Thu, 26 May 2022

Package OmicNavigator updated to version 1.11.5 with previous version 1.8.0 dated 2021-12-01

Title: Open-Source Software for 'Omic' Data Analysis and Visualization
Description: A tool for interactive exploration of the results from 'omics' experiments to facilitate novel discoveries from high-throughput biology. The software includes R functions for the 'bioinformatician' to deposit study metadata and the outputs from statistical analyses (e.g. differential expression, enrichment). These results are then exported to an interactive JavaScript dashboard that can be interrogated on the user's local machine or deployed online to be explored by collaborators. The dashboard includes 'sortable' tables, interactive plots including network visualization, and fine-grained filtering based on statistical significance.
Author: Terrence Ernst [aut] , John Blischak [aut, cre] , Paul Nordlund [aut] , Justin Moore [aut] , Joe Dalen [aut] , Akshay Bhamidipati [aut] , Brett Engelmann [aut], Marco Curado [aut] , Joe LoGrasso [aut] , AbbVie Inc. [cph, fnd]
Maintainer: John Blischak <jdblischak@gmail.com>

Diff between OmicNavigator versions 1.8.0 dated 2021-12-01 and 1.11.5 dated 2022-05-26

 DESCRIPTION                                  |   17 
 LICENSE                                      |    4 
 MD5                                          |  259 +-
 NAMESPACE                                    |  144 -
 NEWS.md                                      | 1411 +++++++------
 R/add.R                                      | 1297 ++++++------
 R/app.R                                      | 1032 ++++-----
 R/check.R                                    | 1056 ++++-----
 R/combine.R                                  |only
 R/data.R                                     |  388 +--
 R/export.R                                   | 1186 +++++------
 R/get.R                                      | 1058 ++++-----
 R/import.R                                   |  171 -
 R/local.R                                    |  222 +-
 R/overlaps.R                                 |  242 +-
 R/plots.R                                    |  741 +++---
 R/print.R                                    |   64 
 R/sanitize.R                                 |  214 -
 R/summary.R                                  |   98 
 R/tests.R                                    |  959 ++++----
 R/upset.R                                    | 1310 ++++++------
 R/utility.R                                  |  408 +--
 R/validate.R                                 |  692 +++---
 R/zzz.R                                      |  174 -
 README.md                                    |  449 ++--
 build/partial.rdb                            |binary
 inst/doc/OmicNavigatorAPI.R                  |  754 +++----
 inst/doc/OmicNavigatorAPI.Rnw                | 1132 +++++-----
 inst/doc/OmicNavigatorAPI.pdf                |binary
 inst/doc/OmicNavigatorUsersGuide.R           | 1034 ++++-----
 inst/doc/OmicNavigatorUsersGuide.Rnw         | 2892 +++++++++++++--------------
 inst/doc/OmicNavigatorUsersGuide.pdf         |binary
 inst/extdata/description-fields-reserved.txt |   94 
 inst/tinytest/testAdd.R                      |  316 +-
 inst/tinytest/testApp.R                      |  920 ++++----
 inst/tinytest/testBugs.R                     |  304 +-
 inst/tinytest/testCheck.R                    | 1066 ++++-----
 inst/tinytest/testCombine.R                  |only
 inst/tinytest/testExport.R                   |  465 ++--
 inst/tinytest/testExtraMetadata.R            |  302 +-
 inst/tinytest/testGet.R                      | 1662 +++++++--------
 inst/tinytest/testGetNumeric.R               |  534 ++--
 inst/tinytest/testImport.R                   |  482 ++--
 inst/tinytest/testOverlaps.R                 |   90 
 inst/tinytest/testPiecemeal.R                |  364 +--
 inst/tinytest/testPlot.R                     | 1923 +++++++++--------
 inst/tinytest/testPrint.R                    |   58 
 inst/tinytest/testSummary.R                  |   68 
 inst/tinytest/testUpset.R                    | 1682 +++++++--------
 inst/tinytest/testUtility.R                  |   34 
 inst/tinytest/testValidate.R                 |  518 ++--
 inst/tinytest/tinytestSettings.R             |   18 
 man/Mm.c2.Rd                                 |   70 
 man/OmicNavigator.Rd                         |   38 
 man/addAnnotations.Rd                        |   70 
 man/addAssays.Rd                             |   60 
 man/addBarcodes.Rd                           |   82 
 man/addEnrichments.Rd                        |   68 
 man/addEnrichmentsLinkouts.Rd                |  120 -
 man/addFeatures.Rd                           |   58 
 man/addMapping.Rd                            |   86 
 man/addMetaFeatures.Rd                       |   66 
 man/addMetaFeaturesLinkouts.Rd               |  128 -
 man/addModels.Rd                             |  102 
 man/addOverlaps.Rd                           |   56 
 man/addPlots.Rd                              |  125 -
 man/addReports.Rd                            |   62 
 man/addResults.Rd                            |   58 
 man/addResultsLinkouts.Rd                    |  128 -
 man/addSamples.Rd                            |   58 
 man/addTests.Rd                              |  118 -
 man/basal.vs.lp.Rd                           |   90 
 man/basal.vs.ml.Rd                           |   90 
 man/cam.BasalvsLP.Rd                         |   82 
 man/cam.BasalvsML.Rd                         |   82 
 man/combineStudies.Rd                        |only
 man/createStudy.Rd                           |  471 ++--
 man/exportStudy.Rd                           |   66 
 man/getAnnotations.Rd                        |   74 
 man/getAssays.Rd                             |   74 
 man/getBarcodeData.Rd                        |   78 
 man/getBarcodes.Rd                           |   74 
 man/getEnrichments.Rd                        |   96 
 man/getEnrichmentsIntersection.Rd            |   97 
 man/getEnrichmentsLinkouts.Rd                |   84 
 man/getEnrichmentsNetwork.Rd                 |   66 
 man/getEnrichmentsTable.Rd                   |   78 
 man/getEnrichmentsUpset.Rd                   |   79 
 man/getFavicons.Rd                           |   56 
 man/getFeatures.Rd                           |   58 
 man/getInstalledStudies.Rd                   |   38 
 man/getLinkFeatures.Rd                       |   52 
 man/getMapping.Rd                            |   70 
 man/getMetaFeatures.Rd                       |   74 
 man/getMetaFeaturesLinkouts.Rd               |   74 
 man/getMetaFeaturesTable.Rd                  |   54 
 man/getModels.Rd                             |   74 
 man/getNodeFeatures.Rd                       |   60 
 man/getOverlaps.Rd                           |   74 
 man/getPackageVersion.Rd                     |   34 
 man/getPlots.Rd                              |   74 
 man/getPlottingData.Rd                       |  126 -
 man/getReportLink.Rd                         |   44 
 man/getReports.Rd                            |   74 
 man/getResults.Rd                            |   90 
 man/getResultsIntersection.Rd                |   99 
 man/getResultsLinkouts.Rd                    |   74 
 man/getResultsTable.Rd                       |   60 
 man/getResultsUpset.Rd                       |   57 
 man/getSamples.Rd                            |   74 
 man/getTests.Rd                              |   78 
 man/getUpsetCols.Rd                          |   42 
 man/group.Rd                                 |   80 
 man/importStudy.Rd                           |   46 
 man/installApp.Rd                            |   66 
 man/installStudy.Rd                          |   42 
 man/lane.Rd                                  |   80 
 man/lcpm.Rd                                  |   70 
 man/listStudies.Rd                           |   54 
 man/plotStudy.Rd                             |   89 
 man/removeStudy.Rd                           |   42 
 man/samplenames.Rd                           |   70 
 man/shared-add.Rd                            |   42 
 man/shared-data.Rd                           |   46 
 man/shared-get.Rd                            |   80 
 man/shared-upset.Rd                          |   61 
 man/startApp.Rd                              |   74 
 man/summary.onStudy.Rd                       |   46 
 man/validateStudy.Rd                         |   38 
 tests/tinytest.R                             |    8 
 vignettes/OmicNavigatorAPI.Rnw               | 1132 +++++-----
 vignettes/OmicNavigatorUsersGuide.Rnw        | 2892 +++++++++++++--------------
 132 files changed, 20309 insertions(+), 19901 deletions(-)

More information about OmicNavigator at CRAN
Permanent link

Package reactable updated to version 0.3.0 with previous version 0.2.3 dated 2020-10-04

Title: Interactive Data Tables Based on 'React Table'
Description: Interactive data tables for R, based on the 'React Table' JavaScript library. Provides an HTML widget that can be used in 'R Markdown' documents and 'Shiny' applications, or viewed from an R console.
Author: Greg Lin [aut, cre], Tanner Linsley [ctb, cph] , Emotion team and other contributors [ctb, cph]
Maintainer: Greg Lin <glin@glin.io>

Diff between reactable versions 0.2.3 dated 2020-10-04 and 0.3.0 dated 2022-05-26

 reactable-0.2.3/reactable/man/reactable_html.Rd                        |only
 reactable-0.3.0/reactable/DESCRIPTION                                  |   13 
 reactable-0.3.0/reactable/MD5                                          |   49 -
 reactable-0.3.0/reactable/NEWS.md                                      |  249 ++++++
 reactable-0.3.0/reactable/R/columns.R                                  |  273 +++++-
 reactable-0.3.0/reactable/R/language.R                                 |   73 +
 reactable-0.3.0/reactable/R/reactable.R                                |  198 +++--
 reactable-0.3.0/reactable/R/utils.R                                    |   93 ++
 reactable-0.3.0/reactable/README.md                                    |   13 
 reactable-0.3.0/reactable/inst/htmlwidgets/reactable.js                |    7 
 reactable-0.3.0/reactable/inst/htmlwidgets/reactable.js.map            |    2 
 reactable-0.3.0/reactable/inst/htmlwidgets/reactable_v1.js             |only
 reactable-0.3.0/reactable/inst/htmlwidgets/reactable_v1.js.LICENSE.txt |only
 reactable-0.3.0/reactable/inst/htmlwidgets/reactable_v1.js.map         |only
 reactable-0.3.0/reactable/man/colDef.Rd                                |   82 +-
 reactable-0.3.0/reactable/man/colFormat.Rd                             |   28 
 reactable-0.3.0/reactable/man/colGroup.Rd                              |   17 
 reactable-0.3.0/reactable/man/reactable-package.Rd                     |    4 
 reactable-0.3.0/reactable/man/reactable.Rd                             |   38 
 reactable-0.3.0/reactable/man/reactableLang.Rd                         |   32 
 reactable-0.3.0/reactable/man/reexports.Rd                             |   32 
 reactable-0.3.0/reactable/man/widget_html.reactable.Rd                 |only
 reactable-0.3.0/reactable/tests/testthat/test-columns.R                |  155 +++
 reactable-0.3.0/reactable/tests/testthat/test-language.R               |   24 
 reactable-0.3.0/reactable/tests/testthat/test-reactable.R              |  396 +++++++---
 reactable-0.3.0/reactable/tests/testthat/test-shiny.R                  |    2 
 reactable-0.3.0/reactable/tests/testthat/test-theme.R                  |    2 
 reactable-0.3.0/reactable/tests/testthat/test-utils.R                  |   68 +
 28 files changed, 1453 insertions(+), 397 deletions(-)

More information about reactable at CRAN
Permanent link

Package sbtools updated to version 1.1.18 with previous version 1.1.17 dated 2021-07-20

Title: USGS ScienceBase Tools
Description: Tools for interacting with U.S. Geological Survey ScienceBase <https://www.sciencebase.gov> interfaces. ScienceBase is a data cataloging and collaborative data management platform. Functions included for querying ScienceBase, and creating and fetching datasets.
Author: David Blodgett [cre], Luke Winslow [aut], Scott Chamberlain [ctb], Alison Appling [ctb], Jordan Read [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>

Diff between sbtools versions 1.1.17 dated 2021-07-20 and 1.1.18 dated 2022-05-26

 sbtools-1.1.17/sbtools/R/item_get_wfs.R               |only
 sbtools-1.1.17/sbtools/R/session_authorized.R         |only
 sbtools-1.1.17/sbtools/man/item_get_wfs.Rd            |only
 sbtools-1.1.18/sbtools/DESCRIPTION                    |   10 -
 sbtools-1.1.18/sbtools/MD5                            |   65 +++++-----
 sbtools-1.1.18/sbtools/NAMESPACE                      |    7 -
 sbtools-1.1.18/sbtools/NEWS.md                        |   15 ++
 sbtools-1.1.18/sbtools/R/AAA.R                        |    6 +
 sbtools-1.1.18/sbtools/R/REST_helpers.R               |   13 ++
 sbtools-1.1.18/sbtools/R/authenticate_sb.R            |   49 ++++++++
 sbtools-1.1.18/sbtools/R/gql_helpers.R                |only
 sbtools-1.1.18/sbtools/R/item_file_download.R         |  107 ++++++++++--------
 sbtools-1.1.18/sbtools/R/item_list_files.R            |   88 +++++++++++++-
 sbtools-1.1.18/sbtools/R/item_replace_files.R         |   54 ++++-----
 sbtools-1.1.18/sbtools/R/item_rm.R                    |   84 +++++++-------
 sbtools-1.1.18/sbtools/R/item_rm_files.R              |   99 +++++++++-------
 sbtools-1.1.18/sbtools/R/item_upload_files.R          |  104 +++++++++++++++++
 sbtools-1.1.18/sbtools/R/query_sb_date.R              |    2 
 sbtools-1.1.18/sbtools/R/sbtools-package.R            |   76 ++++++------
 sbtools-1.1.18/sbtools/R/session_details.R            |   34 +++++
 sbtools-1.1.18/sbtools/R/session_logout.R             |   41 +++---
 sbtools-1.1.18/sbtools/R/session_renew.R              |   28 ++++
 sbtools-1.1.18/sbtools/R/set_endpoint.R               |    8 +
 sbtools-1.1.18/sbtools/R/user_id.R                    |   49 ++++----
 sbtools-1.1.18/sbtools/man/item_append_files.Rd       |    6 -
 sbtools-1.1.18/sbtools/man/item_file_download.Rd      |   18 +--
 sbtools-1.1.18/sbtools/man/item_list_files.Rd         |   33 ++++-
 sbtools-1.1.18/sbtools/man/item_replace_files.Rd      |    7 -
 sbtools-1.1.18/sbtools/man/item_rm_files.Rd           |    7 +
 sbtools-1.1.18/sbtools/man/item_upload_cloud.Rd       |only
 sbtools-1.1.18/sbtools/man/item_upload_create.Rd      |    6 -
 sbtools-1.1.18/sbtools/man/sbtools-package.Rd         |    2 
 sbtools-1.1.18/sbtools/man/session_details.Rd         |   31 +++++
 sbtools-1.1.18/sbtools/tests/testthat/test-REST.R     |   12 +-
 sbtools-1.1.18/sbtools/tests/testthat/test-auth.R     |   89 +++++++++++++-
 sbtools-1.1.18/sbtools/tests/testthat/test_examples.R |   39 +++---
 36 files changed, 842 insertions(+), 347 deletions(-)

More information about sbtools at CRAN
Permanent link

Package packrat updated to version 0.8.0 with previous version 0.7.0 dated 2021-08-20

Title: A Dependency Management System for Projects and their R Package Dependencies
Description: Manage the R packages your project depends on in an isolated, portable, and reproducible way.
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, Aron Atkins, JJ Allaire
Maintainer: Aron Atkins <aron@rstudio.com>

Diff between packrat versions 0.7.0 dated 2021-08-20 and 0.8.0 dated 2022-05-26

 DESCRIPTION                                 |    6 -
 MD5                                         |   43 +++++++------
 R/bitbucket.R                               |   31 ++++++---
 R/cache.R                                   |    5 -
 R/dependencies.R                            |   92 +++++++++++++++++++++++++---
 R/downloader.R                              |   23 -------
 R/github.R                                  |   61 +++++++++++++-----
 R/gitlab.R                                  |   31 ++++++---
 R/library-support.R                         |    1 
 R/options.R                                 |    9 +-
 R/pkg.R                                     |    3 
 R/recursive-package-dependencies.R          |   12 ++-
 R/renv.R                                    |only
 R/restore.R                                 |   20 +++---
 R/utils.R                                   |    2 
 R/zzz.R                                     |    2 
 inst/resources/init-rprofile.R              |    2 
 inst/resources/init.R                       |    2 
 inst/resources/renv.R                       |only
 tests/testthat/packages/packrat/DESCRIPTION |    2 
 tests/testthat/packrat                      |only
 tests/testthat/test-dependencies.R          |   35 ++++++++++
 tests/testthat/test-hash.R                  |   42 ++++++++++++
 tests/testthat/test-options.R               |only
 tools                                       |only
 25 files changed, 310 insertions(+), 114 deletions(-)

More information about packrat at CRAN
Permanent link

Package r4ss updated to version 1.44.0 with previous version 1.36.1 dated 2019-10-18

Title: R Code for Stock Synthesis
Description: A collection of R functions for use with Stock Synthesis, a fisheries stock assessment modeling platform written in ADMB by Dr. Richard D. Methot at the NOAA Northwest Fisheries Science Center. The functions include tools for summarizing and plotting results, manipulating files, visualizing model parameterizations, and various other common stock assessment tasks. This version of '{r4ss}' is compatible with Stock Synthesis versions 3.24 through 3.30 (specifically version 3.30.19.01, from April 2022).
Author: Ian G. Taylor [aut, cre], Ian J. Stewart [aut], Allan C. Hicks [aut], Tommy M. Garrison [aut], Andre E. Punt [aut], John R. Wallace [aut], Chantel R. Wetzel [aut], James T. Thorson [aut], Yukio Takeuchi [aut], Kotaro Ono [aut], Cole C. Monnahan [aut] [...truncated...]
Maintainer: Ian G. Taylor <Ian.Taylor@noaa.gov>

