_manual_input_dfs.Rd |only man/check_epoch_msg_values.Rd |only man/check_input.Rd |only man/check_limits.Rd |only man/check_pupil_cols.Rd |only man/check_start_end_timestamps.Rd |only man/check_time_monotonic.Rd |only man/clean_string.Rd |only man/compute_baseline.Rd |only man/convert_nested_dt.Rd |only man/count_epochs.Rd |only man/counter_bar.Rd |only man/deblink.Rd | 13 man/deblink_pupil.Rd |only man/detransient.Rd | 11 man/detransient_pupil.Rd |only man/detrend.Rd | 11 man/detrend_pupil.Rd |only man/downsample.Rd |only man/downsample_pupil.Rd |only man/draw_na_lines.Rd |only man/draw_random_epochs.Rd |only man/epoch.Rd | 65 man/epoch_and_baseline_block.Rd |only man/epoch_manually.Rd |only man/epoch_only_start_msg.Rd |only man/epoch_pupil.Rd |only man/epoch_start_end_msg.Rd |only man/epoch_start_msg_and_limits.Rd |only man/error_handler.Rd |only man/evaluate_pipeline_step_params.Rd |only man/export_confounds_to_csv.Rd |only man/extract_baseline_epochs.Rd |only man/eyelink_asc_demo_dataset.Rd | 2 man/eyelogger.Rd | 8 man/eyeris_color_palette.Rd |only man/figures/README-timeseries-plot-1.png |binary man/figures/README-timeseries-plot-2.png |binary man/figures/README-timeseries-plot-3.png |only man/figures/README-timeseries-plot-4.png |only man/figures/README-timeseries-plot-5.png |only man/figures/README-timeseries-plot-6.png |only man/figures/README-timeseries-plot-7.png |only man/figures/README-timeseries-plot-8.png |only man/figures/README-unnamed-chunk-3-1.png |binary man/filter_epochs.Rd |only man/find_baseline_structure.Rd |only man/format_call_stack.Rd |only man/get_block_numbers.Rd |only man/get_confounds_for_step.Rd |only man/get_timestamps.Rd |only man/glassbox.Rd | 33 man/index_metadata.Rd |only man/interpolate.Rd | 11 man/interpolate_pupil.Rd |only man/load_asc.Rd | 2 man/lpfilt.Rd | 33 man/lpfilt_pupil.Rd |only man/make_baseline_label.Rd |only man/make_epoch_label.Rd |only man/make_gallery.Rd |only man/make_md_table.Rd |only man/make_md_table_multiline.Rd |only man/make_prog_summary_plot.Rd |only man/make_report.Rd |only man/merge_events_with_timeseries.Rd |only man/normalize_gaze_coords.Rd |only man/parse_call_stack.Rd |only man/parse_eyelink_info.Rd |only man/pipeline_handler.Rd | 27 man/plot.eyeris.Rd | 49 man/plot_detrend_overlay.Rd | 3 man/plot_gaze_heatmap.Rd |only man/plot_pupil_distribution.Rd |only man/plot_with_seed.Rd |only man/print_lightbox_img_html.Rd |only man/print_plots.Rd |only man/process_epoch_and_baselines.Rd |only man/progress_bar.Rd |only man/prompt_user.Rd |only man/render_report.Rd |only man/robust_plot.Rd |only man/sanitize_event_tag.Rd |only man/save_detrend_plots.Rd |only man/save_progressive_summary_plots.Rd |only man/slice_epoch.Rd |only man/slice_epochs_no_limits.Rd |only man/slice_epochs_with_limits.Rd |only man/speed.Rd |only man/summarize_confounds.Rd |only man/tag_blinks.Rd |only man/tag_gaze_coords.Rd |only man/tick.Rd |only man/zscore.Rd | 11 man/zscore_pupil.Rd |only tests/testthat/test-bin.R |only tests/testthat/test-downsample.R |only tests/testthat/test-plot_gaze_heatmap.R |only tests/testthat/test-time_monotonicity.R |only vignettes/anatomy.Rmd | 6 vignettes/complete-pipeline.Rmd | 4 vignettes/custom-extensions.Rmd | 87 vignettes/psychopy-eyetracker-sr-research-plug-in.png |binary vignettes/reports.Rmd | 38 168 files changed, 5893 insertions(+), 1321 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-02-07 0.8.2