Diff between r4ss versions 1.36.1 dated 2019-10-18 and 1.44.0 dated 2022-05-26

 r4ss-1.36.1/r4ss/R/SS_makedatlist.R                       |only
 r4ss-1.36.1/r4ss/R/SStimeseries.R                         |only
 r4ss-1.36.1/r4ss/R/rich.colors.short.R                    |only
 r4ss-1.36.1/r4ss/build                                    |only
 r4ss-1.36.1/r4ss/inst/Shiny                               |only
 r4ss-1.36.1/r4ss/inst/doc                                 |only
 r4ss-1.36.1/r4ss/man/SS_makedatlist.Rd                    |only
 r4ss-1.36.1/r4ss/man/SStimeseries.Rd                      |only
 r4ss-1.36.1/r4ss/vignettes                                |only
 r4ss-1.44.0/r4ss/DESCRIPTION                              |   99 
 r4ss-1.44.0/r4ss/MD5                                      |  447 
 r4ss-1.44.0/r4ss/NAMESPACE                                |   26 
 r4ss-1.44.0/r4ss/NEWS.md                                  |   22 
 r4ss-1.44.0/r4ss/R/NegLogInt_Fn.R                         |  654 -
 r4ss-1.44.0/r4ss/R/PinerPlot.R                            |  444 
 r4ss-1.44.0/r4ss/R/RebuildPlot.R                          | 1040 +-
 r4ss-1.44.0/r4ss/R/SSMethod.Cond.TA1.8.R                  |  412 
 r4ss-1.44.0/r4ss/R/SSMethod.TA1.8.R                       |  516 -
 r4ss-1.44.0/r4ss/R/SS_ForeCatch.R                         |  100 
 r4ss-1.44.0/r4ss/R/SS_RunJitter.R                         |  242 
 r4ss-1.44.0/r4ss/R/SS_Sensi_plot.R                        |only
 r4ss-1.44.0/r4ss/R/SS_changepars.R                        |  529 -
 r4ss-1.44.0/r4ss/R/SS_decision_table_stuff.R              |   61 
 r4ss-1.44.0/r4ss/R/SS_doRetro.R                           |  230 
 r4ss-1.44.0/r4ss/R/SS_fitbiasramp.R                       |  661 -
 r4ss-1.44.0/r4ss/R/SS_html.R                              |  519 -
 r4ss-1.44.0/r4ss/R/SS_makeHTMLdiagnostictable.R           |  188 
 r4ss-1.44.0/r4ss/R/SS_output.R                            | 6773 +++++++-------
 r4ss-1.44.0/r4ss/R/SS_parlines.R                          |  127 
 r4ss-1.44.0/r4ss/R/SS_plots.R                             | 2654 +++--
 r4ss-1.44.0/r4ss/R/SS_profile.R                           |  672 -
 r4ss-1.44.0/r4ss/R/SS_read.R                              |only
 r4ss-1.44.0/r4ss/R/SS_read_summary.R                      |  126 
 r4ss-1.44.0/r4ss/R/SS_readctl.R                           |  288 
 r4ss-1.44.0/r4ss/R/SS_readctl_3.24.R                      | 2086 ++--
 r4ss-1.44.0/r4ss/R/SS_readctl_3.30.R                      | 2923 +++---
 r4ss-1.44.0/r4ss/R/SS_readdat.R                           |  317 
 r4ss-1.44.0/r4ss/R/SS_readdat_2.00.R                      |  589 -
 r4ss-1.44.0/r4ss/R/SS_readdat_3.00.R                      |  827 -
 r4ss-1.44.0/r4ss/R/SS_readdat_3.24.R                      |  793 -
 r4ss-1.44.0/r4ss/R/SS_readdat_3.30.R                      | 1510 +--
 r4ss-1.44.0/r4ss/R/SS_readforecast.R                      |  553 -
 r4ss-1.44.0/r4ss/R/SS_readpar_3.24.R                      |only
 r4ss-1.44.0/r4ss/R/SS_readpar_3.30.R                      |only
 r4ss-1.44.0/r4ss/R/SS_readstarter.R                       |  249 
 r4ss-1.44.0/r4ss/R/SS_readwtatage.R                       |   57 
 r4ss-1.44.0/r4ss/R/SS_recdevs.R                           |  268 
 r4ss-1.44.0/r4ss/R/SS_splitdat.R                          |  135 
 r4ss-1.44.0/r4ss/R/SS_tune_comps.R                        |  754 +
 r4ss-1.44.0/r4ss/R/SS_varadjust.R                         |  200 
 r4ss-1.44.0/r4ss/R/SS_write.R                             |only
 r4ss-1.44.0/r4ss/R/SS_writectl.R                          |   76 
 r4ss-1.44.0/r4ss/R/SS_writectl_3.24.R                     |  599 -
 r4ss-1.44.0/r4ss/R/SS_writectl_3.30.R                     |  959 +
 r4ss-1.44.0/r4ss/R/SS_writedat.R                          |   39 
 r4ss-1.44.0/r4ss/R/SS_writedat_3.24.R                     |  230 
 r4ss-1.44.0/r4ss/R/SS_writedat_3.30.R                     |  293 
 r4ss-1.44.0/r4ss/R/SS_writeforecast.R                     |  290 
 r4ss-1.44.0/r4ss/R/SS_writepar_3.24.R                     |only
 r4ss-1.44.0/r4ss/R/SS_writepar_3.30.R                     |only
 r4ss-1.44.0/r4ss/R/SS_writestarter.R                      |  102 
 r4ss-1.44.0/r4ss/R/SS_writewtatage.R                      |   77 
 r4ss-1.44.0/r4ss/R/SSbiologytables.R                      |  156 
 r4ss-1.44.0/r4ss/R/SSbootstrap.R                          |   63 
 r4ss-1.44.0/r4ss/R/SSexecutivesummary.r                   | 1947 ++--
 r4ss-1.44.0/r4ss/R/SSgetMCMC.R                            |  165 
 r4ss-1.44.0/r4ss/R/SSgetoutput.R                          |  193 
 r4ss-1.44.0/r4ss/R/SSmakeMmatrix.R                        |  162 
 r4ss-1.44.0/r4ss/R/SSmohnsrho.R                           |  180 
 r4ss-1.44.0/r4ss/R/SSplotAgeMatrix.R                      |  238 
 r4ss-1.44.0/r4ss/R/SSplotBiology.R                        | 2865 +++--
 r4ss-1.44.0/r4ss/R/SSplotCatch.R                          | 1018 +-
 r4ss-1.44.0/r4ss/R/SSplotCohortCatch.R                    |  451 
 r4ss-1.44.0/r4ss/R/SSplotComparisons.R                    | 4122 ++++----
 r4ss-1.44.0/r4ss/R/SSplotComps.R                          | 3901 ++++----
 r4ss-1.44.0/r4ss/R/SSplotData.R                           |  489 -
 r4ss-1.44.0/r4ss/R/SSplotDiscard.R                        |  315 
 r4ss-1.44.0/r4ss/R/SSplotDynamicB0.R                      |only
 r4ss-1.44.0/r4ss/R/SSplotIndices.R                        | 1513 +--
 r4ss-1.44.0/r4ss/R/SSplotMCMC_ExtraSelex.R                |   74 
 r4ss-1.44.0/r4ss/R/SSplotMnwt.R                           |  224 
 r4ss-1.44.0/r4ss/R/SSplotMovementMap.R                    |  162 
 r4ss-1.44.0/r4ss/R/SSplotMovementRates.R                  |  500 -
 r4ss-1.44.0/r4ss/R/SSplotNumbers.R                        | 1511 +--
 r4ss-1.44.0/r4ss/R/SSplotPars.R                           | 1017 +-
 r4ss-1.44.0/r4ss/R/SSplotProfile.R                        |  477 
 r4ss-1.44.0/r4ss/R/SSplotRecdevs.R                        |  360 
 r4ss-1.44.0/r4ss/R/SSplotRecdist.R                        |  151 
 r4ss-1.44.0/r4ss/R/SSplotRetroDevs.R                      |  237 
 r4ss-1.44.0/r4ss/R/SSplotRetroRecruits.R                  |  472 
 r4ss-1.44.0/r4ss/R/SSplotSPR.R                            |  631 -
 r4ss-1.44.0/r4ss/R/SSplotSelex.R                          | 1962 ++--
 r4ss-1.44.0/r4ss/R/SSplotSexRatio.R                       |  380 
 r4ss-1.44.0/r4ss/R/SSplotSpawnrecruit.R                   |  669 -
 r4ss-1.44.0/r4ss/R/SSplotSummaryF.R                       |  134 
 r4ss-1.44.0/r4ss/R/SSplotTags.R                           |  813 -
 r4ss-1.44.0/r4ss/R/SSplotTimeseries.R                     | 1123 +-
 r4ss-1.44.0/r4ss/R/SSplotYield.R                          |  452 
 r4ss-1.44.0/r4ss/R/SSsummarize.R                          |  832 -
 r4ss-1.44.0/r4ss/R/SStableComparisons.R                   |  256 
 r4ss-1.44.0/r4ss/R/SSunavailableSpawningOutput.R          |  699 -
 r4ss-1.44.0/r4ss/R/TSCplot.R                              |  253 
 r4ss-1.44.0/r4ss/R/bubble3.R                              |  263 
 r4ss-1.44.0/r4ss/R/check_inputlist.R                      |only
 r4ss-1.44.0/r4ss/R/check_model.R                          |only
 r4ss-1.44.0/r4ss/R/copy_SS_inputs.R                       |only
 r4ss-1.44.0/r4ss/R/file_increment.R                       |only
 r4ss-1.44.0/r4ss/R/getADMBHessian.R                       |   56 
 r4ss-1.44.0/r4ss/R/get_SIS_info.R                         |only
 r4ss-1.44.0/r4ss/R/get_comments.r                         |only
 r4ss-1.44.0/r4ss/R/get_ncol.R                             |only
 r4ss-1.44.0/r4ss/R/helper_fxns.R                          |only
 r4ss-1.44.0/r4ss/R/make_multifig.R                        | 1083 +-
 r4ss-1.44.0/r4ss/R/make_multifig_sexratio.R               |  553 -
 r4ss-1.44.0/r4ss/R/mcmc.nuisance.R                        |  356 
 r4ss-1.44.0/r4ss/R/mcmc.out.R                             |  656 -
 r4ss-1.44.0/r4ss/R/mountains.R                            |  114 
 r4ss-1.44.0/r4ss/R/plotCI.R                               |   26 
 r4ss-1.44.0/r4ss/R/populate_multiple_folders.R            |only
 r4ss-1.44.0/r4ss/R/r4ss-package.R                         |   44 
 r4ss-1.44.0/r4ss/R/r4ss_logo.R                            |   23 
 r4ss-1.44.0/r4ss/R/read.admbFit.R                         |   41 
 r4ss-1.44.0/r4ss/R/run_SS_models.R                        |only
 r4ss-1.44.0/r4ss/R/selShapes.R                            |   22 
 r4ss-1.44.0/r4ss/R/stackpoly.R                            |  106 
 r4ss-1.44.0/r4ss/R/write_fwf4.r                           |only
 r4ss-1.44.0/r4ss/README.md                                |   57 
 r4ss-1.44.0/r4ss/inst/CITATION                            |only
 r4ss-1.44.0/r4ss/inst/WORDLIST                            |only
 r4ss-1.44.0/r4ss/inst/extdata                             |only
 r4ss-1.44.0/r4ss/man/DoProjectPlots.Rd                    |   65 
 r4ss-1.44.0/r4ss/man/NegLogInt_Fn.Rd                      |   59 
 r4ss-1.44.0/r4ss/man/PinerPlot.Rd                         |   61 
 r4ss-1.44.0/r4ss/man/SSMethod.Cond.TA1.8.Rd               |   33 
 r4ss-1.44.0/r4ss/man/SSMethod.TA1.8.Rd                    |   77 
 r4ss-1.44.0/r4ss/man/SS_ForeCatch.Rd                      |   27 
 r4ss-1.44.0/r4ss/man/SS_RunJitter.Rd                      |   92 
 r4ss-1.44.0/r4ss/man/SS_Sensi_plot.Rd                     |only
 r4ss-1.44.0/r4ss/man/SS_changepars.Rd                     |   49 
 r4ss-1.44.0/r4ss/man/SS_decision_table_stuff.Rd           |only
 r4ss-1.44.0/r4ss/man/SS_doRetro.Rd                        |   59 
 r4ss-1.44.0/r4ss/man/SS_fitbiasramp.Rd                    |  210 
 r4ss-1.44.0/r4ss/man/SS_html.Rd                           |   20 
 r4ss-1.44.0/r4ss/man/SS_makeHTMLdiagnostictable.Rd        |    4 
 r4ss-1.44.0/r4ss/man/SS_output.Rd                         |   67 
 r4ss-1.44.0/r4ss/man/SS_parlines.Rd                       |   16 
 r4ss-1.44.0/r4ss/man/SS_plots.Rd                          |  265 
 r4ss-1.44.0/r4ss/man/SS_profile.Rd                        |  173 
 r4ss-1.44.0/r4ss/man/SS_read.Rd                           |only
 r4ss-1.44.0/r4ss/man/SS_read_summary.Rd                   |   16 
 r4ss-1.44.0/r4ss/man/SS_readctl.Rd                        |  201 
 r4ss-1.44.0/r4ss/man/SS_readctl_3.24.Rd                   |  104 
 r4ss-1.44.0/r4ss/man/SS_readctl_3.30.Rd                   |  129 
 r4ss-1.44.0/r4ss/man/SS_readdat.Rd                        |   29 
 r4ss-1.44.0/r4ss/man/SS_readdat_2.00.Rd                   |   17 
 r4ss-1.44.0/r4ss/man/SS_readdat_3.00.Rd                   |   15 
 r4ss-1.44.0/r4ss/man/SS_readdat_3.24.Rd                   |   15 
 r4ss-1.44.0/r4ss/man/SS_readdat_3.30.Rd                   |   15 
 r4ss-1.44.0/r4ss/man/SS_readforecast.Rd                   |   33 
 r4ss-1.44.0/r4ss/man/SS_readpar_3.24.Rd                   |only
 r4ss-1.44.0/r4ss/man/SS_readpar_3.30.Rd                   |only
 r4ss-1.44.0/r4ss/man/SS_readstarter.Rd                    |   10 
 r4ss-1.44.0/r4ss/man/SS_readwtatage.Rd                    |   10 
 r4ss-1.44.0/r4ss/man/SS_recdevs.Rd                        |  120 
 r4ss-1.44.0/r4ss/man/SS_splitdat.Rd                       |  112 
 r4ss-1.44.0/r4ss/man/SS_tune_comps.Rd                     |  228 
 r4ss-1.44.0/r4ss/man/SS_varadjust.Rd                      |   53 
 r4ss-1.44.0/r4ss/man/SS_write.Rd                          |only
 r4ss-1.44.0/r4ss/man/SS_writectl.Rd                       |   33 
 r4ss-1.44.0/r4ss/man/SS_writectl_3.24.Rd                  |   26 
 r4ss-1.44.0/r4ss/man/SS_writectl_3.30.Rd                  |   19 
 r4ss-1.44.0/r4ss/man/SS_writedat.Rd                       |   24 
 r4ss-1.44.0/r4ss/man/SS_writedat_3.24.Rd                  |   23 
 r4ss-1.44.0/r4ss/man/SS_writedat_3.30.Rd                  |   23 
 r4ss-1.44.0/r4ss/man/SS_writeforecast.Rd                  |   20 
 r4ss-1.44.0/r4ss/man/SS_writepar_3.24.Rd                  |only
 r4ss-1.44.0/r4ss/man/SS_writepar_3.30.Rd                  |only
 r4ss-1.44.0/r4ss/man/SS_writestarter.Rd                   |   20 
 r4ss-1.44.0/r4ss/man/SS_writewtatage.Rd                   |   24 
 r4ss-1.44.0/r4ss/man/SSbiologytables.Rd                   |   24 
 r4ss-1.44.0/r4ss/man/SSbootstrap.Rd                       |    5 
 r4ss-1.44.0/r4ss/man/SSdiagsTime2Year.Rd                  |only
 r4ss-1.44.0/r4ss/man/SSexecutivesummary.Rd                |   76 
 r4ss-1.44.0/r4ss/man/SSgetMCMC.Rd                         |   25 
 r4ss-1.44.0/r4ss/man/SSgetoutput.Rd                       |   21 
 r4ss-1.44.0/r4ss/man/SSmakeMmatrix.Rd                     |   65 
 r4ss-1.44.0/r4ss/man/SSmohnsrho.Rd                        |   18 
 r4ss-1.44.0/r4ss/man/SSplotAgeMatrix.Rd                   |   47 
 r4ss-1.44.0/r4ss/man/SSplotBiology.Rd                     |  101 
 r4ss-1.44.0/r4ss/man/SSplotCatch.Rd                       |   90 
 r4ss-1.44.0/r4ss/man/SSplotCohortCatch.Rd                 |   39 
 r4ss-1.44.0/r4ss/man/SSplotComparisons.Rd                 |  232 
 r4ss-1.44.0/r4ss/man/SSplotComps.Rd                       |  167 
 r4ss-1.44.0/r4ss/man/SSplotData.Rd                        |   45 
 r4ss-1.44.0/r4ss/man/SSplotDiscard.Rd                     |   35 
 r4ss-1.44.0/r4ss/man/SSplotDynamicB0.Rd                   |only
 r4ss-1.44.0/r4ss/man/SSplotIndices.Rd                     |   98 
 r4ss-1.44.0/r4ss/man/SSplotMCMC_ExtraSelex.Rd             |   12 
 r4ss-1.44.0/r4ss/man/SSplotMnwt.Rd                        |   36 
 r4ss-1.44.0/r4ss/man/SSplotMovementMap.Rd                 |   24 
 r4ss-1.44.0/r4ss/man/SSplotMovementRates.Rd               |   45 
 r4ss-1.44.0/r4ss/man/SSplotNumbers.Rd                     |   85 
 r4ss-1.44.0/r4ss/man/SSplotPars.Rd                        |   87 
 r4ss-1.44.0/r4ss/man/SSplotProfile.Rd                     |   89 
 r4ss-1.44.0/r4ss/man/SSplotRecdevs.Rd                     |   42 
 r4ss-1.44.0/r4ss/man/SSplotRecdist.Rd                     |   28 
 r4ss-1.44.0/r4ss/man/SSplotRetroRecruits.Rd               |   84 
 r4ss-1.44.0/r4ss/man/SSplotSPR.Rd                         |   60 
 r4ss-1.44.0/r4ss/man/SSplotSelex.Rd                       |  142 
 r4ss-1.44.0/r4ss/man/SSplotSexRatio.Rd                    |   62 
 r4ss-1.44.0/r4ss/man/SSplotSpawnrecruit.Rd                |   75 
 r4ss-1.44.0/r4ss/man/SSplotSummaryF.Rd                    |   48 
 r4ss-1.44.0/r4ss/man/SSplotTags.Rd                        |   54 
 r4ss-1.44.0/r4ss/man/SSplotTimeseries.Rd                  |   71 
 r4ss-1.44.0/r4ss/man/SSplotYield.Rd                       |   46 
 r4ss-1.44.0/r4ss/man/SSsummarize.Rd                       |   28 
 r4ss-1.44.0/r4ss/man/SStableComparisons.Rd                |   30 
 r4ss-1.44.0/r4ss/man/SSunavailableSpawningOutput.Rd       |   20 
 r4ss-1.44.0/r4ss/man/TSCplot.Rd                           |   85 
 r4ss-1.44.0/r4ss/man/add_legend.Rd                        |only
 r4ss-1.44.0/r4ss/man/bubble3.Rd                           |  178 
 r4ss-1.44.0/r4ss/man/check_inputlist.Rd                   |only
 r4ss-1.44.0/r4ss/man/check_model.Rd                       |only
 r4ss-1.44.0/r4ss/man/copy_SS_inputs.Rd                    |only
 r4ss-1.44.0/r4ss/man/file_increment.Rd                    |only
 r4ss-1.44.0/r4ss/man/getADMBHessian.Rd                    |   16 
 r4ss-1.44.0/r4ss/man/get_SIS_info.Rd                      |only
 r4ss-1.44.0/r4ss/man/get_comments.Rd                      |only
 r4ss-1.44.0/r4ss/man/get_dat_new_name.Rd                  |only
 r4ss-1.44.0/r4ss/man/get_last_phase.Rd                    |only
 r4ss-1.44.0/r4ss/man/get_tuning_table.Rd                  |only
 r4ss-1.44.0/r4ss/man/get_tv_parlabs.Rd                    |only
 r4ss-1.44.0/r4ss/man/is.wholenumber.Rd                    |only
 r4ss-1.44.0/r4ss/man/make_multifig.Rd                     |  115 
 r4ss-1.44.0/r4ss/man/make_multifig_sexratio.Rd            |   69 
 r4ss-1.44.0/r4ss/man/mcmc.nuisance.Rd                     |   36 
 r4ss-1.44.0/r4ss/man/mcmc.out.Rd                          |   80 
 r4ss-1.44.0/r4ss/man/mountains.Rd                         |  121 
 r4ss-1.44.0/r4ss/man/plotCI.Rd                            |   93 
 r4ss-1.44.0/r4ss/man/populate_multiple_folders.Rd         |only
 r4ss-1.44.0/r4ss/man/r4ss-package.Rd                      |   79 
 r4ss-1.44.0/r4ss/man/read.admbFit.Rd                      |    2 
 r4ss-1.44.0/r4ss/man/rich.colors.short.Rd                 |    2 
 r4ss-1.44.0/r4ss/man/run_SS_models.Rd                     |only
 r4ss-1.44.0/r4ss/man/save_png.Rd                          |only
 r4ss-1.44.0/r4ss/man/selShapes.Rd                         |    9 
 r4ss-1.44.0/r4ss/man/sspar.Rd                             |only
 r4ss-1.44.0/r4ss/man/stackpoly.Rd                         |   23 
 r4ss-1.44.0/r4ss/man/translate_3.30_to_3.24_Q_setup.Rd    |only
 r4ss-1.44.0/r4ss/man/translate_3.30_to_3.24_var_adjust.Rd |only
 r4ss-1.44.0/r4ss/man/write_fwf4.Rd                        |only
 251 files changed, 40647 insertions(+), 30436 deletions(-)

More information about r4ss at CRAN
Permanent link

Package BoomSpikeSlab updated to version 1.2.5 with previous version 1.2.4 dated 2021-04-06

Title: MCMC for Spike and Slab Regression
Description: Spike and slab regression with a variety of residual error distributions corresponding to Gaussian, Student T, probit, logit, SVM, and a few others. Spike and slab regression is Bayesian regression with prior distributions containing a point mass at zero. The posterior updates the amount of mass on this point, leading to a posterior distribution that is actually sparse, in the sense that if you sample from it many coefficients are actually zeros. Sampling from this posterior distribution is an elegant way to handle Bayesian variable selection and model averaging. See <DOI:10.1504/IJMMNO.2014.059942> for an explanation of the Gaussian case.
Author: Steven L. Scott <steve.the.bayesian@gmail.com>
Maintainer: Steven L. Scott <steve.the.bayesian@gmail.com>

Diff between BoomSpikeSlab versions 1.2.4 dated 2021-04-06 and 1.2.5 dated 2022-05-26

 DESCRIPTION                                        |   12 ++++++------
 MD5                                                |    6 +++---
 inst/tests/tests/testthat/test-nested-regression.R |   17 +++++++++--------
 inst/tests/testthat/test-nested-regression.R       |   17 +++++++++--------
 4 files changed, 27 insertions(+), 25 deletions(-)

More information about BoomSpikeSlab at CRAN
Permanent link

New package ri2 with initial version 0.4.0
Package: ri2
Title: Randomization Inference for Randomized Experiments
Version: 0.4.0
Description: Randomization inference procedures for simple and complex randomized designs, including multi-armed trials, as described in Gerber and Green (2012, ISBN: 978-0393979954). Users formally describe their randomization procedure and test statistic. The randomization distribution of the test statistic under some null hypothesis is efficiently simulated.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: generics, ggplot2, pbapply
Depends: randomizr (>= 0.16.0), estimatr
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-26 16:05:55 UTC; ac2595
Author: Alexander Coppock [aut, cre]
Maintainer: Alexander Coppock <acoppock@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-26 16:20:02 UTC

More information about ri2 at CRAN
Permanent link

Package rego updated to version 1.5.2 with previous version 1.5.1 dated 2022-05-26

Title: Automatic Time Series Forecasting and Missing Value Imputation
Description: Machine learning algorithm for predicting and imputing time series. It can automatically set all the parameters needed, thus in the minimal configuration it only requires the target variable and the dependent variables if present. It can address large problems with hundreds or thousands of dependent variables and problems in which the number of dependent variables is greater than the number of observations. Moreover it can be used not only for time series but also for any other real valued target variable. The algorithm implemented includes a Bayesian stochastic search methodology for model selection and a robust estimation based on bootstrapping. 'rego' is fast because all the code is C++.
Author: Davide Altomare [cre, aut], David Loris [aut]
Maintainer: Davide Altomare <info@channelattribution.io>

Diff between rego versions 1.5.1 dated 2022-05-26 and 1.5.2 dated 2022-05-26

 DESCRIPTION         |    6 +++---
 MD5                 |    6 +++---
 man/rego-package.Rd |    2 +-
 src/rego.cpp        |   10 +++++-----
 4 files changed, 12 insertions(+), 12 deletions(-)

More information about rego at CRAN
Permanent link

Package QuClu updated to version 1.0.1 with previous version 0.1.0 dated 2018-07-30

Title: Quantile-Based Clustering Algorithms
Description: Various quantile-based clustering algorithms: algorithm CU (Common theta and Unscaled variables), algorithm CS (Common theta and Scaled variables through lambda_j), algorithm VU (Variable-wise theta_j and Unscaled variables) and algorithm VW (Variable-wise theta_j and Scaled variables through lambda_j). Hennig, C., Viroli, C., Anderlucci, L. (2019) "Quantile-based clustering." Electronic Journal of Statistics. 13 (2) 4849 - 4883 <doi:10.1214/19-EJS1640>.
Author: Christian Hennig, Cinzia Viroli and Laura Anderlucci
Maintainer: Laura Anderlucci <laura.anderlucci@unibo.it>

Diff between QuClu versions 0.1.0 dated 2018-07-30 and 1.0.1 dated 2022-05-26

 DESCRIPTION       |   13 ++++++-------
 MD5               |   22 ++++++++++++----------
 NAMESPACE         |    1 +
 R/alg.CS.R        |   11 +++++++----
 R/alg.CU.R        |   26 +++++++++++++++++++++-----
 R/alg.VS.R        |   11 ++++++++---
 R/alg.VU.R        |   23 +++++++++++++++++++----
 R/kquantiles.R    |only
 man/alg.CS.Rd     |    5 ++---
 man/alg.CU.Rd     |    7 +++++--
 man/alg.VS.Rd     |    7 ++++---
 man/alg.VU.Rd     |    5 ++++-
 man/kquantiles.Rd |only
 13 files changed, 89 insertions(+), 42 deletions(-)

More information about QuClu at CRAN
Permanent link

Package nnlib2Rcpp updated to version 0.1.9 with previous version 0.1.8 dated 2021-10-30

Title: A Tool for Creating Custom Neural Networks in C++ and using Them in R
Description: Contains a module to define neural networks from custom components and versions of Autoencoder, BP, LVQ, MAM NN.
Author: Vasilis Nikolaidis [aut, cph, cre]
Maintainer: Vasilis Nikolaidis <vnikolaidis@us.uop.gr>

Diff between nnlib2Rcpp versions 0.1.8 dated 2021-10-30 and 0.1.9 dated 2022-05-26

 DESCRIPTION                        |   11 ++++++-----
 MD5                                |   28 ++++++++++++++--------------
 build/partial.rdb                  |binary
 build/vignette.rds                 |binary
 inst/doc/manual.pdf                |binary
 man/Autoencoder.Rd                 |    6 ++----
 man/BP-class.Rd                    |    6 ++++--
 man/LVQs-class.Rd                  |    2 ++
 man/MAM-class.Rd                   |    2 ++
 man/NN-class.Rd                    |    6 ++++--
 man/nnlib2Rcpp.Rd                  |    7 ++++---
 src/Rcpp_BP_supervised_module.cpp  |    9 +++++++++
 src/Rcpp_LVQ_supervised_module.cpp |    9 +++++++++
 src/Rcpp_MAM_supervised_module.cpp |    9 +++++++++
 src/Rcpp_NN_module.cpp             |   13 ++++++++++++-
 15 files changed, 77 insertions(+), 31 deletions(-)

More information about nnlib2Rcpp at CRAN
Permanent link

Package LSDsensitivity updated to version 1.2.2 with previous version 1.2.1 dated 2022-05-15

Title: Sensitivity Analysis Tools for LSD Simulations
Description: Tools for sensitivity analysis of LSD simulation models. Reads object-oriented data produced by LSD simulation models and performs screening and global sensitivity analysis (Sobol decomposition method, Saltelli et al. (2008) ISBN:9780470725177). A Kriging or polynomial meta-model (Kleijnen (2009) <doi:10.1016/j.ejor.2007.10.013>) is estimated using the simulation data to provide the data required by the Sobol decomposition. LSD (Laboratory for Simulation Development) is free software developed by Marco Valente and Marcelo C. Pereira (documentation and downloads available at <https://www.labsimdev.org/>).
Author: Marcelo C. Pereira [aut, cre]
Maintainer: Marcelo C. Pereira <mcper@unicamp.br>

Diff between LSDsensitivity versions 1.2.1 dated 2022-05-15 and 1.2.2 dated 2022-05-26

 DESCRIPTION                                   |    8 ++++----
 MD5                                           |    9 ++++++---
 R/write_resp.R                                |    2 +-
 build/partial.rdb                             |binary
 inst/extdata/ee/Sim2_1_40_median_var1.csv     |only
 inst/extdata/sobol/Sim3_18_27_median_var3.csv |only
 inst/extdata/sobol/Sim3_1_17_median_var3.csv  |only
 7 files changed, 11 insertions(+), 8 deletions(-)

More information about LSDsensitivity at CRAN
Permanent link

Package sparklyr updated to version 1.7.6 with previous version 1.7.5 dated 2022-02-02

Title: R Interface to Apache Spark
Description: R interface to Apache Spark, a fast and general engine for big data processing, see <https://spark.apache.org/>. This package supports connecting to local and remote Apache Spark clusters, provides a 'dplyr' compatible back-end, and provides an interface to Spark's built-in machine learning algorithms.
Author: Javier Luraschi [aut], Kevin Kuo [aut] , Kevin Ushey [aut], JJ Allaire [aut], Samuel Macedo [ctb], Hossein Falaki [aut], Lu Wang [aut], Andy Zhang [aut], Yitao Li [aut] , Jozef Hajnala [ctb], Maciej Szymkiewicz [ctb] , Wil Davis [ctb], Edgar Ruiz [au [...truncated...]
Maintainer: Edgar Ruiz <edgar@rstudio.com>

Diff between sparklyr versions 1.7.5 dated 2022-02-02 and 1.7.6 dated 2022-05-26

 sparklyr-1.7.5/sparklyr/tools/readme/sparklyr-illustration.png |only
 sparklyr-1.7.5/sparklyr/tools/readme/sparklyr-package.png      |only
 sparklyr-1.7.6/sparklyr/DESCRIPTION                            |   25 
 sparklyr-1.7.6/sparklyr/MD5                                    |   90 -
 sparklyr-1.7.6/sparklyr/NAMESPACE                              |   31 
 sparklyr-1.7.6/sparklyr/NEWS.md                                |   12 
 sparklyr-1.7.6/sparklyr/R/config_spark.R                       |    7 
 sparklyr-1.7.6/sparklyr/R/data_interface.R                     |    6 
 sparklyr-1.7.6/sparklyr/R/dbplyr-compat.R                      |only
 sparklyr-1.7.6/sparklyr/R/dbplyr_utils.R                       |    4 
 sparklyr-1.7.6/sparklyr/R/do_spark.R                           |    5 
 sparklyr-1.7.6/sparklyr/R/dplyr_hof.R                          |    2 
 sparklyr-1.7.6/sparklyr/R/dplyr_spark.R                        |   46 -
 sparklyr-1.7.6/sparklyr/R/dplyr_spark_connection.R             |  195 ++--
 sparklyr-1.7.6/sparklyr/R/dplyr_spark_table.R                  |   33 
 sparklyr-1.7.6/sparklyr/R/dplyr_sql.R                          |  166 ++-
 sparklyr-1.7.6/sparklyr/R/livy_connection.R                    |    2 
 sparklyr-1.7.6/sparklyr/R/livy_install.R                       |    2 
 sparklyr-1.7.6/sparklyr/R/ml_clustering_bisecting_kmeans.R     |    6 
 sparklyr-1.7.6/sparklyr/R/ml_feature_sql_transformer_utils.R   |   25 
 sparklyr-1.7.6/sparklyr/R/ml_model_kmeans.R                    |    2 
 sparklyr-1.7.6/sparklyr/R/ml_stat.R                            |    2 
 sparklyr-1.7.6/sparklyr/R/mutation.R                           |    6 
 sparklyr-1.7.6/sparklyr/R/spark_extensions.R                   |    2 
 sparklyr-1.7.6/sparklyr/R/spark_gen_embedded_sources.R         |    2 
 sparklyr-1.7.6/sparklyr/R/stream_operations.R                  |    2 
 sparklyr-1.7.6/sparklyr/R/tidiers_ml_linear_models.R           |   23 
 sparklyr-1.7.6/sparklyr/R/tidiers_ml_logistic_regression.R     |   10 
 sparklyr-1.7.6/sparklyr/R/tidiers_ml_naive_bayes.R             |    1 
 sparklyr-1.7.6/sparklyr/R/tidiers_ml_tree_models.R             |   72 +
 sparklyr-1.7.6/sparklyr/R/tidiers_utils.R                      |   41 
 sparklyr-1.7.6/sparklyr/R/tidyr_fill.R                         |   20 
 sparklyr-1.7.6/sparklyr/R/tidyr_pivot_longer.R                 |   12 
 sparklyr-1.7.6/sparklyr/R/tidyr_pivot_wider.R                  |   47 -
 sparklyr-1.7.6/sparklyr/R/utils.R                              |   17 
 sparklyr-1.7.6/sparklyr/R/zzz.R                                |    7 
 sparklyr-1.7.6/sparklyr/README.md                              |  460 ++++------
 sparklyr-1.7.6/sparklyr/build/partial.rdb                      |binary
 sparklyr-1.7.6/sparklyr/inst/extdata/versions.json             |  268 ++++-
 sparklyr-1.7.6/sparklyr/man/livy_install.Rd                    |    2 
 sparklyr-1.7.6/sparklyr/man/ml_glm_tidiers.Rd                  |   10 
 sparklyr-1.7.6/sparklyr/man/ml_logistic_regression_tidiers.Rd  |    5 
 sparklyr-1.7.6/sparklyr/man/ml_tree_tidiers.Rd                 |   20 
 sparklyr-1.7.6/sparklyr/man/spark_dependency.Rd                |    2 
 sparklyr-1.7.6/sparklyr/man/spark_write_rds.Rd                 |    6 
 sparklyr-1.7.6/sparklyr/man/stream_lag.Rd                      |    2 
 sparklyr-1.7.6/sparklyr/tools/readme/dplyr-ggplot2-1.png       |binary
 sparklyr-1.7.6/sparklyr/tools/readme/sparklyr-diagram.png      |only
 48 files changed, 1114 insertions(+), 584 deletions(-)

More information about sparklyr at CRAN
Permanent link

Package rlas updated to version 1.6.0 with previous version 1.5.3 dated 2022-03-18

Title: Read and Write 'las' and 'laz' Binary File Formats Used for Remote Sensing Data
Description: Read and write 'las' and 'laz' binary file formats. The LAS file format is a public file format for the interchange of 3-dimensional point cloud data between data users. The LAS specifications are approved by the American Society for Photogrammetry and Remote Sensing <https://www.asprs.org/divisions-committees/lidar-division/laser-las-file-format-exchange-activities>. The LAZ file format is an open and lossless compression scheme for binary LAS format versions 1.0 to 1.4 <https://laszip.org/>.
Author: Jean-Romain Roussel [aut, cre, cph], Florian De Boissieu [aut, ctb] , Martin Isenburg [cph] , David Auty [ctb] , Pierrick Marie [ctb] , Tiago de Conto [ctb]
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>

Diff between rlas versions 1.5.3 dated 2022-03-18 and 1.6.0 dated 2022-05-26

 DESCRIPTION                               |   10 -
 MD5                                       |   31 +++--
 NAMESPACE                                 |    2 
 NEWS.md                                   |    4 
 R/RcppExports.R                           |   16 +++
 R/altrep.R                                |only
 R/readLAS.r                               |   13 ++
 R/writeLAS.r                              |   11 ++
 inst/tinytest/test-altrep_iolas.R         |only
 inst/tinytest/test_altrep-serialization.R |only
 inst/tinytest/test_altrep.R               |only
 man/compression.Rd                        |only
 src/Makevars                              |    1 
 src/Makevars.win                          |    1 
 src/RcppExports.cpp                       |   55 ++++++++++
 src/altrep_compact_replication.cpp        |only
 src/altrepisode.h                         |only
 src/rlasstreamer.cpp                      |  159 ++++++++++++++++++++++--------
 src/rlasstreamer.h                        |   19 +++
 src/writeLAS.cpp                          |   60 +++++------
 20 files changed, 288 insertions(+), 94 deletions(-)

More information about rlas at CRAN
Permanent link

Package nloptr updated to version 2.0.3 with previous version 2.0.2 dated 2022-05-19

Title: R Interface to NLopt
Description: Solve optimization problems using an R interface to NLopt. NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. See <https://nlopt.readthedocs.io/en/latest/NLopt_Algorithms/> for more information on the available algorithms. Building from included sources requires 'CMake'. On Linux and 'macOS', if a suitable system build of NLopt (2.7.0 or later) is found, it is used; otherwise, it is built from included sources via 'CMake'. On Windows, NLopt is obtained through 'rwinlib' for 'R <= 4.1.x' or grabbed from the 'Rtools42 toolchain' for 'R >= 4.2.0'.
Author: Jelmer Ypma [aut], Steven G. Johnson [aut] , Hans W. Borchers [ctb], Dirk Eddelbuettel [ctb], Brian Ripley [ctb] , Kurt Hornik [ctb] , Julien Chiquet [ctb], Avraham Adler [ctb] , Xiongtao Dai [ctb], Aymeric Stamm [ctb, cre] , Jeroen Ooms [ctb]
Maintainer: Aymeric Stamm <aymeric.stamm@math.cnrs.fr>

Diff between nloptr versions 2.0.2 dated 2022-05-19 and 2.0.3 dated 2022-05-26

 nloptr-2.0.2/nloptr/src/scripts/nlopt_install.sh |only
 nloptr-2.0.3/nloptr/DESCRIPTION                  |    8 ++++----
 nloptr-2.0.3/nloptr/MD5                          |   15 +++++++--------
 nloptr-2.0.3/nloptr/NEWS.md                      |    6 ++++++
 nloptr-2.0.3/nloptr/README.md                    |    2 ++
 nloptr-2.0.3/nloptr/build/vignette.rds           |binary
 nloptr-2.0.3/nloptr/inst/doc/nloptr.html         |    4 ++--
 nloptr-2.0.3/nloptr/src/scripts/nlopt_cleanup.sh |    4 ++--
 nloptr-2.0.3/nloptr/tools/cmake_call.sh          |   15 ++++++++++-----
 9 files changed, 33 insertions(+), 21 deletions(-)

More information about nloptr at CRAN
Permanent link

Package pbo updated to version 1.3.5 with previous version 1.3.4 dated 2014-05-31

Title: Probability of Backtest Overfitting
Description: Following the method of Bailey et al., computes for a collection of candidate models the probability of backtest overfitting, the performance degradation and probability of loss, and the stochastic dominance.
Author: Matt Barry [aut, cre]
Maintainer: Matt Barry <mrb@softisms.com>

Diff between pbo versions 1.3.4 dated 2014-05-31 and 1.3.5 dated 2022-05-26

 pbo-1.3.4/pbo/tests/test_pbo_function.R  |only
 pbo-1.3.4/pbo/tests/test_pbo_parallel.R  |only
 pbo-1.3.4/pbo/tests/test_pbo_threshold.R |only
 pbo-1.3.5/pbo/DESCRIPTION                |   25 ++++---
 pbo-1.3.5/pbo/MD5                        |   44 +++++++------
 pbo-1.3.5/pbo/NAMESPACE                  |    7 +-
 pbo-1.3.5/pbo/NEWS.md                    |only
 pbo-1.3.5/pbo/R/lattice.pbo.R            |  101 +++++++++++++++----------------
 pbo-1.3.5/pbo/R/pbo-package.R            |    3 
 pbo-1.3.5/pbo/R/pbo.R                    |    9 +-
 pbo-1.3.5/pbo/README.md                  |    6 +
 pbo-1.3.5/pbo/build/vignette.rds         |binary
 pbo-1.3.5/pbo/inst/WORDLIST              |only
 pbo-1.3.5/pbo/inst/doc/pbo.R             |   28 ++++----
 pbo-1.3.5/pbo/inst/doc/pbo.Rmd           |    6 -
 pbo-1.3.5/pbo/inst/doc/pbo.html          |   62 +++++++++----------
 pbo-1.3.5/pbo/man/dotplot.pbo.Rd         |   18 +++--
 pbo-1.3.5/pbo/man/histogram.pbo.Rd       |   17 +++--
 pbo-1.3.5/pbo/man/pbo-package.Rd         |   13 +--
 pbo-1.3.5/pbo/man/pbo.Rd                 |    9 +-
 pbo-1.3.5/pbo/man/pbo_show_config.Rd     |    4 -
 pbo-1.3.5/pbo/man/xyplot.pbo.Rd          |   90 ++++++++++++++++-----------
 pbo-1.3.5/pbo/tests/spelling.R           |only
 pbo-1.3.5/pbo/tests/testthat             |only
 pbo-1.3.5/pbo/tests/testthat.R           |only
 pbo-1.3.5/pbo/vignettes/pbo.Rmd          |    6 -
 26 files changed, 249 insertions(+), 199 deletions(-)

More information about pbo at CRAN
Permanent link

New package MonteCarloSEM with initial version 0.0.4
Package: MonteCarloSEM
Title: Monte Carlo Data Simulation Package
Version: 0.0.4
Description: Monte Carlo simulation allows to test different conditions given to the correct structural equation models. This package runs Monte Carlo simulations under different conditions (such as sample size or normality of data). Within the package data sets can be simulated and run based on the given model. First, continuous and normal data sets are generated based on the given model. Later Fleishman's power method (1978) <DOI:10.1007/BF02293811> is used to add non-normality if exists. When data generation is completed (or when generated data sets are given) model test can also be run. Please cite as "Orçan, F. (2021). MonteCarloSEM: An R Package to Simulate Data for SEM. International Journal of Assessment Tools in Education, 8 (3), 704-713."
License: GPL-3
Encoding: UTF-8
Imports: Matrix, stats, utils, lavaan
Copyright: Fatih Orcan, Turkey
NeedsCompilation: no
Packaged: 2022-05-25 07:30:29 UTC; PC110
Author: Fatih Orcan [aut, cre]
Maintainer: Fatih Orcan <fatihorcan84@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-26 14:30:07 UTC

More information about MonteCarloSEM at CRAN
Permanent link

New package latrend with initial version 1.3.0
Package: latrend
Version: 1.3.0
Date: 2022-05-25
Title: A Framework for Clustering Longitudinal Data
Description: A framework for clustering longitudinal datasets in a standardized way. Provides an interface to existing R packages for clustering longitudinal univariate trajectories, facilitating reproducible and transparent analyses. Additionally, standard tools are provided to support cluster analyses, including repeated estimation, model validation, and model assessment. The interface enables users to compare results between methods, and to implement and evaluate new methods with ease.
Maintainer: Niek Den Teuling <niek.den.teuling@philips.com>
URL: https://github.com/philips-software/latrend
BugReports: https://github.com/philips-software/latrend/issues
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Language: en-US
Depends: R (>= 3.6.0)
Imports: stats, methods, Rdpack, R.utils, assertthat (>= 0.2.1), foreach, data.table (>= 1.12.0), magrittr, matrixStats, rlang, rmarkdown (>= 1.18)
Suggests: testthat (>= 3.0.0), roxygen2 (>= 7.1.0), knitr (>= 1.24), rcmdcheck, pkgdown, devtools, evaluate, lme4, covr, lintr, tinytex, longitudinalData (>= 2.4.1), kml (>= 2.4.1), lcmm (>= 1.9.3), mixtools, flexmix, fda, funFEM, gridExtra, igraph, crimCV, akmedoids (>= 1.3.0), dtwclust, mixAK, clusterCrit, mclust, mclustcomp, psych, qqplotr, doParallel, simTool, dplyr, ggplot2, caret, tibble
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-25 22:57:28 UTC; 310083353
Author: Niek Den Teuling [aut, cre] , Steffen Pauws [ctb], Edwin van den Heuvel [ctb], Copyright © 2022 Koninklijke Philips N.V. [cph]
Repository: CRAN
Date/Publication: 2022-05-26 14:40:05 UTC

More information about latrend at CRAN
Permanent link

Package HACSim updated to version 1.0.6 with previous version 1.0.5 dated 2020-01-07

Title: Iterative Extrapolation of Species' Haplotype Accumulation Curves for Genetic Diversity Assessment
Description: Performs iterative extrapolation of species' haplotype accumulation curves using a nonparametric stochastic (Monte Carlo) optimization method for assessment of specimen sampling completeness based on the approach of Phillips et al. (2015) <doi:10.1515/dna-2015-0008>, Phillips et al. (2019) <doi:10.1002/ece3.4757> and Phillips et al. (2020) <doi: 10.7717/peerj-cs.243>. 'HACSim' outputs a number of useful summary statistics of sampling coverage ("Measures of Sampling Closeness"), including an estimate of the likely required sample size (along with desired level confidence intervals) necessary to recover a given number/proportion of observed unique species' haplotypes. Any genomic marker can be targeted to assess likely required specimen sample sizes for genetic diversity assessment. The method is particularly well-suited to assess sampling sufficiency for DNA barcoding initiatives. Users can also simulate their own DNA sequences according to various models of nucleotide substitution. A Shiny app is also available.
Author: Jarrett D. Phillips [aut, cre], Steven H. French [ctb], Navdeep Singh [ctb]
Maintainer: Jarrett D. Phillips <phillipsjarrett1@gmail.com>

Diff between HACSim versions 1.0.5 dated 2020-01-07 and 1.0.6 dated 2022-05-26

 DESCRIPTION            |   21 +++---
 MD5                    |   55 +++++++++++-----
 NAMESPACE              |    7 ++
 R/HAC.object.R         |    8 ++
 R/HAC.sim.R            |  168 +++++++++++++++++++++++++++++++------------------
 R/HAC.simrep.R         |   43 ++++++++----
 R/launchApp.R          |only
 R/sim.seqs.R           |only
 R/zzz.R                |    9 ++
 build/partial.rdb      |binary
 inst                   |only
 man/HAC.sim.Rd         |    3 
 man/HAC.simrep.Rd      |   48 ++++++++++----
 man/HACClass.Rd        |    3 
 man/HACHypothetical.Rd |   52 ++++++++++-----
 man/HACReal.Rd         |   43 ++++++++----
 man/HACSim-package.Rd  |   58 +++++++++++++++-
 man/accumulate.Rd      |    3 
 man/envr.Rd            |   53 +++++++++++----
 man/launchApp.Rd       |only
 man/sim.seqs.Rd        |only
 src/Makevars           |    1 
 src/accumulate.cpp     |   10 ++
 23 files changed, 418 insertions(+), 167 deletions(-)

More information about HACSim at CRAN
Permanent link

Package ergm.ego updated to version 1.0.1 with previous version 1.0.0 dated 2021-06-23

Title: Fit, Simulate and Diagnose Exponential-Family Random Graph Models to Egocentrically Sampled Network Data
Description: Utilities for managing egocentrically sampled network data and a wrapper around the 'ergm' package to facilitate ERGM inference and simulation from such data. See Krivitsky and Morris (2017) <doi:10.1214/16-AOAS1010>.
Author: Pavel N. Krivitsky [aut, cre] , Steven M. Goodreau [ctb], Martina Morris [ctb], Kirk Li [ctb], Emily N. Beylerian [ctb], Michal Bojanowski [ctb] , Chad Klumb [ctb]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>

Diff between ergm.ego versions 1.0.0 dated 2021-06-23 and 1.0.1 dated 2022-05-26

 ergm.ego-1.0.0/ergm.ego/build/partial.rdb                      |only
 ergm.ego-1.0.1/ergm.ego/DESCRIPTION                            |   24 +-
 ergm.ego-1.0.1/ergm.ego/LICENSE                                |    2 
 ergm.ego-1.0.1/ergm.ego/MD5                                    |   83 ++++------
 ergm.ego-1.0.1/ergm.ego/R/EgoStat.R                            |    8 
 ergm.ego-1.0.1/ergm.ego/R/EgoStat.duration.R                   |    2 
 ergm.ego-1.0.1/ergm.ego/R/EgoStat.node.attr.R                  |    2 
 ergm.ego-1.0.1/ergm.ego/R/InitErgmTerm.R                       |    2 
 ergm.ego-1.0.1/ergm.ego/R/control.ergm.ego.R                   |   25 +--
 ergm.ego-1.0.1/ergm.ego/R/control.simulate.ergm.ego.R          |    2 
 ergm.ego-1.0.1/ergm.ego/R/degreedist.R                         |    4 
 ergm.ego-1.0.1/ergm.ego/R/egor.R                               |    2 
 ergm.ego-1.0.1/ergm.ego/R/ergm.ego.R                           |   32 ++-
 ergm.ego-1.0.1/ergm.ego/R/fmhfit.R                             |    2 
 ergm.ego-1.0.1/ergm.ego/R/gof.ergm.ego.R                       |    2 
 ergm.ego-1.0.1/ergm.ego/R/predict.ergmego.R                    |    2 
 ergm.ego-1.0.1/ergm.ego/R/reweight.egor.R                      |    2 
 ergm.ego-1.0.1/ergm.ego/R/simulate.ergm.ego.R                  |    2 
 ergm.ego-1.0.1/ergm.ego/R/summary.ergm.ego.R                   |    2 
 ergm.ego-1.0.1/ergm.ego/R/summary.statistics.egor.R            |    2 
 ergm.ego-1.0.1/ergm.ego/R/zzz.R                                |   17 --
 ergm.ego-1.0.1/ergm.ego/build/ergm.ego.pdf                     |binary
 ergm.ego-1.0.1/ergm.ego/inst/CITATION                          |   12 -
 ergm.ego-1.0.1/ergm.ego/inst/NEWS.Rd                           |   24 ++
 ergm.ego-1.0.1/ergm.ego/man/control.ergm.ego.Rd                |   27 +--
 ergm.ego-1.0.1/ergm.ego/man/ergm.ego-terms.Rd                  |    6 
 ergm.ego-1.0.1/ergm.ego/man/ergm.ego.Rd                        |   14 +
 ergm.ego-1.0.1/ergm.ego/man/mixingmatrix.egor.Rd               |    2 
 ergm.ego-1.0.1/ergm.ego/src/changestats.c                      |    2 
 ergm.ego-1.0.1/ergm.ego/src/include_stubs.c                    |    2 
 ergm.ego-1.0.1/ergm.ego/src/init.c                             |    2 
 ergm.ego-1.0.1/ergm.ego/tests/testthat.R                       |    2 
 ergm.ego-1.0.1/ergm.ego/tests/testthat/test-EgoStat.R          |    7 
 ergm.ego-1.0.1/ergm.ego/tests/testthat/test-boot_jack.R        |   18 +-
 ergm.ego-1.0.1/ergm.ego/tests/testthat/test-coef_recovery.R    |   45 ++---
 ergm.ego-1.0.1/ergm.ego/tests/testthat/test-degreedist.R       |    9 -
 ergm.ego-1.0.1/ergm.ego/tests/testthat/test-drop.R             |    5 
 ergm.ego-1.0.1/ergm.ego/tests/testthat/test-gof.ergm.ego.R     |    2 
 ergm.ego-1.0.1/ergm.ego/tests/testthat/test-mixingmatrix.R     |    2 
 ergm.ego-1.0.1/ergm.ego/tests/testthat/test-netsize.adj.R      |    6 
 ergm.ego-1.0.1/ergm.ego/tests/testthat/test-predict.ergm.ego.R |   10 -
 ergm.ego-1.0.1/ergm.ego/tests/testthat/test-statmismatch.R     |    4 
 ergm.ego-1.0.1/ergm.ego/tests/testthat/test-table_ppop.R       |    4 
 43 files changed, 214 insertions(+), 210 deletions(-)

More information about ergm.ego at CRAN
Permanent link

Package ctmcd updated to version 1.4.2 with previous version 1.4.1 dated 2019-01-02

Title: Estimating the Parameters of a Continuous-Time Markov Chain from Discrete-Time Data
Description: Functions for estimating Markov generator matrices from discrete-time observations. The implemented approaches comprise diagonal adjustment, weighted adjustment and quasi-optimization of matrix logarithm based candidate solutions, an expectation-maximization algorithm as well as a Gibbs sampler.
Author: Marius Pfeuffer [aut,cre], Greig Smith [ctb], Goncalo dos Reis [ctb], Linda Moestel [ctb], Matthias Fischer [ctb]
Maintainer: Marius Pfeuffer <marius.pfeuffer@fau.de>

Diff between ctmcd versions 1.4.1 dated 2019-01-02 and 1.4.2 dated 2022-05-26

 ctmcd-1.4.1/ctmcd/R/expmMC.R        |only
 ctmcd-1.4.1/ctmcd/man/expmMC.Rd     |only
 ctmcd-1.4.2/ctmcd/DESCRIPTION       |   10 +++++-----
 ctmcd-1.4.2/ctmcd/MD5               |    8 +++-----
 ctmcd-1.4.2/ctmcd/NAMESPACE         |    1 -
 ctmcd-1.4.2/ctmcd/build/partial.rdb |binary
 6 files changed, 8 insertions(+), 11 deletions(-)

More information about ctmcd at CRAN
Permanent link

Package cchsflow updated to version 2.1.0 with previous version 2.0.0 dated 2021-10-25

Title: Transforming and Harmonizing CCHS Variables
Description: Supporting the use of the Canadian Community Health Survey (CCHS) by transforming variables from each cycle into harmonized, consistent versions that span survey cycles (currently, 2001 to 2018). CCHS data used in this library is accessed and adapted in accordance to the Statistics Canada Open Licence Agreement. This package uses rec_with_table(), which was developed from 'sjmisc' rec(). Lüdecke D (2018). "sjmisc: Data and Variable Transformation Functions". Journal of Open Source Software, 3(26), 754. <doi:10.21105/joss.00754>.
Author: Doug Manuel [aut, cph] , Warsame Yusuf [aut], Rostyslav Vyuha [aut], Kitty Chen [aut, cre], Carol Bennett [aut], Yulric Sequeira [ctb], The Ottawa Hospital [cph]
Maintainer: Kitty Chen <kitchen@ohri.ca>

Diff between cchsflow versions 2.0.0 dated 2021-10-25 and 2.1.0 dated 2022-05-26

 DESCRIPTION                                   |   25 
 LICENSE                                       |    2 
 MD5                                           |  258 -
 NAMESPACE                                     |  129 
 NEWS.md                                       | 1011 ++---
 R/RACDPAL.R                                   |  156 
 R/active-transportation.R                     |only
 R/adl.R                                       |  452 +-
 R/age-categorical.R                           |  212 -
 R/alcohol.R                                   | 1670 +++++----
 R/bmi.R                                       |  542 +-
 R/data.R                                      |  961 ++---
 R/depression.R                                |  128 
 R/diet.R                                      |  388 +-
 R/food-insecurity.R                           |   98 
 R/immigration.R                               |  170 
 R/label-utils.R                               |  424 +-
 R/life-satisfaction.R                         |   90 
 R/merge-data.R                                |  126 
 R/number-conditions.R                         |  452 +-
 R/occupation.R                                |  250 -
 R/percent-time-canada.R                       |  298 -
 R/physical-activity.R                         |  268 -
 R/recode-with-table.R                         | 1946 +++++-----
 R/respiratory-condition.R                     | 1050 ++---
 R/smoking.R                                   | 1201 +++---
 R/social-provision.R                          |only
 R/strings.R                                   |  202 -
 R/utility-functions.R                         |   68 
 README.md                                     |  343 -
 build                                         |only
 data/cchs2009_s.RData                         |only
 data/cchs2010_s.RData                         |only
 data/cchs2012_s.RData                         |only
 data/variable_details.RData                   |binary
 data/variables.RData                          |binary
 inst/extdata/sample_variable_details.csv      |    2 
 inst/extdata/variable_details.RData           |only
 inst/extdata/variable_details.csv             | 4805 ++++++++++++++++----------
 inst/extdata/variables.RData                  |only
 inst/extdata/variables.csv                    |  502 +-
 man/ALCDTTM.Rd                                |   70 
 man/ALCDTYP.Rd                                |   80 
 man/ALWDDLY.Rd                                |   54 
 man/ALWDWKY.Rd                                |   64 
 man/ALW_1.Rd                                  |only
 man/ALW_2A1.Rd                                |only
 man/ALW_2A2.Rd                                |only
 man/ALW_2A3.Rd                                |only
 man/ALW_2A4.Rd                                |only
 man/ALW_2A5.Rd                                |only
 man/ALW_2A6.Rd                                |only
 man/ALW_2A7.Rd                                |only
 man/COPD_Emph_der_fun1.Rd                     |  140 
 man/COPD_Emph_der_fun2.Rd                     |  136 
 man/DPSDPP.Rd                                 |   84 
 man/DPSDSF.Rd                                 |   72 
 man/GEN_02A2.Rd                               |  104 
 man/LBFA_31A.Rd                               |   90 
 man/LBFA_31A_a.Rd                             |  104 
 man/LBFA_31A_b.Rd                             |   96 
 man/RACDPAL_fun.Rd                            |  142 
 man/SMKDSTY_fun.Rd                            |only
 man/SMKG040_fun.Rd                            |  140 
 man/SMKG203_fun.Rd                            |only
 man/SMKG207_fun.Rd                            |only
 man/SPS_5_fun.Rd                              |only
 man/active_transport1_fun.Rd                  |only
 man/active_transport2_fun.Rd                  |only
 man/active_transport3_fun.Rd                  |only
 man/adjusted_bmi_fun.Rd                       |  198 -
 man/adl_fun.Rd                                |  238 -
 man/adl_score_5_fun.Rd                        |  162 
 man/age_cat_fun.Rd                            |  130 
 man/binge_drinker_fun.Rd                      |  216 -
 man/bmi_fun.Rd                                |  190 -
 man/bmi_fun_cat.Rd                            |  144 
 man/cchs2001_p.Rd                             |   68 
 man/cchs2003_p.Rd                             |   68 
 man/cchs2005_p.Rd                             |   68 
 man/cchs2007_2008_p.Rd                        |   68 
 man/cchs2009_2010_p.Rd                        |   68 
 man/cchs2009_s.Rd                             |only
 man/cchs2010_p.Rd                             |   76 
 man/cchs2010_s.Rd                             |only
 man/cchs2011_2012_p.Rd                        |   68 
 man/cchs2012_p.Rd                             |   76 
 man/cchs2012_s.Rd                             |only
 man/cchs2013_2014_p.Rd                        |   68 
 man/cchs2014_p.Rd                             |   76 
 man/cchs2015_2016_p.Rd                        |   76 
 man/cchs2017_2018_p.Rd                        |   76 
 man/compare_value_based_on_interval.Rd        |   64 
 man/diet_score_fun.Rd                         |  170 
 man/diet_score_fun_cat.Rd                     |  140 
 man/energy_exp_fun.Rd                         |  238 -
 man/figures/logo.svg                          |   68 
 man/food_insecurity_der.Rd                    |  106 
 man/get_data_variable_name.Rd                 |   60 
 man/if_else2.Rd                               |   78 
 man/immigration_fun.Rd                        |  146 
 man/is_equal.Rd                               |   82 
 man/label_data.Rd                             |   40 
 man/low_drink_long_fun.Rd                     |  250 -
 man/low_drink_score_fun.Rd                    |  156 
 man/low_drink_score_fun1.Rd                   |  176 
 man/low_drink_short_fun.Rd                    |  248 -
 man/merge_rec_data.Rd                         |   94 
 man/multiple_conditions_fun1.Rd               |  194 -
 man/multiple_conditions_fun2.Rd               |  206 -
 man/pack_years_fun.Rd                         |  220 -
 man/pack_years_fun_cat.Rd                     |  148 
 man/pct_time_fun.Rd                           |  148 
 man/pct_time_fun_cat.Rd                       |  134 
 man/rec_with_table.Rd                         |  278 -
 man/recode_columns.Rd                         |   72 
 man/recode_variable_NA_formating.Rd           |   38 
 man/resp_condition_fun1.Rd                    |  144 
 man/resp_condition_fun2.Rd                    |  148 
 man/resp_condition_fun3.Rd                    |  142 
 man/set_data_labels.Rd                        |  100 
 man/smoke_simple_fun.Rd                       |  130 
 man/time_quit_smoking_fun.Rd                  |  118 
 man/variable_details.Rd                       |   42 
 man/variables.Rd                              |   42 
 tests/testdata/rec_with_table_test_data.RData |binary
 tests/testthat.R                              |    8 
 tests/testthat/test-RACDPAL.R                 |   36 
 tests/testthat/test-active-transportation.R   |only
 tests/testthat/test-adl.R                     |   92 
 tests/testthat/test-age-categorical.R         |   22 
 tests/testthat/test-alcohol.R                 |  398 +-
 tests/testthat/test-bmi.R                     |   58 
 tests/testthat/test-data.R                    |  316 -
 tests/testthat/test-diet.R                    |   48 
 tests/testthat/test-immigration.R             |  128 
 tests/testthat/test-label-utils.R             |   36 
 tests/testthat/test-number-conditions.R       |   66 
 tests/testthat/test-physical-activity.R       |   20 
 tests/testthat/test-recode-with-table.R       |   65 
 tests/testthat/test-respiratory-condition.R   |  390 +-
 tests/testthat/test-smoking.R                 |  200 -
 tests/testthat/test-social-provision.R        |only
 tests/testthat/test-utility-functions.R       |   22 
 144 files changed, 15114 insertions(+), 12950 deletions(-)