2024-03-30 0.8.1
2023-09-30 0.8.0
2023-05-09 0.7.9
2023-05-02 0.7.8
2022-08-08 0.7.7
2022-04-05 0.7.6
2021-06-22 0.7.4
2021-04-30 0.7.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-26 1.4.2
2024-04-28 1.4.1
2024-04-23 1.4.0
2023-11-17 1.3.2
2023-10-12 1.3.1
2023-04-18 1.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-28 1.0.0
2021-02-11 0.2.0
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 1.11.0 dated 2025-06-24 and 1.11.1 dated 2025-07-03
DESCRIPTION | 6 +-- MD5 | 26 ++++++++-------- NEWS.md | 10 ++++++ R/update-input.R | 13 +------- inst/www/shared/busy-indicators/busy-indicators.css | 2 - inst/www/shared/shiny-autoreload.js | 2 - inst/www/shared/shiny-showcase.css | 2 - inst/www/shared/shiny-showcase.js | 2 - inst/www/shared/shiny-testmode.js | 2 - inst/www/shared/shiny.js | 31 ++++++++++---------- inst/www/shared/shiny.js.map | 4 +- inst/www/shared/shiny.min.css | 2 - inst/www/shared/shiny.min.js | 26 ++++++++-------- inst/www/shared/shiny.min.js.map | 6 +-- 14 files changed, 69 insertions(+), 65 deletions(-)
Title: Data Visualization Tools for Statistical Analysis Results
Description: Unified plotting tools for statistics commonly used, such as GLM,
time series, PCA families, clustering and survival analysis. The package offers
a single plotting interface for these analysis results and plots in a unified
style using 'ggplot2'.
Author: Masaaki Horikoshi [aut],
Yuan Tang [aut, cre] ,
Austin Dickey [ctb],
Matthias Grenie [ctb],
Ryan Thompson [ctb],
Luciano Selzer [ctb],
Dario Strbenac [ctb],
Kirill Voronin [ctb],
Damir Pulatov [ctb]
Maintainer: Yuan Tang <terrytangyuan@gmail.com>
Diff between ggfortify versions 0.4.17 dated 2024-04-17 and 0.4.18 dated 2025-07-03
ggfortify-0.4.17/ggfortify/build |only ggfortify-0.4.17/ggfortify/inst/doc |only ggfortify-0.4.17/ggfortify/vignettes |only ggfortify-0.4.18/ggfortify/DESCRIPTION | 13 - ggfortify-0.4.18/ggfortify/MD5 | 49 +---- ggfortify-0.4.18/ggfortify/NAMESPACE | 1 ggfortify-0.4.18/ggfortify/NEWS.md | 4 ggfortify-0.4.18/ggfortify/R/fortify_surv.R | 67 +++----- ggfortify-0.4.18/ggfortify/R/ggfortify.R | 1 ggfortify-0.4.18/ggfortify/man/autoplot.survfit.Rd | 2 ggfortify-0.4.18/ggfortify/tests/testthat/test-changepoint.R | 6 ggfortify-0.4.18/ggfortify/tests/testthat/test-plotlib.R | 6 ggfortify-0.4.18/ggfortify/tests/testthat/test-spatial.R | 8 ggfortify-0.4.18/ggfortify/tests/testthat/test-surv.R | 90 ++++++----- 14 files changed, 117 insertions(+), 130 deletions(-)
Title: Irregularly Observed Autoregressive Models
Description: Data sets, functions and scripts with examples to implement autoregressive models for irregularly observed time series. The models available in this package are the irregular autoregressive model (Eyheramendy et al.(2018) <doi:10.1093/mnras/sty2487>), the complex irregular autoregressive model (Elorrieta et al.(2019) <doi:10.1051/0004-6361/201935560>) and the bivariate irregular autoregressive model (Elorrieta et al.(2021) <doi:10.1093/mnras/stab1216>).