More information about cchsflow at CRAN
Permanent link

Package Boom updated to version 0.9.8 with previous version 0.9.7 dated 2021-02-23

Title: Bayesian Object Oriented Modeling
Description: A C++ library for Bayesian modeling, with an emphasis on Markov chain Monte Carlo. Although boom contains a few R utilities (mainly plotting functions), its primary purpose is to install the BOOM C++ library on your system so that other packages can link against it.
Author: Steven L. Scott is the sole author and creator of the BOOM project. Some code in the BOOM libraries has been modified from other open source projects. These include Cephes , NEWUOA , and a modified version of the R math libraries . Original copyrig [...truncated...]
Maintainer: Steven L. Scott <steve.the.bayesian@gmail.com>

Diff between Boom versions 0.9.7 dated 2021-02-23 and 0.9.8 dated 2022-05-26

 Boom-0.9.7/Boom/inst/include/Models/StateSpace/Filters/KalmanStorage.hpp                                    |only
 Boom-0.9.7/Boom/inst/include/Models/StateSpace/MultivariateStateSpaceModelBase.hpp                          |only
 Boom-0.9.7/Boom/inst/include/Models/StateSpace/MultivariateStateSpaceRegressionModel.hpp                    |only
 Boom-0.9.7/Boom/inst/include/Models/StateSpace/PosteriorSamplers/MultivariateStateSpaceModelSampler.hpp     |only
 Boom-0.9.7/Boom/inst/include/Models/StateSpace/PosteriorSamplers/MvStateSpaceRegressionPosteriorSampler.hpp |only
 Boom-0.9.7/Boom/inst/include/Models/StateSpace/PosteriorSamplers/SharedLocalLevelPosteriorSampler.hpp       |only
 Boom-0.9.7/Boom/src/Models/StateSpace/MultivariateStateSpaceModelBase.cpp                                   |only
 Boom-0.9.7/Boom/src/Models/StateSpace/MultivariateStateSpaceRegressionModel.cpp                             |only
 Boom-0.9.7/Boom/src/Models/StateSpace/PosteriorSamplers/MultivariateStateSpaceModelSampler.cpp              |only
 Boom-0.9.7/Boom/src/Models/StateSpace/PosteriorSamplers/MvStateSpaceRegressionPosteriorSampler.cpp          |only
 Boom-0.9.7/Boom/src/Models/StateSpace/PosteriorSamplers/SharedLocalLevelPosteriorSampler.cpp                |only
 Boom-0.9.7/Boom/src/math/cephes/rgamma.cpp                                                                  |only
 Boom-0.9.8/Boom/DESCRIPTION                                                                                 |    8 
 Boom-0.9.8/Boom/MD5                                                                                         |  522 ++---
 Boom-0.9.8/Boom/NAMESPACE                                                                                   |   12 
 Boom-0.9.8/Boom/R/prior_specification.R                                                                     |   14 
 Boom-0.9.8/Boom/inst/include/LinAlg/Array.hpp                                                               |    7 
 Boom-0.9.8/Boom/inst/include/LinAlg/ArrayIterator.hpp                                                       |   24 
 Boom-0.9.8/Boom/inst/include/LinAlg/Matrix.hpp                                                              |   18 
 Boom-0.9.8/Boom/inst/include/LinAlg/Selector.hpp                                                            |    7 
 Boom-0.9.8/Boom/inst/include/LinAlg/SpdMatrix.hpp                                                           |   12 
 Boom-0.9.8/Boom/inst/include/LinAlg/SubMatrix.hpp                                                           |   16 
 Boom-0.9.8/Boom/inst/include/LinAlg/Vector.hpp                                                              |    6 
 Boom-0.9.8/Boom/inst/include/LinAlg/VectorView.hpp                                                          |    2 
 Boom-0.9.8/Boom/inst/include/LinAlg/VectorViewIterator.hpp                                                  |   25 
 Boom-0.9.8/Boom/inst/include/Models/DataTypes.hpp                                                           |   14 
 Boom-0.9.8/Boom/inst/include/Models/Glm/ChoiceData.hpp                                                      |    3 
 Boom-0.9.8/Boom/inst/include/Models/Glm/Glm.hpp                                                             |    3 
 Boom-0.9.8/Boom/inst/include/Models/Glm/GlmCoefs.hpp                                                        |    8 
 Boom-0.9.8/Boom/inst/include/Models/Glm/IndependentRegressionModels.hpp                                     |   11 
 Boom-0.9.8/Boom/inst/include/Models/Glm/MultinomialLogitModel.hpp                                           |    7 
 Boom-0.9.8/Boom/inst/include/Models/Glm/MvnGivenX.hpp                                                       |   66 
 Boom-0.9.8/Boom/inst/include/Models/Glm/PosteriorSamplers/BigAssSpikeSlabSampler.hpp                        |only
 Boom-0.9.8/Boom/inst/include/Models/Glm/PosteriorSamplers/BinomialLogitSpikeSlabSampler.hpp                 |    3 
 Boom-0.9.8/Boom/inst/include/Models/Glm/PosteriorSamplers/BregVsSampler.hpp                                 |   17 
 Boom-0.9.8/Boom/inst/include/Models/Glm/PosteriorSamplers/IndependentRegressionModelsPosteriorSampler.hpp   |   21 
 Boom-0.9.8/Boom/inst/include/Models/Glm/PosteriorSamplers/MultinomialLogitCompositeSpikeSlabSampler.hpp     |   12 
 Boom-0.9.8/Boom/inst/include/Models/Glm/PosteriorSamplers/PoissonRegressionAuxMixSampler.hpp                |    1 
 Boom-0.9.8/Boom/inst/include/Models/Glm/PosteriorSamplers/PoissonRegressionSpikeSlabSampler.hpp             |    3 
 Boom-0.9.8/Boom/inst/include/Models/Glm/PosteriorSamplers/RegressionSemiconjugateSampler.hpp                |    4 
 Boom-0.9.8/Boom/inst/include/Models/Glm/PosteriorSamplers/SpikeSlabSampler.hpp                              |   25 
 Boom-0.9.8/Boom/inst/include/Models/Glm/PosteriorSamplers/TRegressionSpikeSlabSampler.hpp                   |    6 
 Boom-0.9.8/Boom/inst/include/Models/Glm/RegressionModel.hpp                                                 |  106 +
 Boom-0.9.8/Boom/inst/include/Models/Glm/RegressionSlabPrior.hpp                                             |only
 Boom-0.9.8/Boom/inst/include/Models/Glm/VariableSelectionPrior.hpp                                          |    3 
 Boom-0.9.8/Boom/inst/include/Models/Hierarchical/HierarchicalGammaModel.hpp                                 |    2 
 Boom-0.9.8/Boom/inst/include/Models/Hierarchical/HierarchicalModel.hpp                                      |    2 
 Boom-0.9.8/Boom/inst/include/Models/Hierarchical/HierarchicalZeroInflatedGammaModel.hpp                     |    2 
 Boom-0.9.8/Boom/inst/include/Models/Hierarchical/HierarchicalZeroInflatedPoissonModel.hpp                   |    2 
 Boom-0.9.8/Boom/inst/include/Models/IRT/IRT.hpp                                                             |    3 
 Boom-0.9.8/Boom/inst/include/Models/Impute/MixedDataImputerWithErrorCorrection.hpp                          |    2 
 Boom-0.9.8/Boom/inst/include/Models/MarkovModel.hpp                                                         |    2 
 Boom-0.9.8/Boom/inst/include/Models/Mixtures/DirichletProcessMvnModel.hpp                                   |   26 
 Boom-0.9.8/Boom/inst/include/Models/Mixtures/identify_permutation.hpp                                       |only
 Boom-0.9.8/Boom/inst/include/Models/ModelTypes.hpp                                                          |   18 
 Boom-0.9.8/Boom/inst/include/Models/ParamTypes.hpp                                                          |    2 
 Boom-0.9.8/Boom/inst/include/Models/Policies/IID_DataPolicy.hpp                                             |    2 
 Boom-0.9.8/Boom/inst/include/Models/Policies/PriorPolicy.hpp                                                |   16 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/AbsorbingMarkovConjSampler.hpp                        |    2 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/BetaBinomialPosteriorSampler.hpp                      |    3 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/BetaBinomialSampler.hpp                               |    1 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/BetaPosteriorSampler.hpp                              |    4 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/CompositeModelSampler.hpp                             |    1 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/CorrelationSampler.hpp                                |   10 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/DirichletPosteriorSampler.hpp                         |    2 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/ExchangeableDirichletSampler.hpp                      |    5 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/ExponentialGammaSampler.hpp                           |    8 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/FiniteMixturePosteriorSampler.hpp                     |    7 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/FixedProbBinomialSampler.hpp                          |    1 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/GammaPosteriorSampler.hpp                             |    7 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/GaussianConjSampler.hpp                               |    3 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/GaussianMeanSampler.hpp                               |   16 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/GaussianVarSampler.hpp                                |    3 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/GenericGaussianVarianceSampler.hpp                    |    3 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/GenericStudentSampler.hpp                             |only
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/IndependentMvnConjSampler.hpp                         |    9 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/IndependentMvnVarSampler.hpp                          |    4 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/MarkovConjSampler.hpp                                 |   15 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/MarkovConjShrinkageSampler.hpp                        |    2 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/MultinomialDirichletSampler.hpp                       |    8 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/MvnConjSampler.hpp                                    |    4 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/MvnIndependentVarianceSampler.hpp                     |    9 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/MvnMeanSampler.hpp                                    |   19 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/MvnVarSampler.hpp                                     |   10 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/PoissonGammaPosteriorSampler.hpp                      |    3 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/PoissonGammaSampler.hpp                               |    8 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/PosteriorSampler.hpp                                  |    9 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/ProductDirichletPosteriorSampler.hpp                  |    7 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/SepStratSampler.hpp                                   |    9 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/ZeroInflatedGammaPosteriorSampler.hpp                 |    9 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/ZeroInflatedLognormalPosteriorSampler.hpp             |   10 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/ZeroInflatedPoissonSampler.hpp                        |    2 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/ZeroMeanGaussianConjSampler.hpp                       |    7 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/ZeroMeanMvnConjSampler.hpp                            |   10 
 Boom-0.9.8/Boom/inst/include/Models/PosteriorSamplers/ZeroMeanMvnIndependenceSampler.hpp                    |    8 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/AggregatedStateSpaceRegression.hpp                           |   14 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/DynamicInterceptRegression.hpp                               |   39 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/DynamicRegression.hpp                                        |   62 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/Filters/ConditionalIidKalmanFilter.hpp                       |   69 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/Filters/ConditionallyIndependentKalmanFilter.hpp             |   60 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/Filters/KalmanFilterBase.hpp                                 |   30 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/Filters/KalmanTools.hpp                                      |   26 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/Filters/MultivariateKalmanFilterBase.hpp                     |  193 -
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/Filters/ScalarKalmanFilter.hpp                               |   19 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/Filters/SparseKalmanTools.hpp                                |   10 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/Filters/SparseMatrix.hpp                                     |  731 ++++++-
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/Multivariate                                                 |only
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/PosteriorSamplers/DynamicRegressionArPosteriorSampler.hpp    |    3 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/PosteriorSamplers/DynamicRegressionDirectGibbs.hpp           |   49 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/PosteriorSamplers/DynamicRegressionPosteriorSampler.hpp      |    7 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/PosteriorSamplers/StateSpaceLogitPosteriorSampler.hpp        |    3 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/PosteriorSamplers/StateSpacePoissonPosteriorSampler.hpp      |    3 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/PosteriorSamplers/StateSpacePosteriorSampler.hpp             |    4 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/StateModelVector.hpp                                         |  146 -
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/StateModels/GeneralSeasonalStateModel.hpp                    |  164 +
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/StateModels/LocalLevelStateModel.hpp                         |  170 -
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/StateModels/PosteriorSamplers                                |only
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/StateModels/RegressionHolidayStateModel.hpp                  |   15 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/StateModels/SemilocalLinearTrend.hpp                         |    5 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/StateModels/StateModel.hpp                                   |   27 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/StateSpaceLogitModel.hpp                                     |   48 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/StateSpaceModel.hpp                                          |   38 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/StateSpaceModelBase.hpp                                      |  161 +
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/StateSpacePoissonModel.hpp                                   |   13 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/StateSpaceRegressionModel.hpp                                |   38 
 Boom-0.9.8/Boom/inst/include/Models/StateSpace/StateSpaceStudentRegressionModel.hpp                         |   30 
 Boom-0.9.8/Boom/inst/include/Models/TimeSeries/PosteriorSamplers/ArPosteriorSampler.hpp                     |    4 
 Boom-0.9.8/Boom/inst/include/Models/TimeSeries/PosteriorSamplers/ArSpikeSlabSampler.hpp                     |    3 
 Boom-0.9.8/Boom/inst/include/cpputil/Date.hpp                                                               |   10 
 Boom-0.9.8/Boom/inst/include/cpputil/Ptr.hpp                                                                |   12 
 Boom-0.9.8/Boom/inst/include/cpputil/ThreadTools.hpp                                                        |    3 
 Boom-0.9.8/Boom/inst/include/cpputil/string_utils.hpp                                                       |    8 
 Boom-0.9.8/Boom/inst/include/distributions.hpp                                                              |    2 
 Boom-0.9.8/Boom/inst/include/numopt/LinearAssignment.hpp                                                    |only
 Boom-0.9.8/Boom/inst/include/numopt/MarkovDecisionProcess.hpp                                               |only
 Boom-0.9.8/Boom/inst/include/numopt/Qlearning.hpp                                                           |only
 Boom-0.9.8/Boom/inst/include/numopt/linear_assignment                                                       |only
 Boom-0.9.8/Boom/inst/include/r_interface/prior_specification.hpp                                            |   34 
 Boom-0.9.8/Boom/inst/include/stats/DataTable.hpp                                                            |   33 
 Boom-0.9.8/Boom/inst/include/uint.hpp                                                                       |    4 
 Boom-0.9.8/Boom/man/MvnGivenSigmaMatrixPrior.Rd                                                             |only
 Boom-0.9.8/Boom/src/Bmath/mlutils.cpp                                                                       |   30 
 Boom-0.9.8/Boom/src/Bmath/plogis.cpp                                                                        |   11 
 Boom-0.9.8/Boom/src/LinAlg/Array.cpp                                                                        |   31 
 Boom-0.9.8/Boom/src/LinAlg/Eigen.cpp                                                                        |    3 
 Boom-0.9.8/Boom/src/LinAlg/LU.cpp                                                                           |   22 
 Boom-0.9.8/Boom/src/LinAlg/Matrix.cpp                                                                       |   56 
 Boom-0.9.8/Boom/src/LinAlg/SWEEP.cpp                                                                        |    3 
 Boom-0.9.8/Boom/src/LinAlg/Selector.cpp                                                                     |   12 
 Boom-0.9.8/Boom/src/LinAlg/SpdMatrix.cpp                                                                    |   28 
 Boom-0.9.8/Boom/src/LinAlg/SubMatrix.cpp                                                                    |   88 
 Boom-0.9.8/Boom/src/LinAlg/Vector.cpp                                                                       |    9 
 Boom-0.9.8/Boom/src/LinAlg/VectorView.cpp                                                                   |   16 
 Boom-0.9.8/Boom/src/Makevars                                                                                |   11 
 Boom-0.9.8/Boom/src/Models/BinomialModel.cpp                                                                |    5 
 Boom-0.9.8/Boom/src/Models/FiniteMixtureModel.cpp                                                           |    2 
 Boom-0.9.8/Boom/src/Models/GaussianModel.cpp                                                                |    2 
 Boom-0.9.8/Boom/src/Models/Glm/GlmCoefs.cpp                                                                 |   18 
 Boom-0.9.8/Boom/src/Models/Glm/MultinomialLogitModel.cpp                                                    |    2 
 Boom-0.9.8/Boom/src/Models/Glm/PoissonRegressionModel.cpp                                                   |    2 
 Boom-0.9.8/Boom/src/Models/Glm/PosteriorSamplers/BigAssSpikeSlabSampler.cpp                                 |only
 Boom-0.9.8/Boom/src/Models/Glm/PosteriorSamplers/BinomialLogitSpikeSlabSampler.cpp                          |   11 
 Boom-0.9.8/Boom/src/Models/Glm/PosteriorSamplers/BregVsSampler.cpp                                          |    2 
 Boom-0.9.8/Boom/src/Models/Glm/PosteriorSamplers/PoissonRegressionAuxMixSampler.cpp                         |    9 
 Boom-0.9.8/Boom/src/Models/Glm/PosteriorSamplers/PoissonRegressionSpikeSlabSampler.cpp                      |   14 
 Boom-0.9.8/Boom/src/Models/Glm/PosteriorSamplers/RegressionSemiconjugateSampler.cpp                         |    4 
 Boom-0.9.8/Boom/src/Models/Glm/PosteriorSamplers/SpikeSlabDaRegressionSampler.cpp                           |    2 
 Boom-0.9.8/Boom/src/Models/Glm/PosteriorSamplers/SpikeSlabSampler.cpp                                       |   14 
 Boom-0.9.8/Boom/src/Models/Glm/PosteriorSamplers/ZeroInflatedLognormalRegressionPosteriorSampler.cpp        |    2 
 Boom-0.9.8/Boom/src/Models/Glm/RegressionModel.cpp                                                          |  102 
 Boom-0.9.8/Boom/src/Models/Glm/RegressionSlabPrior.cpp                                                      |only
 Boom-0.9.8/Boom/src/Models/Glm/VariableSelectionPrior.cpp                                                   |    3 
 Boom-0.9.8/Boom/src/Models/HMM/HmmDataImputer.cpp                                                           |    3 
 Boom-0.9.8/Boom/src/Models/IRT/PartialCreditModel.cpp                                                       |    9 
 Boom-0.9.8/Boom/src/Models/Impute/MixedDataImputer.cpp                                                      |   12 
 Boom-0.9.8/Boom/src/Models/Impute/MixedDataImputerWithErrorCorrection.cpp                                   |    4 
 Boom-0.9.8/Boom/src/Models/Impute/MvRegCopulaDataImputer.cpp                                                |    3 
 Boom-0.9.8/Boom/src/Models/MarkovModel.cpp                                                                  |   11 
 Boom-0.9.8/Boom/src/Models/Mixtures/DirichletProcessMixture.cpp                                             |    8 
 Boom-0.9.8/Boom/src/Models/Mixtures/DirichletProcessMvnModel.cpp                                            |   11 
 Boom-0.9.8/Boom/src/Models/Mixtures/PosteriorSamplers/DirichletProcessMvnCollapsedGibbsSampler.cpp          |    7 
 Boom-0.9.8/Boom/src/Models/Mixtures/identify_permutation.cpp                                                |only
 Boom-0.9.8/Boom/src/Models/MultinomialModel.cpp                                                             |    2 
 Boom-0.9.8/Boom/src/Models/PoissonModel.cpp                                                                 |    2 
 Boom-0.9.8/Boom/src/Models/Policies/PriorPolicy.cpp                                                         |   29 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/AbsorbingMarkovConjSampler.cpp                                 |    8 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/BetaBinomialPosteriorSampler.cpp                               |    7 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/BetaBinomialSampler.cpp                                        |    6 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/BetaPosteriorSampler.cpp                                       |    8 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/CompositeModelSampler.cpp                                      |    5 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/CorrelationSampler.cpp                                         |    8 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/DirichletPosteriorSampler.cpp                                  |    7 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/ExchangeableDirichletSampler.cpp                               |    7 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/ExponentialGammaSampler.cpp                                    |   33 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/FixedProbBinomialSampler.cpp                                   |    9 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/GammaPosteriorSampler.cpp                                      |   19 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/GaussianConjSampler.cpp                                        |   11 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/GaussianMeanSampler.cpp                                        |   28 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/GaussianVarSampler.cpp                                         |    8 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/GenericGaussianVarianceSampler.cpp                             |    8 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/GenericStudentSampler.cpp                                      |only
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/IndependentMvnConjSampler.cpp                                  |   16 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/IndependentMvnVarSampler.cpp                                   |   20 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/MarkovConjSampler.cpp                                          |   13 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/MultinomialDirichletSampler.cpp                                |   14 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/MvnConjSampler.cpp                                             |    7 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/MvnIndependentVarianceSampler.cpp                              |   22 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/MvnMeanSampler.cpp                                             |   14 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/MvnVarSampler.cpp                                              |   15 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/PoissonGammaPosteriorSampler.cpp                               |   15 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/PoissonGammaSampler.cpp                                        |   44 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/PosteriorSampler.cpp                                           |    6 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/ProductDirichletPosteriorSampler.cpp                           |   16 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/SepStratSampler.cpp                                            |   18 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/ZeroInflatedGammaPosteriorSampler.cpp                          |   13 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/ZeroInflatedLognormalPosteriorSampler.cpp                      |    8 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/ZeroInflatedPoissonSampler.cpp                                 |    9 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/ZeroMeanGaussianConjSampler.cpp                                |   17 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/ZeroMeanMvnConjSampler.cpp                                     |    7 
 Boom-0.9.8/Boom/src/Models/PosteriorSamplers/ZeroMeanMvnIndependenceSampler.cpp                             |   10 
 Boom-0.9.8/Boom/src/Models/ProductVectorModel.cpp                                                           |    2 
 Boom-0.9.8/Boom/src/Models/SpdModel.cpp                                                                     |    6 
 Boom-0.9.8/Boom/src/Models/StateSpace/AggregatedStateSpaceRegression.cpp                                    |   27 
 Boom-0.9.8/Boom/src/Models/StateSpace/DynamicInterceptRegression.cpp                                        |   26 
 Boom-0.9.8/Boom/src/Models/StateSpace/DynamicRegression.cpp                                                 |   68 
 Boom-0.9.8/Boom/src/Models/StateSpace/Filters/ConditionalIidKalmanFilter.cpp                                |  171 -
 Boom-0.9.8/Boom/src/Models/StateSpace/Filters/ConditionallyIndependentKalmanFilter.cpp                      |  219 --
 Boom-0.9.8/Boom/src/Models/StateSpace/Filters/KalmanFilterBase.cpp                                          |   17 
 Boom-0.9.8/Boom/src/Models/StateSpace/Filters/KalmanTools.cpp                                               |   31 
 Boom-0.9.8/Boom/src/Models/StateSpace/Filters/MultivariateKalmanFilterBase.cpp                              |  196 +
 Boom-0.9.8/Boom/src/Models/StateSpace/Filters/ScalarKalmanFilter.cpp                                        |   74 
 Boom-0.9.8/Boom/src/Models/StateSpace/Filters/SparseKalmanTools.cpp                                         |  122 -
 Boom-0.9.8/Boom/src/Models/StateSpace/Filters/SparseMatrix.cpp                                              | 1027 ++++++++--
 Boom-0.9.8/Boom/src/Models/StateSpace/Multivariate                                                          |only
 Boom-0.9.8/Boom/src/Models/StateSpace/PosteriorSamplers/DynamicRegressionArPosteriorSampler.cpp             |   10 
 Boom-0.9.8/Boom/src/Models/StateSpace/PosteriorSamplers/DynamicRegressionDirectGibbs.cpp                    |    4 
 Boom-0.9.8/Boom/src/Models/StateSpace/PosteriorSamplers/DynamicRegressionPosteriorSampler.cpp               |   29 
 Boom-0.9.8/Boom/src/Models/StateSpace/PosteriorSamplers/StateSpaceLogitPosteriorSampler.cpp                 |   21 
 Boom-0.9.8/Boom/src/Models/StateSpace/PosteriorSamplers/StateSpacePoissonPosteriorSampler.cpp               |   18 
 Boom-0.9.8/Boom/src/Models/StateSpace/PosteriorSamplers/StateSpacePosteriorSampler.cpp                      |    5 
 Boom-0.9.8/Boom/src/Models/StateSpace/PosteriorSamplers/StudentLocalLinearTrendPosteriorSampler.cpp         |   57 
 Boom-0.9.8/Boom/src/Models/StateSpace/StateModelVector.cpp                                                  |   88 
 Boom-0.9.8/Boom/src/Models/StateSpace/StateModels/GeneralSeasonalStateModel.cpp                             |only
 Boom-0.9.8/Boom/src/Models/StateSpace/StateModels/Holiday.cpp                                               |    1 
 Boom-0.9.8/Boom/src/Models/StateSpace/StateModels/LocalLevelStateModel.cpp                                  |  258 --
 Boom-0.9.8/Boom/src/Models/StateSpace/StateModels/PosteriorSamplers                                         |only
 Boom-0.9.8/Boom/src/Models/StateSpace/StateModels/test_utils/StudentLocalLinearTrendTestModule.cpp          |    6 
 Boom-0.9.8/Boom/src/Models/StateSpace/StateSpaceLogitModel.cpp                                              |   65 
 Boom-0.9.8/Boom/src/Models/StateSpace/StateSpaceModel.cpp                                                   |   65 
 Boom-0.9.8/Boom/src/Models/StateSpace/StateSpaceModelBase.cpp                                               |  141 +
 Boom-0.9.8/Boom/src/Models/StateSpace/StateSpacePoissonModel.cpp                                            |   68 
 Boom-0.9.8/Boom/src/Models/StateSpace/StateSpaceRegressionModel.cpp                                         |   59 
 Boom-0.9.8/Boom/src/Models/StateSpace/StateSpaceStudentRegressionModel.cpp                                  |   61 
 Boom-0.9.8/Boom/src/Models/TimeSeries/ArModel.cpp                                                           |    4 
 Boom-0.9.8/Boom/src/Models/ZeroInflatedGammaModel.cpp                                                       |    7 
 Boom-0.9.8/Boom/src/Models/ZeroInflatedLognormalModel.cpp                                                   |    9 
 Boom-0.9.8/Boom/src/boom_r_tools.cpp                                                                        |    4 
 Boom-0.9.8/Boom/src/cpputil/ThreadTools.cpp                                                                 |    4 
 Boom-0.9.8/Boom/src/cpputil/report_error.cpp                                                                |    1 
 Boom-0.9.8/Boom/src/cpputil/split.cpp                                                                       |    8 
 Boom-0.9.8/Boom/src/distributions/dirichlet.cpp                                                             |   15 
 Boom-0.9.8/Boom/src/distributions/rng.cpp                                                                   |    3 
 Boom-0.9.8/Boom/src/distributions/student_fix.cpp                                                           |   10 
 Boom-0.9.8/Boom/src/distributions/trun_exp.cpp                                                              |    3 
 Boom-0.9.8/Boom/src/distributions/trun_logit.cpp                                                            |   14 
 Boom-0.9.8/Boom/src/math/cephes/cephes_rgamma.cpp                                                           |only
 Boom-0.9.8/Boom/src/numopt/LinearAssignment.cpp                                                             |only
 Boom-0.9.8/Boom/src/numopt/MarkovDecisionProcess.cpp                                                        |only
 Boom-0.9.8/Boom/src/numopt/Qlearning.cpp                                                                    |only
 Boom-0.9.8/Boom/src/prior_specification.cpp                                                                 |   22 
 Boom-0.9.8/Boom/src/stats/DataTable.cpp                                                                     |   58 
 Boom-0.9.8/Boom/src/stats/Design.cpp                                                                        |    2 
 272 files changed, 5449 insertions(+), 2321 deletions(-)