Author: Elorrieta Felipe [aut, cre],
Ojeda Cesar [aut],
Eyheramendy Susana [aut],
Palma Wilfredo [aut]
Maintainer: Elorrieta Felipe <felipe.elorrieta@usach.cl>
Diff between iAR versions 1.3.0 dated 2025-03-10 and 1.3.1 dated 2025-07-03
iAR-1.3.0/iAR/man/CiARfit.Rd |only iAR-1.3.1/iAR/DESCRIPTION | 8 +- iAR-1.3.1/iAR/MD5 | 53 ++++++++-------- iAR-1.3.1/iAR/R/00_multidata.R | 66 ++++++++++++++++++-- iAR-1.3.1/iAR/R/00_unidata.R | 77 +++++++++++++++++------- iAR-1.3.1/iAR/R/01_BiARclass.R | 40 +++++++++++- iAR-1.3.1/iAR/R/01_CiARclass.R | 66 ++++++++++++++++---- iAR-1.3.1/iAR/R/01_iARclass.R | 118 +++++++++++++++++++++++++++++++++---- iAR-1.3.1/iAR/R/02_sim.R | 57 +++++++++++++++-- iAR-1.3.1/iAR/R/07_interpolation.R | 2 iAR-1.3.1/iAR/R/RcppExports.R | 4 - iAR-1.3.1/iAR/R/agn.R | 2 iAR-1.3.1/iAR/R/cvnovag.R | 2 iAR-1.3.1/iAR/R/cvnovar.R | 2 iAR-1.3.1/iAR/R/iAR.R | 10 --- iAR-1.3.1/iAR/README.md |only iAR-1.3.1/iAR/build/partial.rdb |binary iAR-1.3.1/iAR/man/BiAR.Rd | 23 +++++-- iAR-1.3.1/iAR/man/CiAR.Rd | 41 +++++++++--- iAR-1.3.1/iAR/man/agn.Rd | 2 iAR-1.3.1/iAR/man/cvnovag.Rd | 2 iAR-1.3.1/iAR/man/cvnovar.Rd | 2 iAR-1.3.1/iAR/man/iAR-package.Rd |only iAR-1.3.1/iAR/man/iAR.Rd | 58 ++++++++---------- iAR-1.3.1/iAR/man/interpolation.Rd | 1 iAR-1.3.1/iAR/man/multidata.Rd | 28 ++++++-- iAR-1.3.1/iAR/man/sim.Rd | 23 ++++++- iAR-1.3.1/iAR/man/unidata.Rd | 25 +++++-- iAR-1.3.1/iAR/src/CiARfit.cpp | 4 - 29 files changed, 547 insertions(+), 169 deletions(-)
Title: Collection of Utility Functions for Data Analysis and Computing
Description: Provides a collection of utility functions commonly used in data analysis and scientific computing. Includes functions for parallel processing, matrix operations, correlation calculations, and other computational tasks to streamline R workflows.
Author: Meng Xu [aut, cre]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between thisutils versions 0.0.4 dated 2025-06-17 and 0.0.5 dated 2025-07-03
DESCRIPTION | 12 MD5 | 30 + NAMESPACE | 8 R/computation.R |only R/log_message.R |only R/utils.R | 691 +++++++++++++++++++++++++----------------- man/capitalize.Rd |only man/check_sparsity.Rd | 2 man/download.Rd |only man/invoke_fun.Rd |only man/log_message.Rd | 111 ++++++ man/normalization.Rd | 22 - man/parallelize_fun.Rd | 10 man/r_square.Rd | 2 man/remove_space.Rd |only man/rescale.Rd |only man/simulate_sparse_matrix.Rd | 2 man/str_wrap.Rd |only man/thisutils-package.Rd | 2 man/try_get.Rd |only man/unnest_fun.Rd |only 21 files changed, 575 insertions(+), 317 deletions(-)