More information about Boom at CRAN
Permanent link

Package sboost updated to version 0.1.2 with previous version 0.1.1 dated 2019-04-08

Title: Machine Learning with AdaBoost on Decision Stumps
Description: Creates classifier for binary outcomes using Adaptive Boosting (AdaBoost) algorithm on decision stumps with a fast C++ implementation. For a description of AdaBoost, see Freund and Schapire (1997) <doi:10.1006/jcss.1997.1504>. This type of classifier is nonlinear, but easy to interpret and visualize. Feature vectors may be a combination of continuous (numeric) and categorical (string, factor) elements. Methods for classifier assessment, predictions, and cross-validation also included.
Author: Jadon Wagstaff [aut, cre]
Maintainer: Jadon Wagstaff <jadonw@gmail.com>

Diff between sboost versions 0.1.1 dated 2019-04-08 and 0.1.2 dated 2022-05-26

 sboost-0.1.1/sboost/tests                            |only
 sboost-0.1.2/sboost/DESCRIPTION                      |    8 +-
 sboost-0.1.2/sboost/MD5                              |   36 ++++-----
 sboost-0.1.2/sboost/NEWS.md                          |    8 +-
 sboost-0.1.2/sboost/R/assess.R                       |   24 +++---
 sboost-0.1.2/sboost/R/mean.R                         |only
 sboost-0.1.2/sboost/R/predict.R                      |   39 +++++++++
 sboost-0.1.2/sboost/R/regression.R                   |only
 sboost-0.1.2/sboost/R/sboost.R                       |   75 ++++++++++---------
 sboost-0.1.2/sboost/man/assess.Rd                    |   24 +++---
 sboost-0.1.2/sboost/man/malware.Rd                   |    6 +
 sboost-0.1.2/sboost/man/mushrooms.Rd                 |    6 +
 sboost-0.1.2/sboost/man/predict.sboost_classifier.Rd |    3 
 sboost-0.1.2/sboost/man/sboost.Rd                    |   41 +++++-----
 sboost-0.1.2/sboost/man/validate.Rd                  |   10 ++
 sboost-0.1.2/sboost/src/RcppExports.cpp              |    5 +
 sboost-0.1.2/sboost/src/init.c                       |    8 +-
 sboost-0.1.2/sboost/src/mean_stump.c                 |only
 sboost-0.1.2/sboost/src/regression_stump.c           |only
 19 files changed, 181 insertions(+), 112 deletions(-)

More information about sboost at CRAN
Permanent link

Package ProjectionBasedClustering updated to version 1.1.8 with previous version 1.1.6 dated 2020-12-11

Title: Projection Based Clustering
Description: A clustering approach applicable to every projection method is proposed here. The two-dimensional scatter plot of any projection method can construct a topographic map which displays unapparent data structures by using distance and density information of the data. The generalized U*-matrix renders this visualization in the form of a topographic map, which can be used to automatically define the clusters of high-dimensional data. The whole system is based on Thrun and Ultsch, "Using Projection based Clustering to Find Distance and Density based Clusters in High-Dimensional Data" <DOI:10.1007/s00357-020-09373-2>. Selecting the correct projection method will result in a visualization in which mountains surround each cluster. The number of clusters can be determined by counting valleys on the topographic map. Most projection methods are wrappers for already available methods in R. By contrast, the neighbor retrieval visualizer (NeRV) is based on C++ source code of the 'dredviz' software package, and the Curvilinear Component Analysis (CCA) is translated from 'MATLAB' ('SOM Toolbox' 2.0) to R.
Author: Michael Thrun [aut, cre, cph], Florian Lerch [aut], Felix Pape [aut], Tim Schreier [aut], Luis Winckelmann [aut], Kristian Nybo [cph], Jarkko Venna [cph]
Maintainer: Michael Thrun <m.thrun@gmx.net>

Diff between ProjectionBasedClustering versions 1.1.6 dated 2020-12-11 and 1.1.8 dated 2022-05-26

 DESCRIPTION                                    |   10 
 MD5                                            |   53 -
 NAMESPACE                                      |    3 
 R/PlotProjectedPoints.R                        |    4 
 R/ProjectionBasedClustering.R                  |    6 
 R/helperTopographicIsland.R                    |only
 R/interactiveClustering.R                      | 1118 +++++++------------------
 R/interactiveGeneralizedUmatrixIsland.R        |  889 -------------------
 R/interactiveGeneralizedUmatrixIsland_ggplot.R |only
 R/interactiveGeneralizedUmatrixIsland_plotly.R |only
 R/interactiveProjectionBasedClustering.R       |   26 
 README.md                                      |only
 build                                          |only
 man/CCA.Rd                                     |    4 
 man/ICA.Rd                                     |    2 
 man/Isomap.Rd                                  |    2 
 man/KruskalStress.Rd                           |    2 
 man/MDS.Rd                                     |    2 
 man/NeRV.rd                                    |    4 
 man/PCA.Rd                                     |    2 
 man/PlotProjectedPoints.Rd                     |   93 +-
 man/Projection2Bestmatches.Rd                  |    2 
 man/ProjectionBasedClustering.Rd               |    2 
 man/ProjectionPursuit.Rd                       |    2 
 man/SammonsMapping.Rd                          |    2 
 man/interactiveClustering.Rd                   |   19 
 man/interactiveGeneralizedUmatrixIsland.Rd     |  117 +-
 man/interactiveProjectionBasedClustering.Rd    |   22 
 man/tSNE.Rd                                    |    2 
 src/RcppExports.cpp                            |    5 
 30 files changed, 561 insertions(+), 1832 deletions(-)

More information about ProjectionBasedClustering at CRAN
Permanent link

Package plotROC updated to version 2.3.0 with previous version 2.2.1 dated 2018-06-23

Title: Generate Useful ROC Curve Charts for Print and Interactive Use
Description: Most ROC curve plots obscure the cutoff values and inhibit interpretation and comparison of multiple curves. This attempts to address those shortcomings by providing plotting and interactive tools. Functions are provided to generate an interactive ROC curve plot for web use, and print versions. A Shiny application implementing the functions is also included.
Author: Michael C. Sachs [aut, cre], Robert W. Corty [ctb], Luis Crouch [ctb]
Maintainer: Michael C. Sachs <sachsmc@gmail.com>

Diff between plotROC versions 2.2.1 dated 2018-06-23 and 2.3.0 dated 2022-05-26

 DESCRIPTION                   |   21 
 MD5                           |   76 -
 NAMESPACE                     |   97 -
 NEWS                          |  209 +--
 R/calculate_roc.R             |  523 ++++---
 R/deprecated.R                |  278 ++--
 R/geom_roc.R                  |  816 ++++++------
 R/geom_rocci.R                |  561 ++++----
 R/interactive_roc.R           |  368 ++---
 R/plotROC-package.R           |   94 -
 R/style_roc.R                 |  210 +--
 README.md                     |  141 +-
 build/vignette.rds            |binary
 inst/doc/examples.R           |  364 ++---
 inst/doc/examples.Rmd         |  691 +++++-----
 inst/doc/examples.html        | 2769 ++++++++++++++++++++----------------------
 man/calc_auc.Rd               |   53 
 man/calculate_multi_roc.Rd    |   46 
 man/calculate_roc.Rd          |   66 -
 man/direct_label.Rd           |   63 
 man/export_interactive_roc.Rd |  110 -
 man/geom_roc.Rd               |  302 ++--
 man/geom_rocci.Rd             |  243 +--
 man/getD3.Rd                  |   24 
 man/ggroc.Rd                  |   96 -
 man/melt_roc.Rd               |   62 
 man/multi_ggroc.Rd            |  104 -
 man/plotROC.Rd                |   97 -
 man/plot_interactive_roc.Rd   |   42 
 man/plot_journal_roc.Rd       |   79 -
 man/roc_key.Rd                |   38 
 man/shiny_plotROC.Rd          |   22 
 man/stat_roc.Rd               |  208 +--
 man/stat_rocci.Rd             |  242 +--
 man/style_roc.Rd              |   74 -
 man/verify_d.Rd               |   54 
 tests/testthat/Rplots.pdf     |binary
 tests/testthat/test-calc.R    |  136 +-
 vignettes/examples.Rmd        |  691 +++++-----
 39 files changed, 5093 insertions(+), 4977 deletions(-)

More information about plotROC at CRAN
Permanent link

New package OPTtesting with initial version 1.0.0
Package: OPTtesting
Title: Optimal Testing
Version: 1.0.0
Maintainer: Lijia Wang <lijiawan@usc.edu>
Description: Optimal testing under general dependence. The R package implements procedures proposed in Wang, Han, and Tong (2022). The package includes parameter estimation procedures, the computation for the posterior probabilities, and the testing procedure.
Encoding: UTF-8
Imports: rootSolve, quantreg, RSpectra, stats
Suggests: MASS
License: GPL-2
NeedsCompilation: no
Packaged: 2022-05-26 00:51:46 UTC; cocow
Author: Lijia Wang [aut, cre, cph], Xu Han [aut], Xin Tong [aut]
Repository: CRAN
Date/Publication: 2022-05-26 13:30:09 UTC

More information about OPTtesting at CRAN
Permanent link

New package mapbayr with initial version 0.7.3
Package: mapbayr
Title: MAP-Bayesian Estimation of PK Parameters
Version: 0.7.3
Description: Performs maximum a posteriori Bayesian estimation of individual pharmacokinetic parameters from a model defined in 'mrgsolve', typically for model-based therapeutic drug monitoring. Internally computes an objective function value from model and data, performs optimization and returns predictions in a convenient format. The performance of the package was described by Le Louedec et al (2021) <doi:10.1002/psp4.12689>.
License: GPL-3
Encoding: UTF-8
Imports: dplyr, ggplot2, magrittr, mrgsolve (>= 1.0.0), optimx, progress, purrr, rlang, stringr, tibble, tidyr
URL: https://github.com/FelicienLL/mapbayr
BugReports: https://github.com/FelicienLL/mapbayr/issues
Suggests: knitr, minqa, testthat (>= 3.0.0)
Depends: R (>= 2.10)
LazyData: true
NeedsCompilation: no
Packaged: 2022-05-25 15:13:49 UTC; le_louedec
Author: Felicien Le Louedec [aut, cre] , Kyle T Baron [ctb]
Maintainer: Felicien Le Louedec <felicienlelouedec@proton.me>
Repository: CRAN
Date/Publication: 2022-05-26 13:30:02 UTC

More information about mapbayr at CRAN
Permanent link

Package effectsize updated to version 0.7.0 with previous version 0.6.0.1 dated 2022-01-26

Title: Indices of Effect Size and Standardized Parameters
Description: Provide utilities to work with indices of effect size and standardized parameters for a wide variety of models (see list of supported models using the function 'insight::supported_models()'), allowing computation of and conversion between indices such as Cohen's d, r, odds, etc.
Author: Mattan S. Ben-Shachar [aut, cre] , Dominique Makowski [aut] , Daniel Luedecke [aut] , Indrajeet Patil [aut] , Brenton M. Wiernik [aut] , Ken Kelley [ctb], David Stanley [ctb], Jessica Burnett [rev] , Johannes Karreth [rev]
Maintainer: Mattan S. Ben-Shachar <matanshm@post.bgu.ac.il>

Diff between effectsize versions 0.6.0.1 dated 2022-01-26 and 0.7.0 dated 2022-05-26

 effectsize-0.6.0.1/effectsize/R/standardize.models.R                       |only
 effectsize-0.6.0.1/effectsize/R/standardize_info.R                         |only
 effectsize-0.6.0.1/effectsize/R/standardize_parameters.R                   |only
 effectsize-0.6.0.1/effectsize/R/utils_standardize.R                        |only
 effectsize-0.6.0.1/effectsize/inst/doc/bayesian_models.R                   |only
 effectsize-0.6.0.1/effectsize/inst/doc/bayesian_models.Rmd                 |only
 effectsize-0.6.0.1/effectsize/inst/doc/bayesian_models.html                |only
 effectsize-0.6.0.1/effectsize/inst/doc/standardize_parameters.R            |only
 effectsize-0.6.0.1/effectsize/inst/doc/standardize_parameters.Rmd          |only
 effectsize-0.6.0.1/effectsize/inst/doc/standardize_parameters.html         |only
 effectsize-0.6.0.1/effectsize/man/standardize.default.Rd                   |only
 effectsize-0.6.0.1/effectsize/man/standardize_info.Rd                      |only
 effectsize-0.6.0.1/effectsize/man/standardize_parameters.Rd                |only
 effectsize-0.6.0.1/effectsize/tests/testthat/test-standardize_models.R     |only
 effectsize-0.6.0.1/effectsize/tests/testthat/test-standardize_parameters.R |only
 effectsize-0.6.0.1/effectsize/vignettes/bayesian_models.Rmd                |only
 effectsize-0.6.0.1/effectsize/vignettes/standardize_parameters.Rmd         |only
 effectsize-0.7.0/effectsize/DESCRIPTION                                    |   29 
 effectsize-0.7.0/effectsize/MD5                                            |  182 +-
 effectsize-0.7.0/effectsize/NAMESPACE                                      |   66 -
 effectsize-0.7.0/effectsize/NEWS.md                                        |   20 
 effectsize-0.7.0/effectsize/R/cohens_d.R                                   |   39 
 effectsize-0.7.0/effectsize/R/common_language.R                            |    5 
 effectsize-0.7.0/effectsize/R/convert_between_OR_to_RR.R                   |    2 
 effectsize-0.7.0/effectsize/R/convert_between_common_language.R            |    2 
 effectsize-0.7.0/effectsize/R/convert_stat_chisq.R                         |  150 +-
 effectsize-0.7.0/effectsize/R/convert_stat_to_anova.R                      |   56 
 effectsize-0.7.0/effectsize/R/effectsize.BFBayesFactor.R                   |  180 +-
 effectsize-0.7.0/effectsize/R/effectsize.R                                 |   11 
 effectsize-0.7.0/effectsize/R/effectsize.htest.R                           |  478 ++++---
 effectsize-0.7.0/effectsize/R/equivalence_test.R                           |    2 
 effectsize-0.7.0/effectsize/R/eta_squared.R                                |  142 +-
 effectsize-0.7.0/effectsize/R/eta_squared_posterior.R                      |  124 -
 effectsize-0.7.0/effectsize/R/format_standardize.R                         |    2 
 effectsize-0.7.0/effectsize/R/interpret.R                                  |   18 
 effectsize-0.7.0/effectsize/R/interpret_cfa_fit.R                          |   19 
 effectsize-0.7.0/effectsize/R/interpret_r.R                                |    3 
 effectsize-0.7.0/effectsize/R/is_effectsize_name.R                         |    6 
 effectsize-0.7.0/effectsize/R/plot.R                                       |    8 
 effectsize-0.7.0/effectsize/R/print.effectsize_table.R                     |  266 ++--
 effectsize-0.7.0/effectsize/R/print.rules.R                                |   96 +
 effectsize-0.7.0/effectsize/R/rank_effectsizes.R                           |   37 
 effectsize-0.7.0/effectsize/R/reexports.R                                  |   33 
 effectsize-0.7.0/effectsize/R/sd_pooled.R                                  |   14 
 effectsize-0.7.0/effectsize/R/utils.R                                      |only
 effectsize-0.7.0/effectsize/R/utils_validate_input_data.R                  |  251 ++-
 effectsize-0.7.0/effectsize/R/xtab.R                                       |  176 ++
 effectsize-0.7.0/effectsize/R/zzz.R                                        |only
 effectsize-0.7.0/effectsize/README.md                                      |   80 -
 effectsize-0.7.0/effectsize/build/partial.rdb                              |binary
 effectsize-0.7.0/effectsize/build/vignette.rds                             |binary
 effectsize-0.7.0/effectsize/inst/doc/anovaES.R                             |   33 
 effectsize-0.7.0/effectsize/inst/doc/anovaES.Rmd                           |   66 +
 effectsize-0.7.0/effectsize/inst/doc/anovaES.html                          |  501 ++++++-
 effectsize-0.7.0/effectsize/inst/doc/convert.Rmd                           |    4 
 effectsize-0.7.0/effectsize/inst/doc/convert.html                          |  335 ++++-
 effectsize-0.7.0/effectsize/inst/doc/effectsize.R                          |   15 
 effectsize-0.7.0/effectsize/inst/doc/effectsize.Rmd                        |   36 
 effectsize-0.7.0/effectsize/inst/doc/effectsize.html                       |  630 +++++++--
 effectsize-0.7.0/effectsize/inst/doc/effectsize_API.Rmd                    |   18 
 effectsize-0.7.0/effectsize/inst/doc/effectsize_API.html                   |  320 ++++-
 effectsize-0.7.0/effectsize/inst/doc/from_test_statistics.html             |  354 ++++-
 effectsize-0.7.0/effectsize/inst/doc/interpret.Rmd                         |    4 
 effectsize-0.7.0/effectsize/inst/doc/interpret.html                        |  390 +++++-
 effectsize-0.7.0/effectsize/inst/doc/simple_htests.R                       |   81 -
 effectsize-0.7.0/effectsize/inst/doc/simple_htests.Rmd                     |  131 +-
 effectsize-0.7.0/effectsize/inst/doc/simple_htests.html                    |  638 +++++++---
 effectsize-0.7.0/effectsize/man/F_to_eta2.Rd                               |   56 
 effectsize-0.7.0/effectsize/man/chisq_to_phi.Rd                            |   69 -
 effectsize-0.7.0/effectsize/man/cles.Rd                                    |    6 
 effectsize-0.7.0/effectsize/man/cohens_d.Rd                                |   14 
 effectsize-0.7.0/effectsize/man/effectsize.Rd                              |   12 
 effectsize-0.7.0/effectsize/man/effectsize_CIs.Rd                          |   48 
 effectsize-0.7.0/effectsize/man/es_info.Rd                                 |    2 
 effectsize-0.7.0/effectsize/man/eta_squared.Rd                             |  100 -
 effectsize-0.7.0/effectsize/man/interpret.Rd                               |    2 
 effectsize-0.7.0/effectsize/man/interpret_gfi.Rd                           |   15 
 effectsize-0.7.0/effectsize/man/interpret_r.Rd                             |   10 
 effectsize-0.7.0/effectsize/man/phi.Rd                                     |  137 +-
 effectsize-0.7.0/effectsize/man/print.effectsize_table.Rd                  |   17 
 effectsize-0.7.0/effectsize/man/rank_biserial.Rd                           |   10 
 effectsize-0.7.0/effectsize/man/reexports.Rd                               |   18 
 effectsize-0.7.0/effectsize/man/rules.Rd                                   |    2 
 effectsize-0.7.0/effectsize/man/sd_pooled.Rd                               |    7 
 effectsize-0.7.0/effectsize/tests/testthat/test-convert_between.R          |    4 
 effectsize-0.7.0/effectsize/tests/testthat/test-convert_statistic.R        |    4 
 effectsize-0.7.0/effectsize/tests/testthat/test-effectsize.R               |  161 +-
 effectsize-0.7.0/effectsize/tests/testthat/test-eta_squared.R              |  266 ++--
 effectsize-0.7.0/effectsize/tests/testthat/test-eta_squared_posterior.R    |   46 
 effectsize-0.7.0/effectsize/tests/testthat/test-helpers.R                  |   48 
 effectsize-0.7.0/effectsize/tests/testthat/test-interpret.R                |   18 
 effectsize-0.7.0/effectsize/tests/testthat/test-plot.R                     |only
 effectsize-0.7.0/effectsize/tests/testthat/test-printing.R                 |  176 ++
 effectsize-0.7.0/effectsize/tests/testthat/test-rankES.R                   |   53 
 effectsize-0.7.0/effectsize/tests/testthat/test-standardized_differences.R |   11 
 effectsize-0.7.0/effectsize/tests/testthat/test-xtab.R                     |   34 
 effectsize-0.7.0/effectsize/vignettes/anovaES.Rmd                          |   66 +
 effectsize-0.7.0/effectsize/vignettes/convert.Rmd                          |    4 
 effectsize-0.7.0/effectsize/vignettes/effectsize.Rmd                       |   36 
 effectsize-0.7.0/effectsize/vignettes/effectsize_API.Rmd                   |   18 
 effectsize-0.7.0/effectsize/vignettes/interpret.Rmd                        |    4 
 effectsize-0.7.0/effectsize/vignettes/simple_htests.Rmd                    |  131 +-
 102 files changed, 5277 insertions(+), 2381 deletions(-)

More information about effectsize at CRAN
Permanent link

New package FAVAR with initial version 0.1.3
Package: FAVAR
Title: Bayesian Analysis of a FAVAR Model
Version: 0.1.3
Description: Estimate a FAVAR model by a Bayesian method, based on Bernanke et al. (2005) <DOI:10.1162/0033553053327452>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: ggplot2, bvartools, foreach, magrittr, MCMCpack, coda, dplyr, doParallel, Matrix
Depends: R (>= 3.5.0)
Suggests: testthat, vars, patchwork
NeedsCompilation: no
Packaged: 2022-05-26 02:32:20 UTC; yangnay
Author: Pu Chen [aut, cre] , Chen Chen [aut], Gary Koop [cph], Dimitris Korobilis [cph]
Maintainer: Pu Chen <shengnehs@qq.com>
Repository: CRAN
Date/Publication: 2022-05-26 13:30:12 UTC

More information about FAVAR at CRAN
Permanent link

New package BiCausality with initial version 0.1.1
Package: BiCausality
Title: Binary Causality Inference Framework
Version: 0.1.1
Maintainer: Chainarong Amornbunchornvej <grandca@gmail.com>
Description: A framework to infer causality on binary data using techniques in frequent pattern mining and estimation statistics. Given a set of individual vectors S={x} where x(i) is a realization value of binary variable i, the framework infers empirical causal relations of binary variables i,j from S in a form of causal graph G=(V,E) where V is a set of nodes representing binary variables and there is an edge from i to j in E if the variable i causes j. The framework determines dependency among variables as well as analyzing confounding factors before deciding whether i causes j. The publication of this package is at <arXiv:2205.06131>.
License: MIT + file LICENSE
URL: https://github.com/DarkEyes/BiCausality
BugReports: https://github.com/DarkEyes/BiCausality/issues
Depends: R (>= 3.5.0)
Encoding: UTF-8
LazyData: TRUE
Suggests: knitr, rmarkdown, markdown, igraph
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-26 03:53:52 UTC; 006005
Author: Chainarong Amornbunchornvej [aut, cre]
Repository: CRAN
Date/Publication: 2022-05-26 13:30:15 UTC

More information about BiCausality at CRAN
Permanent link

Package ergm.userterms (with last version 3.10.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2019-05-15 3.10.0
2018-08-25 3.9.0
2013-11-28 3.1.1
2013-04-27 3.1-0
2013-01-30 3.0-2
2012-03-08 3.0-1
2011-02-03 1.0

Permanent link
Package rego updated to version 1.5.1 with previous version 1.4.1 dated 2022-05-10

Title: Automatic Time Series Forecasting and Missing Value Imputation
Description: Machine learning algorithm for predicting and imputing time series. It can automatically set all the parameters needed, thus in the minimal configuration it only requires the target variable and the dependent variables if present. It can address large problems with hundreds or thousands of dependent variables and problems in which the number of dependent variables is greater than the number of observations. Moreover it can be used not only for time series but also for any other real valued target variable. The algorithm implemented includes a Bayesian stochastic search methodology for model selection and a robust estimation based on bootstrapping. 'rego' is fast because all the code is C++.
Author: Davide Altomare [cre, aut], David Loris [aut]
Maintainer: Davide Altomare <info@channelattribution.io>

Diff between rego versions 1.4.1 dated 2022-05-10 and 1.5.1 dated 2022-05-26

 DESCRIPTION         |    8 
 MD5                 |   12 -
 R/rego.R            |   63 +++---
 man/rego-package.Rd |    4 
 man/regpred.Rd      |    7 
 src/rego.cpp        |  541 +++++++++++++++++++++++++++++++++-------------------
 src/rego.h          |    6 
 7 files changed, 408 insertions(+), 233 deletions(-)

More information about rego at CRAN
Permanent link

Package SoupX updated to version 1.6.1 with previous version 1.5.2 dated 2021-05-17

Title: Single Cell mRNA Soup eXterminator
Description: Quantify, profile and remove ambient mRNA contamination (the "soup") from droplet based single cell RNA-seq experiments. Implements the method described in Young et al. (2018) <doi:10.1101/303727>.
Author: Matthew Daniel Young
Maintainer: Matthew Daniel Young <my4@sanger.ac.uk>

Diff between SoupX versions 1.5.2 dated 2021-05-17 and 1.6.1 dated 2022-05-26

 DESCRIPTION                |    8 
 MD5                        |   22 
 R/autoEstCont.R            |    9 
 R/load10X.R                |   16 
 R/plotFunctions.R          |    2 
 R/setProperties.R          |    8 
 README.md                  |    9 
 inst/doc/pbmcTutorial.R    |    1 
 inst/doc/pbmcTutorial.Rmd  |    8 
 inst/doc/pbmcTutorial.html | 1602 +++++++++++++++++++++++++++------------------
 man/autoEstCont.Rd         |    3 
 vignettes/pbmcTutorial.Rmd |    8 
 12 files changed, 1047 insertions(+), 649 deletions(-)

More information about SoupX at CRAN
Permanent link

Package DendroSync updated to version 0.1.4 with previous version 0.1.3 dated 2019-05-30

Title: A Set of Tools for Calculating Spatial Synchrony Between Tree-Ring Chronologies
Description: Provides functions for the calculation and plotting of synchrony in tree growth from tree-ring width chronologies (TRW index). It combines variance-covariance (VCOV) mixed modelling with functions that quantify the degree to which the TRW chronologies contain a common temporal signal. It also implements temporal trends in spatial synchrony using a moving window. These methods can also be used with other kind of ecological variables that have temporal autocorrelation corrected.
Author: Josu G. Alday , Tatiana A. Shestakova , Victor Resco de Dios , Jordi Voltas
Maintainer: Josu G. Alday <josucham@gmail.com>

Diff between DendroSync versions 0.1.3 dated 2019-05-30 and 0.1.4 dated 2022-05-26

 DESCRIPTION          |   14 +++++++-------
 MD5                  |   18 +++++++++---------
 NAMESPACE            |    1 +
 NEWS.md              |    9 +++++++++
 R/dendro.varcov.R    |    2 +-
 R/sync.plot.R        |    4 ++--
 R/sync.trend.plot.R  |    5 +++--
 README.md            |    2 +-
 man/conifersIP.Rd    |    6 ++++--
 man/dendro.varcov.Rd |    2 +-
 10 files changed, 38 insertions(+), 25 deletions(-)

More information about DendroSync at CRAN
Permanent link

New package FGLMtrunc with initial version 0.1.0
Package: FGLMtrunc
Title: Truncated Functional Generalized Linear Models
Version: 0.1.0
Date: 2022-05-21
Author: Xi Liu [aut], Chau Tran [aut, cre], Alexander Petersen [aut]
Maintainer: Chau Tran <chautran@ucsb.edu>
Description: An implementation of the methodologies described in Xi Liu, Afshin A. Divani, and Alexander Petersen (2022) <doi:10.1016/j.csda.2022.107421>, including truncated functional linear and truncated functional logistic regression models.
License: GPL-2
Depends: R (>= 3.6.0)
Imports: foreach, glmnet, splines2
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
Suggests: knitr, xfun, rmarkdown
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: yes
Packaged: 2022-05-25 14:52:03 UTC; chautran
Repository: CRAN
Date/Publication: 2022-05-26 08:20:02 UTC

More information about FGLMtrunc at CRAN
Permanent link

New package BioRssay with initial version 1.0.0
Package: BioRssay
Title: Analyze Bioassays and Probit Graphs
Version: 1.0.0
Maintainer: Piyal Karunarathne <piyalkarumail@yahoo.com>
Description: A robust framework for analyzing mortality data from bioassays for one or several strains/lines/populations.
License: AGPL (>= 3)
Imports: colorspace
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5)
Suggests: markdown, rmarkdown, knitr, testthat (>= 2.0.0), covr
VignetteBuilder: knitr
URL: https://milesilab.github.io/BioRssay/
BugReports: https://github.com/milesilab/BioRssay/issues/
NeedsCompilation: no
Packaged: 2022-05-25 09:24:39 UTC; piyalkarunarathne
Author: Piyal Karunarathne [aut, cre] , Pascal Milesi [aut] , Pierrick Labbe [aut]
Repository: CRAN
Date/Publication: 2022-05-26 08:20:05 UTC

More information about BioRssay at CRAN
Permanent link

New package async with initial version 0.2.1
Package: async
Title: Asynchronous Code Constructs: Generators, Yield, Async, Await
Version: 0.2.1
Date: 2022-05-15
URL: https://crowding.github.io/async/, https://github.com/crowding/async/
BugReports: https://github.com/crowding/async/issues
Description: Write sequential-looking code that pauses and resumes. gen() creates a generator, an iterator that returns a value and pauses each time it reaches a yield() call. async() creates a promise, which runs until it reaches a call to await(), then resumes when information is available. These work similarly to generator and async constructs from 'Python' or 'JavaScript'. Objects produced are compatible with the 'iterators' and 'promises' packages.
License: GPL-2
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: nseval (>= 0.4), iterators, itertools, later, promises
Suggests: rmarkdown, testthat (>= 3.0.0), knitr, magrittr, audio, profvis, covr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-25 05:52:07 UTC; peter
Author: Peter Meilstrup [aut, cre]
Maintainer: Peter Meilstrup <peter.meilstrup@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-26 08:30:02 UTC

More information about async at CRAN
Permanent link

Package Neighboot (with last version 1.0.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-09-21 1.0.0

Permanent link
Package MorphoTools2 updated to version 1.0.0.0 with previous version 0.9.1.2 dated 2022-02-03

Title: Multivariate Morphometric Analysis
Description: Tools for multivariate analyses of morphological data, wrapped in one package, to make the workflow convenient and fast. Statistical and graphical tools provide a comprehensive framework for checking and manipulating input data, statistical analyses, and visualization of results. Several methods are provided for the analysis of raw data, to make the dataset ready for downstream analyses. Integrated statistical methods include hierarchical classification, principal component analysis, principal coordinates analysis, non-metric multidimensional scaling, and multiple discriminant analyses: canonical, stepwise, and classificatory (linear, quadratic, and the non-parametric k nearest neighbours). The philosophy of the package will be described in Šlenker et al. (in prep).
Author: Marek Šlenker [aut, cre] Petr Koutecký [ctb] Karol Marhold [ctb]
Maintainer: Marek Šlenker <marek.slenker@savba.sk>

Diff between MorphoTools2 versions 0.9.1.2 dated 2022-02-03 and 1.0.0.0 dated 2022-05-26

 DESCRIPTION                                             |    8 
 MD5                                                     |  353 +-
 NAMESPACE                                               |  222 -
 R/BoxMTest.R                                            |   24 
 R/SampsPopsTax.R                                        |   54 
 R/boxplots.R                                            |  178 -
 R/calcDistance.R                                        |  108 
 R/cda.calc.R                                            |  332 -
 R/centaurea.R                                           |    6 
 R/classif.knn.R                                         |  144 
 R/classif.lda.R                                         |  128 
 R/classif.qda.R                                         |  132 
 R/classifMatrix.R                                       |  132 
 R/classifSample.knn.R                                   |  156 
 R/classifSample.lda.R                                   |   90 
 R/classifSample.qda.R                                   |   88 
 R/clust.R                                               |   72 
 R/correlations.R                                        |  100 
 R/descrStatistics.R                                     |  350 +-
 R/export.res.R                                          |  124 
 R/helperMethods.R                                       |  130 
 R/histCharacter.R                                       |  178 -
 R/keep.itemInMorphodataObject.R                         |  240 -
 R/knn.select.R                                          |  148 
 R/missingDataTable.R                                    |  198 -
 R/na.meanSubst.R                                        |   56 
 R/newObject.R                                           |  270 -
 R/nmds.calc.R                                           |  100 
 R/pca.calc.R                                            |  122 
 R/pcoa.calc.R                                           |  122 
 R/plot.3Dpoints.R                                       |  286 -
 R/plot.R                                                |   48 
 R/plot.addEllipses.R                                    |  192 -
 R/plot.addLabels.characters.R                           |  212 -
 R/plot.addLabels.points.R                               |  166 
 R/plot.addLegend.R                                      |  230 -
 R/plot.addSpiders.R                                     |  196 -
 R/plot.characters.R                                     |  264 -
 R/plot.points.R                                         |  550 +--
 R/popul.otu.R                                           |   40 
 R/print.R                                               |  120 
 R/qq.R                                                  |  180 -
 R/read.morphodata.R                                     |   72 
 R/remove.itemFromMorphodataObject.R                     |  244 -
 R/shapirowilk.R                                         |   96 
 R/stepdisc.calc.R                                       |  308 -
 R/summary.R                                             |  282 -
 R/transformCharacter.R                                  |   36 
 R/viewMorphodata.R                                      |   14 
 R/zzz.R                                                 |   27 
 README.md                                               |   70 
 build/vignette.rds                                      |binary
 inst/CITATION                                           |only
 inst/doc/MorphoTools2_tutorial.R                        | 1388 ++++----
 inst/doc/MorphoTools2_tutorial.Rmd                      | 2666 ++++++++--------
 inst/doc/MorphoTools2_tutorial.pdf                      |binary
 inst/extdata/centaurea.txt                              | 1306 +++----
 man/boxMTest.Rd                                         |   94 
 man/boxplotCharacter.Rd                                 |  140 
 man/cda.calc.Rd                                         |  112 
 man/cdadata.Rd                                          |   64 
 man/centaurea.Rd                                        |   64 
 man/characters.Rd                                       |   58 
 man/classif.lda.Rd                                      |  182 -
 man/classif.matrix.Rd                                   |   72 
 man/classifSample.lda.Rd                                |  182 -
 man/classifdata.Rd                                      |   40 
 man/clust.Rd                                            |  142 
 man/cormat.Rd                                           |   92 
 man/descrTaxon.Rd                                       |  104 
 man/exportRes.Rd                                        |   70 
 man/head.morphodata.Rd                                  |   88 
 man/histCharacter.Rd                                    |   92 
 man/keepTaxon.Rd                                        |  106 
 man/knn.select.Rd                                       |   96 
 man/missingCharactersTable.Rd                           |   54 
 man/missingSamplesTable.Rd                              |   54 
 man/morphodata.Rd                                       |   36 
 man/naMeanSubst.Rd                                      |   80 
 man/nmds.calc.Rd                                        |  166 
 man/nmdsdata.Rd                                         |   54 
 man/pca.calc.Rd                                         |  104 
 man/pcadata.Rd                                          |   62 
 man/pcoa.calc.Rd                                        |  160 
 man/pcoadata.Rd                                         |   56 
 man/plot3Dpoints.Rd                                     |  108 
 man/plotAddEllipses.Rd                                  |  108 
 man/plotAddLabels.characters.Rd                         |   88 
 man/plotAddLabels.points.Rd                             |  100 
 man/plotAddLegend.Rd                                    |  108 
 man/plotAddSpiders.Rd                                   |  102 
 man/plotCharacters.Rd                                   |  104 
 man/plotPoints.Rd                                       |  128 
 man/populOTU.Rd                                         |   72 
 man/qqnormCharacter.Rd                                  |   82 
 man/read.morphodata.Rd                                  |  140 
 man/removeTaxon.Rd                                      |  108 
 man/shapiroWilkTest.Rd                                  |   68 
 man/stepdisc.calc.Rd                                    |   84 
 man/summary.Rd                                          |   74 
 man/transformCharacter.Rd                               |  122 
 man/viewMorphodata.Rd                                   |   50 
 tests/testFiles/Impatiens_Pektinata.txt                 |   54 
 tests/testFiles/Impatiens_individuals.txt               | 1132 +++---
 tests/testFiles/bin.txt                                 |   54 
 tests/testFiles/sample.txt                              | 1306 +++----
 tests/testFiles/samplePlnaMatica.txt                    | 1226 +++----
 tests/testFiles/sample_NaNs.txt                         | 1306 +++----
 tests/testFiles/sample_Na_celyZnak.txt                  | 1306 +++----
 tests/testFiles/sample_decComa.txt                      | 1306 +++----
 tests/testFiles/sample_mockup.exported.txt              |   34 
 tests/testFiles/sample_mockup.txt                       |   34 
 tests/testFiles/sample_numericNames.txt                 |   10 
 tests/testFiles/sample_whitespaceDelim.txt              | 1282 +++----
 tests/testFiles/shortFile.txt                           |   12 
 tests/testthat.R                                        |   14 
 tests/testthat/test.boxplot.character.R                 |   32 
 tests/testthat/test.calcDistance.R                      |  150 
 tests/testthat/test.cda.calc.R                          |  164 
 tests/testthat/test.checkClass.R                        |   42 
 tests/testthat/test.classif.knn.R                       |  104 
 tests/testthat/test.classif.lda.R                       |  102 
 tests/testthat/test.classifMatrix.R                     |  202 -
 tests/testthat/test.classifSample.knn.R                 |  218 -
 tests/testthat/test.classifSample.lda.R                 |  192 -
 tests/testthat/test.clust.R                             |  132 
 tests/testthat/test.cormat.R                            |   34 
 tests/testthat/test.cormat.signifTest.R                 |   36 
 tests/testthat/test.delete.charecter.R                  |  112 
 tests/testthat/test.delete.population.R                 |   40 
 tests/testthat/test.delete.sample.R                     |  120 
 tests/testthat/test.delete.taxon.R                      |   40 
 tests/testthat/test.descrByGroup.R                      |   80 
 tests/testthat/test.export.res.R                        |  102 
 tests/testthat/test.formatDescrStatistic.R              |   64 
 tests/testthat/test.giveMeNiceBoxPlot.R                 |   42 
 tests/testthat/test.keep.charecter.R                    |  132 
 tests/testthat/test.keep.population.R                   |   66 
 tests/testthat/test.keep.sample.R                       |  132 
 tests/testthat/test.keep.taxon.R                        |   76 
 tests/testthat/test.missingCharactersTable.R            |   72 
 tests/testthat/test.missingSamplesTable.R               |   70 
 tests/testthat/test.morphodataFromDataFrame.R           |   78 
 tests/testthat/test.na.meanSubst.R                      |   72 
 tests/testthat/test.newCdadata.R                        |   34 
 tests/testthat/test.newMorphodata.R                     |   30 
 tests/testthat/test.newPcadata.R                        |   28 
 tests/testthat/test.newPcoadata.R                       |   28 
 tests/testthat/test.pca.calc.R                          |   92 
 tests/testthat/test.pcoa.calc.R                         |   62 
 tests/testthat/test.plot.addEllipse.R                   |   68 
 tests/testthat/test.plot.addLabels.characters_hist.R    |   48 
 tests/testthat/test.plot.addLabels.characters_scatter.R |   62 
 tests/testthat/test.plot.addLabels.points_hist.R        |   36 
 tests/testthat/test.plot.addSpiders.R                   |   66 
 tests/testthat/test.plot.characters.cdadata_hist.R      |   58 
 tests/testthat/test.plot.characters.cdadata_scatter.R   |   32 
 tests/testthat/test.plot.characters.pcadata.R           |   56 
 tests/testthat/test.plot.points.cdadata_hist.R          |  102 
 tests/testthat/test.plot.points.cdadata_scatter.R       |   52 
 tests/testthat/test.plot.points.pcadata.R               |   52 
 tests/testthat/test.plot.points.pcoadata.R              |   52 
 tests/testthat/test.plot3Dpoints.cdadata.R              |   46 
 tests/testthat/test.plot3Dpoints.pcadata.R              |   48 
 tests/testthat/test.popul.otu.R                         |   52 
 tests/testthat/test.populations.R                       |   26 
 tests/testthat/test.read.morphodata.R                   |   70 
 tests/testthat/test.removeByColumn.R                    |  112 
 tests/testthat/test.samples.R                           |   26 
 tests/testthat/test.setValuesForVector.R                |   72 
 tests/testthat/test.summary.cdadata.R                   |   38 
 tests/testthat/test.summary.classifdata.R               |   32 
 tests/testthat/test.summary.morphodata.R                |   30 
 tests/testthat/test.summary.pcadata.R                   |   36 
 tests/testthat/test.summary.pcoadata.R                  |   36 
 tests/testthat/test.taxa.R                              |   26 
 tests/testthat/test.transformCharacter.R                |   36 
 vignettes/MorphoTools2_tutorial.Rmd                     | 2666 ++++++++--------
 178 files changed, 16861 insertions(+), 16859 deletions(-)

More information about MorphoTools2 at CRAN
Permanent link

Package OUwie (with last version 2.6) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-02-04 2.6
2020-10-20 2.5
2020-08-04 2.4
2020-06-25 2.3
2020-06-15 2.2
2020-05-12 2.1
2019-12-06 1.57
2019-06-11 1.53
2016-06-18 1.50
2016-02-28 1.49
2016-01-07 1.48
2015-09-05 1.46
2015-03-09 1.45
2015-02-19 1.44
2014-07-26 1.43
2014-04-01 1.42
2014-03-14 1.41
2014-02-18 1.40
2014-02-10 1.39
2014-02-03 1.38
2013-12-11 1.37
2013-11-22 1.36
2013-11-11 1.35
2013-05-24 1.34
2013-03-23 1.33
2013-01-30 1.32
2012-11-26 1.31
2012-11-11 1.30
2012-09-10 1.27
2012-06-13 1.24
2012-05-04 1.21
2012-04-17 1.18
2012-03-15 1.17
2012-03-14 1.16
2012-03-02 1.15
2012-02-21 1.13
2011-12-20 1.10
2011-09-17 1.2

Permanent link
Package bisect (with last version 0.9.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2018-04-16 0.9.0

Permanent link

Wed, 25 May 2022

New package mixedCCA with initial version 1.5.2
Package: mixedCCA
Title: Sparse Canonical Correlation Analysis for High-Dimensional Mixed Data
Version: 1.5.2
Date: 2022-05-25
Maintainer: Irina Gaynanova <irinag@stat.tamu.edu>
Description: Semi-parametric approach for sparse canonical correlation analysis which can handle mixed data types: continuous, binary and truncated continuous. Bridge functions are provided to connect Kendall's tau to latent correlation under the Gaussian copula model. The methods are described in Yoon, Carroll and Gaynanova (2020) <doi:10.1093/biomet/asaa007> and Yoon, Mueller and Gaynanova (2020) <doi:10.1080/10618600.2021.1882468>.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.0.1), stats, MASS
Imports: Rcpp, pcaPP, Matrix, fMultivar, mnormt, irlba
NeedsCompilation: yes
LinkingTo: Rcpp, RcppArmadillo
Packaged: 2022-05-25 18:16:48 UTC; irinag
Author: Grace Yoon [aut] , Mingze Huang [ctb] , Irina Gaynanova [aut, cre]
Repository: CRAN
Date/Publication: 2022-05-25 23:10:02 UTC

More information about mixedCCA at CRAN
Permanent link

New package scar with initial version 0.2-2
Package: scar
Version: 0.2-2
Date: 2022-05-25
Title: Shape-Constrained Additive Regression: a Maximum Likelihood Approach
Author: Yining Chen and Richard Samworth
Maintainer: Yining Chen <y.chen101@lse.ac.uk>
Depends: R (>= 3.0.0)
Suggests: gam, mgcv, scam
Description: Computes the maximum likelihood estimator of the generalised additive and index regression with shape constraints. Each additive component function is assumed to obey one of the nine possible shape restrictions: linear, increasing, decreasing, convex, convex increasing, convex decreasing, concave, concave increasing, or concave decreasing. For details, see Chen and Samworth (2016) <doi:10.1111/rssb.12137>.
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2022-05-25 16:13:43 UTC; chen
Repository: CRAN
Date/Publication: 2022-05-25 22:50:02 UTC

More information about scar at CRAN
Permanent link

Package rpartScore updated to version 1.0-2 with previous version 1.0-1 dated 2012-12-08

Title: Classification Trees for Ordinal Responses
Description: Recursive partitioning methods to build classification trees for ordinal responses within the CART framework. Trees are grown using the Generalized Gini impurity function, where the misclassification costs are given by the absolute or squared differences in scores assigned to the categories of the response. Pruning is based on the total misclassification rate or on the total misclassification cost.
Author: Giuliano Galimberti, Gabriele Soffritti, Matteo Di Maso
Maintainer: Giuliano Galimberti <giuliano.galimberti@unibo.it>

Diff between rpartScore versions 1.0-1 dated 2012-12-08 and 1.0-2 dated 2022-05-25

 DESCRIPTION               |   18 +++++++--------
 MD5                       |   21 +++++++++--------
 NAMESPACE                 |    2 -
 build                     |only
 inst/CITATION             |   17 ++++++++------
 man/evalMedian.Rd         |    9 +++----
 man/evalMode.Rd           |    8 +++---
 man/initScore.Rd          |   10 ++++----
 man/rpartScore-package.Rd |   55 ++++++++++++++++++----------------------------
 man/rpartScore.Rd         |   51 ++++++++++++++++--------------------------
 man/splitAbs.Rd           |    8 +++---
 man/splitQuad.Rd          |    8 +++---
 12 files changed, 94 insertions(+), 113 deletions(-)

More information about rpartScore at CRAN
Permanent link

Package MapGAM updated to version 1.2-6 with previous version 1.2-5 dated 2019-07-27

Title: Mapping Smoothed Effect Estimates from Individual-Level Data
Description: Contains functions for mapping odds ratios, hazard ratios, or other effect estimates using individual-level data such as case-control study data, using generalized additive models (GAMs) or Cox models for smoothing with a two-dimensional predictor (e.g., geolocation or exposure to chemical mixtures) while adjusting linearly for confounding variables, using methods described by Kelsall and Diggle (1998), Webster at al. (2006), and Bai et al. (2020). Includes convenient functions for mapping point estimates and confidence intervals, efficient control sampling, and permutation tests for the null hypothesis that the two-dimensional predictor is not associated with the outcome variable (adjusting for confounders).
Author: Lu Bai, Scott Bartell, Robin Bliss, and Veronica Vieira
Maintainer: Scott Bartell <sbartell@uci.edu>

Diff between MapGAM versions 1.2-5 dated 2019-07-27 and 1.2-6 dated 2022-05-25

 ChangeLog             |  246 +++++++++++++-----------
 DESCRIPTION           |   10 -
 MD5                   |   26 +-
 R/MapGAM.version.R    |   53 ++---
 R/colormap.R          |   12 -
 R/modgam.R            |  495 +++++++++++++++++++++++++-------------------------
 R/predgrid.R          |    4 
 R/sampcont.R          |  116 ++++++-----
 R/summary.gamcox.R    |   90 ++++-----
 R/summary.modgam.R    |   11 -
 R/trimdata.R          |    6 
 man/MapGAM-package.Rd |   16 -
 man/modgam.Rd         |   10 -
 man/sampcont.Rd       |   13 +
 14 files changed, 579 insertions(+), 529 deletions(-)

More information about MapGAM at CRAN
Permanent link

New package markovchain with initial version 0.8.9
Package: markovchain
Title: Easy Handling Discrete Time Markov Chains
Version: 0.8.9
Date: 2022-05-24
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Description: Functions and S4 methods to create and manage discrete time Markov chains more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of their structural proprieties) analysis are provided. See Spedicato (2017) <doi:10.32614/RJ-2017-036>.
License: GPL-2
Depends: R (>= 4.0.0), methods
Imports: igraph, Matrix, expm, stats4, parallel, Rcpp (>= 1.0.2), RcppParallel, utils, stats, grDevices
Suggests: knitr, testthat, diagram, DiagrammeR, msm, Rsolnp, rmarkdown, ctmcd, bookdown, rticles
Enhances: etm
VignetteBuilder: utils, knitr
LinkingTo: Rcpp, RcppParallel, RcppArmadillo (>= 0.9.600.4.0)
SystemRequirements: GNU make
LazyLoad: yes
ByteCompile: yes
Encoding: UTF-8
BugReports: https://github.com/spedygiorgio/markovchain/issues
URL: https://github.com/spedygiorgio/markovchain/
NeedsCompilation: yes
Packaged: 2022-05-25 18:16:37 UTC; giorgio
Author: Giorgio Alfredo Spedicato [aut, cre] , Tae Seung Kang [aut], Sai Bhargav Yalamanchi [aut], Mildenberger Thoralf [ctb] , Deepak Yadav [aut], Ignacio Cordon [aut] , Vandit Jain [ctb], Toni Giorgino [ctb] , Richel J.C. Bilderbeek [ctb] , Daniel Ebbert [ [...truncated...]
Repository: CRAN
Date/Publication: 2022-05-25 22:50:05 UTC

More information about markovchain at CRAN
Permanent link

New package GLIDE with initial version 1.0.5
Package: GLIDE
Title: Global and Individual Tests for Direct Effects
Version: 1.0.5
Date: 2022-05-20
Author: James Dai [aut, cre], Xiaoyu Wang [aut]
Maintainer: James Dai <jdai@fredhutch.org>
Description: Global and individual tests for pleiotropy and direct effects in Mendelian randomization studies. Refer to J. Y. Dai, U. Peters, X. Wang, J. Kocarnik et al. AJE (2018) <doi:10.1093/aje/kwy177>.
Depends: R (>= 2.10)
Imports: MASS,foreach,parallel,doParallel
LazyLoad: no
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2022-05-25 21:53:18 UTC; xwang234
Repository: CRAN
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
Date/Publication: 2022-05-25 23:00:02 UTC

More information about GLIDE at CRAN
Permanent link

Package dcurves updated to version 0.3.0 with previous version 0.2.0 dated 2021-07-20

Title: Decision Curve Analysis for Model Evaluation
Description: Diagnostic and prognostic models are typically evaluated with measures of accuracy that do not address clinical consequences. Decision-analytic techniques allow assessment of clinical outcomes, but often require collection of additional information may be cumbersome to apply to models that yield a continuous result. Decision curve analysis is a method for evaluating and comparing prediction models that incorporates clinical consequences, requires only the data set on which the models are tested, and can be applied to models that have either continuous or dichotomous results. See the following references for details on the methods: Vickers (2006) <doi:10.1177/0272989X06295361>, Vickers (2008) <doi:10.1186/1472-6947-8-53>, and Pfeiffer (2020) <doi:10.1002/bimj.201800240>.
Author: Daniel D. Sjoberg [aut, cre, cph], Emily Vertosick [ctb]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>

Diff between dcurves versions 0.2.0 dated 2021-07-20 and 0.3.0 dated 2022-05-25

 DESCRIPTION                             |   23 
 MD5                                     |   47 -
 NAMESPACE                               |    1 
 NEWS.md                                 |   44 +
 R/dca.r                                 |  256 +--------
 R/plot.R                                |    2 
 R/print.R                               |    1 
 R/standardize_net_benefit.R             |    5 
 R/test_consequences.R                   |only
 README.md                               |    5 
 build/partial.rdb                       |only
 build/vignette.rds                      |binary
 inst/WORDLIST                           |    1 
 inst/doc/dca.R                          |    2 
 inst/doc/dca.Rmd                        |    6 
 inst/doc/dca.html                       |  839 +++++++++++++++++++++++++-------
 man/dca.Rd                              |    2 
 man/dcurves-package.Rd                  |   20 
 man/df_binary.Rd                        |   52 -
 man/df_case_control.Rd                  |   50 -
 man/df_surv.Rd                          |   54 +-
 man/figures/two-by-two-table.png        |only
 man/print.dca.Rd                        |    1 
 man/test_consequences.Rd                |only
 tests/testthat/test-dca.R               |   15 
 tests/testthat/test-test_consequences.R |only
 vignettes/dca.Rmd                       |    6 
 27 files changed, 915 insertions(+), 517 deletions(-)

More information about dcurves at CRAN
Permanent link

Package catIrt updated to version 0.5.1 with previous version 0.5-0 dated 2014-10-05

Title: Simulate IRT-Based Computerized Adaptive Tests
Description: Functions designed to simulate data that conform to basic unidimensional IRT models (for now 3-parameter binary response models and graded response models) along with Post-Hoc CAT simulations of those models given various item selection methods, ability estimation methods, and termination criteria. See Wainer (2000) <doi:10.4324/9781410605931>, van der Linden & Pashley (2010) <doi:10.1007/978-0-387-85461-8_1>, and Eggen (1999) <doi:10.1177/01466219922031365> for more details.
Author: Steven Nydick [cre, aut]
Maintainer: Steven Nydick <swnydick@gmail.com>

Diff between catIrt versions 0.5-0 dated 2014-10-05 and 0.5.1 dated 2022-05-25

 catIrt-0.5-0/catIrt/inst/NEWS.Rd          |only
 catIrt-0.5.1/catIrt/DESCRIPTION           |   29 ++++++++----
 catIrt-0.5.1/catIrt/MD5                   |   47 ++++++++++++++------
 catIrt-0.5.1/catIrt/NAMESPACE             |   15 +++++-
 catIrt-0.5.1/catIrt/NEWS.md               |only
 catIrt-0.5.1/catIrt/R/bmeEst.R            |   57 +++++++++++-------------
 catIrt-0.5.1/catIrt/R/eapEst.R            |   69 +++++++++++++++---------------
 catIrt-0.5.1/catIrt/R/mleEst.R            |   47 +++++++++-----------
 catIrt-0.5.1/catIrt/R/wleEst.R            |   56 +++++++++++-------------
 catIrt-0.5.1/catIrt/README.md             |only
 catIrt-0.5.1/catIrt/inst/ARRT_Updates     |only
 catIrt-0.5.1/catIrt/inst/TODO.rtf         |only
 catIrt-0.5.1/catIrt/man/FI.Rd             |    4 -
 catIrt-0.5.1/catIrt/man/KL.Rd             |    2 
 catIrt-0.5.1/catIrt/man/catIrt-package.Rd |    4 -
 catIrt-0.5.1/catIrt/man/catIrt.Rd         |    4 -
 catIrt-0.5.1/catIrt/man/itChoose.Rd       |    2 
 catIrt-0.5.1/catIrt/man/mleEst.Rd         |    7 +--
 catIrt-0.5.1/catIrt/man/simIrt.Rd         |    2 
 catIrt-0.5.1/catIrt/src/catIrt_init.c     |only
 20 files changed, 189 insertions(+), 156 deletions(-)

More information about catIrt at CRAN
Permanent link

Package usethis updated to version 2.1.6 with previous version 2.1.5 dated 2021-12-09

Title: Automate Package and Project Setup
Description: Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and more.
Author: Hadley Wickham [aut] , Jennifer Bryan [aut, cre] , Malcolm Barrett [aut] , RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>

Diff between usethis versions 2.1.5 dated 2021-12-09 and 2.1.6 dated 2022-05-25

 usethis-2.1.5/usethis/tests/testthat/teardown.R                   |only
 usethis-2.1.6/usethis/DESCRIPTION                                 |   14 
 usethis-2.1.6/usethis/MD5                                         |  153 +++++-----
 usethis-2.1.6/usethis/NAMESPACE                                   |    1 
 usethis-2.1.6/usethis/NEWS.md                                     |   28 +
 usethis-2.1.6/usethis/R/badge.R                                   |   28 +
 usethis-2.1.6/usethis/R/code-of-conduct.R                         |   34 +-
 usethis-2.1.6/usethis/R/course.R                                  |    5 
 usethis-2.1.6/usethis/R/create.R                                  |   17 -
 usethis-2.1.6/usethis/R/data-table.R                              |   18 -
 usethis-2.1.6/usethis/R/data.R                                    |    6 
 usethis-2.1.6/usethis/R/description.R                             |    2 
 usethis-2.1.6/usethis/R/git-default-branch.R                      |    2 
 usethis-2.1.6/usethis/R/github-actions.R                          |  145 ++++++---
 usethis-2.1.6/usethis/R/github-labels.R                           |    9 
 usethis-2.1.6/usethis/R/github-pages.R                            |   17 -
 usethis-2.1.6/usethis/R/issue.R                                   |    6 
 usethis-2.1.6/usethis/R/package.R                                 |   25 +
 usethis-2.1.6/usethis/R/pkgdown.R                                 |   11 
 usethis-2.1.6/usethis/R/pr.R                                      |    6 
 usethis-2.1.6/usethis/R/r.R                                       |   35 ++
 usethis-2.1.6/usethis/R/readme.R                                  |   11 
 usethis-2.1.6/usethis/R/release.R                                 |  104 +++++-
 usethis-2.1.6/usethis/R/roxygen.R                                 |   62 ++--
 usethis-2.1.6/usethis/R/tidy-upkeep.R                             |   40 ++
 usethis-2.1.6/usethis/R/tidyverse.R                               |    8 
 usethis-2.1.6/usethis/R/use_github_file.R                         |    6 
 usethis-2.1.6/usethis/R/usethis-package.R                         |    6 
 usethis-2.1.6/usethis/R/utils-github.R                            |   51 ++-
 usethis-2.1.6/usethis/R/version.R                                 |   34 +-
 usethis-2.1.6/usethis/R/vignette.R                                |    1 
 usethis-2.1.6/usethis/R/vscode.R                                  |only
 usethis-2.1.6/usethis/README.md                                   |   56 +--
 usethis-2.1.6/usethis/inst/templates/CODE_OF_CONDUCT.md           |   41 +-
 usethis-2.1.6/usethis/inst/templates/testthat.R                   |    8 
 usethis-2.1.6/usethis/inst/templates/vscode-c_cpp_properties.json |only
 usethis-2.1.6/usethis/inst/templates/vscode-debug.R               |only
 usethis-2.1.6/usethis/inst/templates/vscode-launch.json           |only
 usethis-2.1.6/usethis/man/badges.Rd                               |    9 
 usethis-2.1.6/usethis/man/create_from_github.Rd                   |   20 -
 usethis-2.1.6/usethis/man/git_protocol.Rd                         |    6 
 usethis-2.1.6/usethis/man/github_actions.Rd                       |   25 +
 usethis-2.1.6/usethis/man/tidyverse.Rd                            |    8 
 usethis-2.1.6/usethis/man/use_code_of_conduct.Rd                  |    4 
 usethis-2.1.6/usethis/man/use_course_details.Rd                   |   42 +-
 usethis-2.1.6/usethis/man/use_data.Rd                             |    9 
 usethis-2.1.6/usethis/man/use_data_table.Rd                       |   14 
 usethis-2.1.6/usethis/man/use_description.Rd                      |    6 
 usethis-2.1.6/usethis/man/use_github_file.Rd                      |    6 
 usethis-2.1.6/usethis/man/use_github_pages.Rd                     |    8 
 usethis-2.1.6/usethis/man/use_pkgdown.Rd                          |    2 
 usethis-2.1.6/usethis/man/use_r.Rd                                |   36 ++
 usethis-2.1.6/usethis/man/use_readme_rmd.Rd                       |   11 
 usethis-2.1.6/usethis/man/use_roxygen_md.Rd                       |   12 
 usethis-2.1.6/usethis/man/use_version.Rd                          |   23 -
 usethis-2.1.6/usethis/man/usethis-package.Rd                      |    2 
 usethis-2.1.6/usethis/man/zip-utils.Rd                            |    6 
 usethis-2.1.6/usethis/tests/testthat/_snaps/badge.md              |   12 
 usethis-2.1.6/usethis/tests/testthat/_snaps/course.md             |   13 
 usethis-2.1.6/usethis/tests/testthat/_snaps/git-default-branch.md |    2 
 usethis-2.1.6/usethis/tests/testthat/_snaps/github-actions.md     |   22 -
 usethis-2.1.6/usethis/tests/testthat/_snaps/lifecycle.md          |    2 
 usethis-2.1.6/usethis/tests/testthat/_snaps/package.md            |   25 +
 usethis-2.1.6/usethis/tests/testthat/_snaps/release.md            |   21 +
 usethis-2.1.6/usethis/tests/testthat/_snaps/tibble.md             |    2 
 usethis-2.1.6/usethis/tests/testthat/_snaps/tidy-upkeep.md        |   24 +
 usethis-2.1.6/usethis/tests/testthat/_snaps/tidyverse.md          |    2 
 usethis-2.1.6/usethis/tests/testthat/_snaps/ui.md                 |   15 
 usethis-2.1.6/usethis/tests/testthat/_snaps/use_import_from.md    |   15 
 usethis-2.1.6/usethis/tests/testthat/_snaps/utils-github.md       |   16 -
 usethis-2.1.6/usethis/tests/testthat/_snaps/vignette.md           |   10 
 usethis-2.1.6/usethis/tests/testthat/setup.R                      |    4 
 usethis-2.1.6/usethis/tests/testthat/test-badge.R                 |    9 
 usethis-2.1.6/usethis/tests/testthat/test-data.R                  |   12 
 usethis-2.1.6/usethis/tests/testthat/test-github-actions.R        |   20 +
 usethis-2.1.6/usethis/tests/testthat/test-package.R               |    8 
 usethis-2.1.6/usethis/tests/testthat/test-release.R               |    8 
 usethis-2.1.6/usethis/tests/testthat/test-roxygen.R               |   18 +
 usethis-2.1.6/usethis/tests/testthat/test-tidy-upkeep.R           |    4 
 usethis-2.1.6/usethis/tests/testthat/test-utils-github.R          |    4 
 80 files changed, 1053 insertions(+), 454 deletions(-)

More information about usethis at CRAN
Permanent link

Package hapassoc updated to version 1.2-9 with previous version 1.2-8 dated 2015-05-10

Title: Inference of Trait Associations with SNP Haplotypes and Other Attributes using the EM Algorithm
Description: The following R functions are used for inference of trait associations with haplotypes and other covariates in generalized linear models. The functions are developed primarily for data collected in cohort or cross-sectional studies. They can accommodate uncertain haplotype phase and handle missing genotypes at some SNPs.
Author: K. Burkett <kburkett@uottawa.ca>, B. McNeney <mcneney@sfu.ca>, J. Graham <jgraham@stat.sfu.ca>, with code for case-control data contributed by Zhijian Chen <z11chen@math.uwaterloo.ca>
Maintainer: K. Burkett <kburkett@uottawa.ca>

Diff between hapassoc versions 1.2-8 dated 2015-05-10 and 1.2-9 dated 2022-05-25

 DESCRIPTION           |    8 ++++----
 MD5                   |   13 +++++++------
 NAMESPACE             |    5 +++++
 build/vignette.rds    |binary
 inst/CITATION         |    4 ++--
 inst/ChangeLog        |    4 ++++
 inst/doc/hapassoc.pdf |binary
 src/hapassoc_init.c   |only
 8 files changed, 22 insertions(+), 12 deletions(-)

More information about hapassoc at CRAN
Permanent link

Package vetiver updated to version 0.1.5 with previous version 0.1.4 dated 2022-04-28

Title: Version, Share, Deploy, and Monitor Models
Description: The goal of 'vetiver' is to provide fluent tooling to version, share, deploy, and monitor a trained model. Functions handle both recording and checking the model's input data prototype, and predicting from a remote API endpoint. The 'vetiver' package is extensible, with generics that can support many kinds of models.
Author: Julia Silge [cre, aut] , RStudio [cph, fnd]
Maintainer: Julia Silge <julia.silge@rstudio.com>

Diff between vetiver versions 0.1.4 dated 2022-04-28 and 0.1.5 dated 2022-05-25

 vetiver-0.1.4/vetiver/inst/rmarkdown/templates/vetiver_dashboard |only
 vetiver-0.1.5/vetiver/DESCRIPTION                                |   31 ++++---
 vetiver-0.1.5/vetiver/MD5                                        |   40 +++++-----
 vetiver-0.1.5/vetiver/NAMESPACE                                  |   22 +++--
 vetiver-0.1.5/vetiver/NEWS.md                                    |    6 +
 vetiver-0.1.5/vetiver/R/endpoint.R                               |   18 +++-
 vetiver-0.1.5/vetiver/R/monitor.R                                |only
 vetiver-0.1.5/vetiver/R/vetiver-package.R                        |   15 +--
 vetiver-0.1.5/vetiver/R/write-docker.R                           |    1 
 vetiver-0.1.5/vetiver/README.md                                  |   14 ++-
 vetiver-0.1.5/vetiver/inst/doc/model-card.html                   |    2 
 vetiver-0.1.5/vetiver/inst/doc/vetiver.R                         |    3 
 vetiver-0.1.5/vetiver/inst/doc/vetiver.Rmd                       |    3 
 vetiver-0.1.5/vetiver/inst/doc/vetiver.html                      |   10 +-
 vetiver-0.1.5/vetiver/man/vetiver-package.Rd                     |    7 +
 vetiver-0.1.5/vetiver/man/vetiver_compute_metrics.Rd             |only
 vetiver-0.1.5/vetiver/man/vetiver_endpoint.Rd                    |    4 -
 vetiver-0.1.5/vetiver/tests/testthat/_snaps/caret.md             |    2 
 vetiver-0.1.5/vetiver/tests/testthat/_snaps/monitor              |only
 vetiver-0.1.5/vetiver/tests/testthat/_snaps/monitor.md           |only
 vetiver-0.1.5/vetiver/tests/testthat/test-caret.R                |    6 -
 vetiver-0.1.5/vetiver/tests/testthat/test-monitor.R              |only
 vetiver-0.1.5/vetiver/tests/testthat/test-predict.R              |    1 
 vetiver-0.1.5/vetiver/vignettes/vetiver.Rmd                      |    3 
 24 files changed, 110 insertions(+), 78 deletions(-)

More information about vetiver at CRAN
Permanent link

Package tidypredict updated to version 0.4.9 with previous version 0.4.8 dated 2020-10-28

Title: Run Predictions Inside the Database
Description: It parses a fitted 'R' model object, and returns a formula in 'Tidy Eval' code that calculates the predictions. It works with several databases back-ends because it leverages 'dplyr' and 'dbplyr' for the final 'SQL' translation of the algorithm. It currently supports lm(), glm(), randomForest(), ranger(), earth(), xgb.Booster.complete(), cubist(), and ctree() models.
Author: Max Kuhn [aut, cre], Edgar Ruiz [aut]
Maintainer: Max Kuhn <max@rstudio.com>

Diff between tidypredict versions 0.4.8 dated 2020-10-28 and 0.4.9 dated 2022-05-25

 DESCRIPTION                      |   47 +--
 LICENSE                          |only
 MD5                              |  130 ++++----
 NEWS.md                          |   10 
 R/model-cubist.R                 |   26 -
 R/model-lm.R                     |    6 
 R/model-rf.R                     |   55 ++-
 R/model-xgboost.R                |    2 
 R/predict-column.R               |    2 
 R/to_sql.R                       |    4 
 README.md                        |   44 +-
 build/vignette.rds               |binary
 inst/doc/cubist.Rmd              |    2 
 inst/doc/cubist.html             |  277 +++++++-----------
 inst/doc/glm.Rmd                 |    2 
 inst/doc/glm.html                |  252 +++++++---------
 inst/doc/lm.Rmd                  |    2 
 inst/doc/lm.html                 |  351 ++++++++++-------------
 inst/doc/mars.Rmd                |    2 
 inst/doc/mars.html               |  347 +++++++++--------------
 inst/doc/non-r.Rmd               |    2 
 inst/doc/non-r.html              |  300 ++++++++-----------
 inst/doc/ranger.Rmd              |    2 
 inst/doc/ranger.html             |  231 +++++----------
 inst/doc/regression.Rmd          |    2 
 inst/doc/regression.html         |   42 --
 inst/doc/rf.R                    |    7 
 inst/doc/rf.Rmd                  |   10 
 inst/doc/rf.html                 |  233 +++++----------
 inst/doc/save.Rmd                |    2 
 inst/doc/save.html               |  265 +++++++----------
 inst/doc/sql.R                   |    7 
 inst/doc/sql.Rmd                 |   13 
 inst/doc/sql.html                |  369 +++++++++++-------------
 inst/doc/tree.Rmd                |    2 
 inst/doc/tree.html               |   44 +-
 inst/doc/xgboost.Rmd             |    2 
 inst/doc/xgboost.html            |  587 +++++++++++++++++----------------------
 man/tidypredict-package.Rd       |    9 
 tests/testthat/_snaps            |only
 tests/testthat/test-acceptable.R |    7 
 tests/testthat/test-cubist.R     |   11 
 tests/testthat/test-earth.R      |    9 
 tests/testthat/test-list.R       |    8 
 tests/testthat/test-party.R      |    5 
 tests/testthat/test-ranger.R     |    9 
 tests/testthat/test-rf.R         |   14 
 tests/testthat/test-sql.R        |    6 
 tests/testthat/test-tester.R     |    4 
 tests/testthat/test_glm.R        |    9 
 tests/testthat/test_lm.R         |    9 
 tests/testthat/test_xgboost.R    |   17 -
 vignettes/cubist.Rmd             |    2 
 vignettes/glm.Rmd                |    2 
 vignettes/lm.Rmd                 |    2 
 vignettes/mars.Rmd               |    2 
 vignettes/non-r.Rmd              |    2 
 vignettes/ranger.Rmd             |    2 
 vignettes/regression.Rmd         |    2 
 vignettes/rf.Rmd                 |   10 
 vignettes/save.Rmd               |    2 
 vignettes/sql.Rmd                |   13 
 vignettes/tree.Rmd               |    2 
 vignettes/xgboost.Rmd            |    2 
 64 files changed, 1689 insertions(+), 2152 deletions(-)

More information about tidypredict at CRAN
Permanent link

Package swCRTdesign updated to version 3.2 with previous version 3.1 dated 2019-10-25

Title: Stepped Wedge Cluster Randomized Trial (SW CRT) Design
Description: A set of tools for examining the design and analysis aspects of stepped wedge cluster randomized trials (SW CRT) based on a repeated cross-sectional sampling scheme (Hussey MA and Hughes JP (2007) Contemporary Clinical Trials 28:182-191. <doi:10.1016/j.cct.2006.05.007>).
Author: Jim Hughes, Navneet R. Hakhu, Emily Voldal, and Fan Xia
Maintainer: Jim Hughes <jphughes@uw.edu>

Diff between swCRTdesign versions 3.1 dated 2019-10-25 and 3.2 dated 2022-05-25

 DESCRIPTION                |   12 ++++++------
 MD5                        |   10 ++++++----
 NAMESPACE                  |    2 +-
 R/swGlmPwr.R               |only
 man/swCRTdesign-package.Rd |   10 ++++++----
 man/swGlmPwr.Rd            |only
 man/swPwr.Rd               |    6 +++---
 7 files changed, 22 insertions(+), 18 deletions(-)

More information about swCRTdesign at CRAN
Permanent link

Package PUPAIM updated to version 0.3.1 with previous version 0.3.0 dated 2022-05-12

Title: A Collection of Physical and Chemical Adsorption Isotherm Models
Description: The PUPAIM R package can generally fit any adsorption experimental data to any of the 55 available adsorption isotherm models - 32 nonlinear models and 23 linear models. This package provides parameter estimation, model accuracy analysis, model error analysis, and adsorption plot created using the package 'ggplot2'. This package will help the users for a much easier way of adsorption model data fitting.
Author: Keith T. Ostan [aut] , Paul Angelo C. Manlapaz [aut] , Jemimah Christine L. Mesias [aut] , Chester C. Deocaris [aut, ths, cre]
Maintainer: Chester C. Deocaris <ccdeocaris@pup.edu.ph>

Diff between PUPAIM versions 0.3.0 dated 2022-05-12 and 0.3.1 dated 2022-05-25

 PUPAIM-0.3.0/PUPAIM/R/PUPAIM.R                         |only
 PUPAIM-0.3.0/PUPAIM/R/henryLM.r                        |only
 PUPAIM-0.3.0/PUPAIM/R/volmeranalysis.R                 |only
 PUPAIM-0.3.0/PUPAIM/man/PUPAIM.Rd                      |only
 PUPAIM-0.3.0/PUPAIM/man/henry.LM.Rd                    |only
 PUPAIM-0.3.1/PUPAIM/DESCRIPTION                        |   12 -
 PUPAIM-0.3.1/PUPAIM/MD5                                |  198 ++++++++---------
 PUPAIM-0.3.1/PUPAIM/NAMESPACE                          |    6 
 PUPAIM-0.3.1/PUPAIM/R/BETLM.r                          |    2 
 PUPAIM-0.3.1/PUPAIM/R/BETanalysis.R                    |    5 
 PUPAIM-0.3.1/PUPAIM/R/FS3analysis.R                    |   11 
 PUPAIM-0.3.1/PUPAIM/R/FS4analysis.R                    |    7 
 PUPAIM-0.3.1/PUPAIM/R/SSLangmuir1analysis.R            |   13 -
 PUPAIM-0.3.1/PUPAIM/R/SSLangmuir2analysis.R            |   13 -
 PUPAIM-0.3.1/PUPAIM/R/SSLangmuir3.R                    |    2 
 PUPAIM-0.3.1/PUPAIM/R/SSLangmuir3analysis.R            |   13 -
 PUPAIM-0.3.1/PUPAIM/R/SSLangmuir4analysis.R            |   13 -
 PUPAIM-0.3.1/PUPAIM/R/aranovichanalysis.R              |    6 
 PUPAIM-0.3.1/PUPAIM/R/bauduanalysis.R                  |    8 
 PUPAIM-0.3.1/PUPAIM/R/dubininradushkevichLM.R          |    4 
 PUPAIM-0.3.1/PUPAIM/R/dubininradushkevichanalysis.R    |    9 
 PUPAIM-0.3.1/PUPAIM/R/elovichLM.r                      |    6 
 PUPAIM-0.3.1/PUPAIM/R/elovichanalysis.r                |   16 -
 PUPAIM-0.3.1/PUPAIM/R/floryhugginsLM.R                 |    8 
 PUPAIM-0.3.1/PUPAIM/R/floryhugginsanalysis.R           |   21 +
 PUPAIM-0.3.1/PUPAIM/R/fowlerguggenheimLM.R             |   12 -
 PUPAIM-0.3.1/PUPAIM/R/fowlerguggenheimanalysis.R       |   15 -
 PUPAIM-0.3.1/PUPAIM/R/freundlichLM.R                   |    6 
 PUPAIM-0.3.1/PUPAIM/R/freundlichanalysis.R             |    7 
 PUPAIM-0.3.1/PUPAIM/R/halseyLM.R                       |    4 
 PUPAIM-0.3.1/PUPAIM/R/halseyanalysis.R                 |    9 
 PUPAIM-0.3.1/PUPAIM/R/harkinsjuraLM.R                  |    4 
 PUPAIM-0.3.1/PUPAIM/R/harkinsjuraanalysis.R            |    8 
 PUPAIM-0.3.1/PUPAIM/R/henryanalysis.r                  |only
 PUPAIM-0.3.1/PUPAIM/R/hillLM.R                         |    2 
 PUPAIM-0.3.1/PUPAIM/R/hillanalysis.R                   |   14 -
 PUPAIM-0.3.1/PUPAIM/R/hilldeboerLM.R                   |    8 
 PUPAIM-0.3.1/PUPAIM/R/hilldeboeranalysis.R             |   13 -
 PUPAIM-0.3.1/PUPAIM/R/jossensLM.r                      |    4 
 PUPAIM-0.3.1/PUPAIM/R/jossensanalysis.r                |   15 -
 PUPAIM-0.3.1/PUPAIM/R/jovanovicLM.R                    |    6 
 PUPAIM-0.3.1/PUPAIM/R/jovanovicanalysis.R              |    5 
 PUPAIM-0.3.1/PUPAIM/R/kahnanalysis.R                   |    8 
 PUPAIM-0.3.1/PUPAIM/R/kiselevLM.R                      |    7 
 PUPAIM-0.3.1/PUPAIM/R/kiselevanalysis.R                |   11 
 PUPAIM-0.3.1/PUPAIM/R/koblecarrigananalysis.R          |    5 
 PUPAIM-0.3.1/PUPAIM/R/koblecorriganLM.R                |    4 
 PUPAIM-0.3.1/PUPAIM/R/langmuir1LM.R                    |only
 PUPAIM-0.3.1/PUPAIM/R/langmuir2LM.R                    |only
 PUPAIM-0.3.1/PUPAIM/R/langmuir3LM.R                    |only
 PUPAIM-0.3.1/PUPAIM/R/langmuir4LM.R                    |only
 PUPAIM-0.3.1/PUPAIM/R/langmuiranalysis.R               |   15 -
 PUPAIM-0.3.1/PUPAIM/R/marckzewskijaroniecanalysis.r    |    8 
 PUPAIM-0.3.1/PUPAIM/R/radkeprausnitzanalysis.R         |    9 
 PUPAIM-0.3.1/PUPAIM/R/radkepraustnitzLM.R              |    2 
 PUPAIM-0.3.1/PUPAIM/R/redlichpetersonLM.R              |    2 
 PUPAIM-0.3.1/PUPAIM/R/redlichpetersonanalysis.R        |    5 
 PUPAIM-0.3.1/PUPAIM/R/sipsLM.R                         |    2 
 PUPAIM-0.3.1/PUPAIM/R/sipsanalysis.R                   |   13 -
 PUPAIM-0.3.1/PUPAIM/R/temkinLM.R                       |   12 -
 PUPAIM-0.3.1/PUPAIM/R/temkinanalysis.r                 |    5 
 PUPAIM-0.3.1/PUPAIM/R/tothanalysis.R                   |   10 
 PUPAIM-0.3.1/PUPAIM/R/volmeranalysis.r                 |only
 PUPAIM-0.3.1/PUPAIM/R/webervanvlietanalysis.r          |    7 
 PUPAIM-0.3.1/PUPAIM/inst/doc/PUPAIM.R                  |    2 
 PUPAIM-0.3.1/PUPAIM/inst/doc/PUPAIM.Rmd                |    9 
 PUPAIM-0.3.1/PUPAIM/inst/doc/PUPAIM.html               |   89 ++++++-
 PUPAIM-0.3.1/PUPAIM/man/FS3analysis.Rd                 |    6 
 PUPAIM-0.3.1/PUPAIM/man/FS4analysis.Rd                 |    2 
 PUPAIM-0.3.1/PUPAIM/man/SSLangmuir3.Rd                 |    2 
 PUPAIM-0.3.1/PUPAIM/man/bauduanalysis.Rd               |    2 
 PUPAIM-0.3.1/PUPAIM/man/dubininradushkevichanalysis.Rd |    2 
 PUPAIM-0.3.1/PUPAIM/man/dubininraduskevich.LM.Rd       |    2 
 PUPAIM-0.3.1/PUPAIM/man/elovich.LM.Rd                  |    4 
 PUPAIM-0.3.1/PUPAIM/man/elovichanalysis.Rd             |   12 -
 PUPAIM-0.3.1/PUPAIM/man/floryhuggins.LM.Rd             |   10 
 PUPAIM-0.3.1/PUPAIM/man/floryhugginsanalysis.Rd        |   10 
 PUPAIM-0.3.1/PUPAIM/man/fowlerguggenheim.LM.Rd         |   12 -
 PUPAIM-0.3.1/PUPAIM/man/fowlerguggenheimanalysis.Rd    |   10 
 PUPAIM-0.3.1/PUPAIM/man/freundlich.LM.Rd               |    4 
 PUPAIM-0.3.1/PUPAIM/man/freundlichanalysis.Rd          |    2 
 PUPAIM-0.3.1/PUPAIM/man/halsey.LM.Rd                   |    2 
 PUPAIM-0.3.1/PUPAIM/man/halseyanalysis.Rd              |    4 
 PUPAIM-0.3.1/PUPAIM/man/harkinsjura.LM.Rd              |    2 
 PUPAIM-0.3.1/PUPAIM/man/harkinsjuraanalysis.Rd         |    2 
 PUPAIM-0.3.1/PUPAIM/man/henryanalysis.Rd               |only
 PUPAIM-0.3.1/PUPAIM/man/hillanalysis.Rd                |    4 
 PUPAIM-0.3.1/PUPAIM/man/hilldeboer.LM.Rd               |   10 
 PUPAIM-0.3.1/PUPAIM/man/hilldeboeranalysis.Rd          |   10 
 PUPAIM-0.3.1/PUPAIM/man/jossens.LM.Rd                  |    2 
 PUPAIM-0.3.1/PUPAIM/man/jossensanalysis.Rd             |   14 -
 PUPAIM-0.3.1/PUPAIM/man/jovanovic.LM.Rd                |    4 
 PUPAIM-0.3.1/PUPAIM/man/kahnanalysis.Rd                |    2 
 PUPAIM-0.3.1/PUPAIM/man/kiselev.LM.Rd                  |    8 
 PUPAIM-0.3.1/PUPAIM/man/kiselevanalysis.Rd             |    8 
 PUPAIM-0.3.1/PUPAIM/man/koblecarrigan.LM.Rd            |    2 
 PUPAIM-0.3.1/PUPAIM/man/langmuir1.LM.Rd                |only
 PUPAIM-0.3.1/PUPAIM/man/langmuir2.LM.Rd                |only
 PUPAIM-0.3.1/PUPAIM/man/langmuir3.LM.Rd                |only
 PUPAIM-0.3.1/PUPAIM/man/langmuir4.LM.Rd                |only
 PUPAIM-0.3.1/PUPAIM/man/langmuiranalysis.Rd            |only
 PUPAIM-0.3.1/PUPAIM/man/marckzewskijaroniecanalysis.Rd |    2 
 PUPAIM-0.3.1/PUPAIM/man/radkeprausnitzanalysis.Rd      |    4 
 PUPAIM-0.3.1/PUPAIM/man/temkin.LM.Rd                   |    4 
 PUPAIM-0.3.1/PUPAIM/man/temkinanalysis.Rd              |   48 ----
 PUPAIM-0.3.1/PUPAIM/man/tothanalysis.Rd                |only
 PUPAIM-0.3.1/PUPAIM/man/volmeranalysis.Rd              |   10 
 PUPAIM-0.3.1/PUPAIM/man/webervanvlietanalysis.Rd       |    8 
 PUPAIM-0.3.1/PUPAIM/vignettes/PUPAIM.Rmd               |    9 
 109 files changed, 537 insertions(+), 432 deletions(-)

More information about PUPAIM at CRAN
Permanent link

New package traitdataform with initial version 0.6.8
Package: traitdataform
Title: Formatting and Harmonizing Ecological Trait-Data
Version: 0.6.8
Date: 2022-05-25
Description: Assistance for handling ecological trait data and applying the Ecological Trait-Data Standard terminology (Schneider et al. 2019 <doi:10.1111/2041-210X.13288>). There are two major use cases: (1) preparation of own trait datasets for publication, and (2) harmonizing trait datasets from different sources by re-formatting them into a unified format. See 'traitdataform' website for full documentation.
License: MIT + file LICENSE
LazyData: TRUE
Depends: R (>= 2.10)
Imports: data.table, stats, reshape2, taxize, getPass, units, suppdata, curl, XML, RCurl, plyr
URL: https://ecologicaltraitdata.github.io/traitdataform/, https://github.com/ecologicaltraitdata/traitdataform
BugReports: https://github.com/ecologicaltraitdata/traitdataform/issues
VignetteBuilder: knitr
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat
NeedsCompilation: no
Packaged: 2022-05-25 14:26:48 UTC; Flo
Author: Florian D. Schneider [aut, cre] , Caterina Penone [ctb] , Andreas Ostrowski [ctb] , Dennis Heimann [ctb], Felix Neff [ctb], Markus J. Ankenbrand [ctb], Jessica Burnett [ctb], Inaki Ucar [ctb], Matthias Grenie [ctb]
Maintainer: Florian D. Schneider <florian.dirk.schneider@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-25 15:10:02 UTC

More information about traitdataform at CRAN
Permanent link

Package StereoMorph updated to version 1.6.7 with previous version 1.6.5 dated 2022-05-12

Title: Stereo Camera Calibration and Reconstruction
Description: Functions for the collection of 3D points and curves using a stereo camera setup.
Author: Aaron Olsen, Annat Haber
Maintainer: Aaron Olsen <aarolsen@gmail.com>

Diff between StereoMorph versions 1.6.5 dated 2022-05-12 and 1.6.7 dated 2022-05-25

 DESCRIPTION                                             |    8 -
 MD5                                                     |   16 +--
 R/XML4R2listLines.R                                     |    9 +
 R/digitizeImages.R                                      |    2 
 R/list2XML4R.R                                          |   81 ++++++++--------
 R/readShapes.R                                          |    6 -
 R/readXMLLines.R                                        |    9 +
 inst/extdata/apps/digitizeImages/session_parameters.txt |    2 
 man/StereoMorph-package.Rd                              |    4 
 9 files changed, 81 insertions(+), 56 deletions(-)

More information about StereoMorph at CRAN
Permanent link

Package pogit updated to version 1.3.0 with previous version 1.2.0 dated 2019-01-17

Title: Bayesian Variable Selection for a Poisson-Logistic Model
Description: Bayesian variable selection for regression models of under-reported count data as well as for (overdispersed) Poisson, negative binomal and binomial logit regression models using spike and slab priors.
Author: Michaela Dvorzak [aut, cre], Helga Wagner [aut]
Maintainer: Michaela Dvorzak <m.dvorzak@gmx.at>

Diff between pogit versions 1.2.0 dated 2019-01-17 and 1.3.0 dated 2022-05-25

 DESCRIPTION                |   11 ++++++-----
 MD5                        |   45 +++++++++++++++++++++++----------------------
 R/logitBvs.R               |   13 ++++++++-----
 R/negbinBvs.R              |   11 +++++++----
 R/pogitBvs.R               |   16 ++++++++++------
 R/poissonBvs.R             |   15 +++++++++------
 R/simul1.R                 |    2 +-
 R/simul2.R                 |    2 +-
 build                      |only
 inst/CITATION              |    2 +-
 inst/NEWS.Rd               |    6 ++++++
 man/cervical.Rd            |    6 ++++--
 man/cervical_validation.Rd |    6 ++++--
 man/logitBvs.Rd            |   32 ++++++++++++++++++++++----------
 man/negbinBvs.Rd           |   27 +++++++++++++++++++--------
 man/plot.pogit.Rd          |   12 ++++++++++--
 man/pogit-package.Rd       |    4 ++--
 man/pogitBvs.Rd            |   38 ++++++++++++++++++++++++++------------
 man/poissonBvs.Rd          |   29 ++++++++++++++++++++---------
 man/simul1.Rd              |    8 +++++---
 man/simul2.Rd              |    8 +++++---
 man/simul_binomial.Rd      |    6 ++++--
 man/simul_pois1.Rd         |    6 ++++--
 man/simul_pois2.Rd         |    6 ++++--
 24 files changed, 201 insertions(+), 110 deletions(-)

More information about pogit at CRAN
Permanent link

Package habCluster updated to version 1.0.5 with previous version 1.0.3 dated 2022-05-18

Title: Detecting Spatial Clustering Based on Connection Cost Between Grids
Description: Based on landscape connectivity, spatial boundaries were identified using community detection algorithm at grid level. Methods using raster as input and the value of each cell of the raster is the "smoothness" to indicate how easy the cell connecting with neighbor cells. Details about the 'habCluster' package methods can be found in Zhang et al. <bioRxiv:2022.05.06.490926>.
Author: Qiang Dai
Maintainer: Qiang Dai <daiqiang@cib.ac.cn>

Diff between habCluster versions 1.0.3 dated 2022-05-18 and 1.0.5 dated 2022-05-25

 DESCRIPTION                              |    8 ++++----
 MD5                                      |   24 +++++++++++++-----------
 NEWS.md                                  |    8 ++++++++
 R/cluster.R                              |    6 +++---
 R/raster2Graph.R                         |   13 ++++++++++++-
 inst/WORDLIST                            |only
 inst/doc/introduction-to-habCluster.html |    6 +++---
 man/cluster.Rd                           |    4 +++-
 man/figures/README-Greedy_plot-1.png     |binary
 man/figures/README-cluster-1.png         |binary
 man/figures/README-discard-1.png         |binary
 man/raster2Graph.Rd                      |    4 +++-
 src/getEdge.cpp                          |    2 +-
 tests/spelling.R                         |only
 14 files changed, 50 insertions(+), 25 deletions(-)

More information about habCluster at CRAN
Permanent link

Package GeneralizedUmatrix updated to version 1.2.4 with previous version 1.2.2 dated 2021-01-12

Title: Credible Visualization for Two-Dimensional Projections of Data
Description: Projections are common dimensionality reduction methods, which represent high-dimensional data in a two-dimensional space. However, when restricting the output space to two dimensions, which results in a two dimensional scatter plot (projection) of the data, low dimensional similarities do not represent high dimensional distances coercively [Thrun, 2018] <DOI: 10.1007/978-3-658-20540-9>. This could lead to a misleading interpretation of the underlying structures [Thrun, 2018]. By means of the 3D topographic map the generalized Umatrix is able to depict errors of these two-dimensional scatter plots. The package is derived from the book of Thrun, M.C.: "Projection Based Clustering through Self-Organization and Swarm Intelligence" (2018) <DOI:10.1007/978-3-658-20540-9> and the main algorithm called simplified self-organizing map for dimensionality reduction methods is published in <DOI: 10.1016/j.mex.2020.101093>.
Author: Michael Thrun [aut, cre, cph] , Felix Pape [ctb, ctr], Tim Schreier [ctb, ctr], Luis Winckelman [ctb, ctr], Quirin Stier [ctb, ctr], Alfred Ultsch [ths]
Maintainer: Michael Thrun <m.thrun@gmx.net>

Diff between GeneralizedUmatrix versions 1.2.2 dated 2021-01-12 and 1.2.4 dated 2022-05-25

 GeneralizedUmatrix-1.2.2/GeneralizedUmatrix/src/packagename_init.c           |only
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/DESCRIPTION                      |   20 
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/MD5                              |   45 
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/NAMESPACE                        |   29 
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/R/DefaultColorSequence.R         |only
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/R/GeneralizedUmatrix.R           |  695 
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/R/LowLand.R                      |only
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/R/RcppExports.R                  |    4 
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/R/ReduceToLowLand.R              |only
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/R/TopviewTopographicMap.R        |  264 
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/R/Uheights4Data.R                |only
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/R/UniqueBestMatchingUnits.R      |only
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/R/plotTopographicMap.R           |    2 
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/R/sESOM4BMUs.R                   |  202 
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/build/partial.rdb                |binary
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/build/vignette.rds               |binary
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/inst/doc/GeneralizedUmatrix.html |12817 ++++++----
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/man/GeneralizedUmatrix.Rd        |   19 
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/man/LowLand.Rd                   |only
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/man/ReduceToLowLand.Rd           |only
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/man/TopviewTopographicMap.Rd     |   26 
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/man/Uheights4Data.Rd             |only
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/man/UniqueBestMatchingUnits.Rd   |only
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/man/sESOM4BMUs.Rd                |   11 
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/src/Makevars                     |   22 
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/src/Makevars.win                 |   27 
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/src/RcppExports.cpp              |   37 
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/src/trainstepC.cpp               |   15 
 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/src/trainstepC2.cpp              |only
 29 files changed, 9070 insertions(+), 5165 deletions(-)

More information about GeneralizedUmatrix at CRAN
Permanent link

New package discnorm with initial version 0.2.1
Package: discnorm
Title: Test for Discretized Normality in Ordinal Data
Version: 0.2.1
Description: Tests whether multivariate ordinal data may stem from discretizing a multivariate normal distribution. The test is described by Foldnes and Grønneberg (2019) <doi:10.1080/10705511.2019.1673168>. In addition, an adjusted polychoric correlation estimator is provided that takes marginal knowledge into account, as described by Grønneberg and Foldnes (2022) <doi:10.1037/met0000495>.
License: GPL (>= 2)
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Imports: lavaan (>= 0.6.10), arules, sirt, MASS, pbivnorm, cubature, copula, mnormt, GoFKernel
NeedsCompilation: no
Packaged: 2022-05-25 10:00:38 UTC; njaalfoldnes
Author: Njål Foldnes [aut, cre], Steffen Groenneberg [aut]
Maintainer: Njål Foldnes <njal.foldnes@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-25 15:20:02 UTC

More information about discnorm at CRAN
Permanent link

New package cdcatR with initial version 1.0.6
Package: cdcatR
Title: Cognitive Diagnostic Computerized Adaptive Testing
Version: 1.0.6
Date: 2022-05-25
Description: Provides a set of functions for conducting cognitive diagnostic computerized adaptive testing applications (Chen, 2009) <DOI:10.1007/s11336-009-9123-2>). It includes different item selection rules such us the global discrimination index (Kaplan, de la Torre, and Barrada (2015) <DOI:10.1177/0146621614554650>) and the nonparametric selection method (Chang, Chiu, and Tsai (2019) <DOI:10.1177/0146621618813113>), as well as several stopping rules. Functions for generating item banks and responses are also provided. To guide item bank calibration, model comparison at the item level can be conducted using the two-step likelihood ratio test statistic by Sorrel, de la Torre, Abad and Olea (2017) <DOI:10.1027/1614-2241/a000131>.
License: GPL-3
LazyData: TRUE
Depends: R (>= 3.5.0)
Imports: cdmTools (>= 1.0.1), GDINA (>= 2.2.0), ggplot2 (>= 3.3.0), cowplot, foreach, doSNOW, NPCD, stats
Suggests: CDM
URL: https://github.com/miguel-sorrel/cdcatR
BugReports: https://github.com/miguel-sorrel/cdcatR/issues
Encoding: UTF-8
Author: Miguel A. Sorrel [aut, cre, cph], Pablo Najera [aut, cph], Francisco J. Abad [aut, cph]
Maintainer: Miguel A. Sorrel <miguel.sorrel@uam.es>
NeedsCompilation: no
Packaged: 2022-05-25 09:44:50 UTC; msorr
Repository: CRAN
Date/Publication: 2022-05-25 15:10:08 UTC

More information about cdcatR at CRAN
Permanent link

Package bpr updated to version 1.0.5 with previous version 1.0.4 dated 2021-09-22

Title: Fitting Bayesian Poisson Regression
Description: Posterior sampling and inference for Bayesian Poisson regression models. The model specification makes use of Gaussian (or conditionally Gaussian) prior distributions on the regression coefficients. Details on the algorithm are found in D'Angelo and Canale (2021) <arXiv:2109.09520>.
Author: Laura D'Angelo
Maintainer: Laura D'Angelo <laura.dangelo@live.com>

Diff between bpr versions 1.0.4 dated 2021-09-22 and 1.0.5 dated 2022-05-25

 DESCRIPTION                         |   10 +++---
 MD5                                 |    8 ++---
 build/partial.rdb                   |binary
 src/is_polya_adaptive.cpp           |   23 +++++---------
 src/is_polya_horseshoe_adaptive.cpp |   56 +++++++++++++-----------------------
 5 files changed, 39 insertions(+), 58 deletions(-)

More information about bpr at CRAN
Permanent link

New package alookr with initial version 0.3.6
Package: alookr
Title: Model Classifier for Binary Classification
Version: 0.3.6
Description: A collection of tools that support data splitting, predictive modeling, and model evaluation. A typical function is to split a dataset into a training dataset and a test dataset. Then compare the data distribution of the two datasets. Another feature is to support the development of predictive models and to compare the performance of several predictive models, helping to select the best model.
Depends: R (>= 3.2.0), ggplot2 (>= 3.0.0), randomForest
Imports: caTools, cli (>= 1.1.0), dlookr, dplyr (>= 0.7.6), future, ggmosaic, MASS, MLmetrics, methods, party, purrr, ROCR, ranger, rlang, rpart, stats, tibble, tidyr, tidyselect, xgboost, glmnet
Suggests: knitr, ISLR, mice, mlbench, rmarkdown, stringi
Author: Choonghyun Ryu [aut, cre]
Maintainer: Choonghyun Ryu <choonghyun.ryu@gmail.com>
BugReports: https://github.com/choonghyunryu/alookr/issues
License: GPL-2 | file LICENSE
Encoding: UTF-8
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2022-05-25 07:14:47 UTC; choonghyunryu
Repository: CRAN
Date/Publication: 2022-05-25 15:20:05 UTC

More information about alookr at CRAN
Permanent link

Package radmixture (with last version 0.0.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2017-03-13 0.0.1

Permanent link
Package RFpredInterval updated to version 1.0.6 with previous version 1.0.5 dated 2022-01-20

Title: Prediction Intervals with Random Forests and Boosted Forests
Description: Implements various prediction interval methods with random forests and boosted forests. The package has two main functions: pibf() produces prediction intervals with boosted forests (PIBF) as described in Alakus et al. (2021) <arXiv:2106.08217> and rfpi() builds 15 distinct variations of prediction intervals with random forests (RFPI) proposed by Roy and Larocque (2020) <doi:10.1177/0962280219829885>.
Author: Cansu Alakus [aut, cre], Denis Larocque [aut], Aurelie Labbe [aut], Hemant Ishwaran [ctb] , Udaya B. Kogalur [ctb]
Maintainer: Cansu Alakus <cansu.alakus@hec.ca>

Diff between RFpredInterval versions 1.0.5 dated 2022-01-20 and 1.0.6 dated 2022-05-25

 DESCRIPTION                   |    8 ++++----
 MD5                           |   24 ++++++++++++------------
 NEWS.md                       |    3 +++
 R/RFpredInterval-package.R    |   30 +++++++++++++++---------------
 R/formpi.functions.R          |    2 +-
 R/piall.R                     |   29 +++++++++++++++++++++++++----
 R/pibf.R                      |   29 +++++++++++++++++++++++++----
 R/rfpi.R                      |   29 +++++++++++++++++++++++++----
 R/utilities.R                 |   20 ++++++++++----------
 README.md                     |    2 --
 configure                     |   18 +++++++++---------
 configure.ac                  |    2 +-
 man/RFpredInterval-package.Rd |   29 +++++++++++++++--------------
 13 files changed, 145 insertions(+), 80 deletions(-)

More information about RFpredInterval at CRAN
Permanent link

Package GAIPE updated to version 1.1 with previous version 1.0 dated 2013-04-17

Title: Graphical Extension with Accuracy in Parameter Estimation (GAIPE)
Description: Implements graphical extension with accuracy in parameter estimation (AIPE) on RMSEA for sample size planning in structural equation modeling based on Lin, T.-Z. & Weng, L.-J. (2014) <doi: 10.1080/10705511.2014.915380>. And, it can also implement AIPE on RMSEA and power analysis on RMSEA.
Author: Tzu-Yao Lin
Maintainer: Yao Lin <zaiyaolin@gmail.com>

Diff between GAIPE versions 1.0 dated 2013-04-17 and 1.1 dated 2022-05-25

 DESCRIPTION          |   20 +---
 MD5                  |   23 ++--
 NAMESPACE            |    6 +
 NEWS                 |only
 R/AIPE.RMSEA.R       |   38 +++++--
 R/CI.RMSEA.R         |  201 ++++++++++++++++++++++++++++++++--------
 R/GAIPE.RMSEA.R      |  253 ++++++++++++++++++++++++++++++++-------------------
 R/PA.RMSEA.R         |   91 ++++++++++++------
 man/AIPE.RMSEA.Rd    |    4 
 man/CI.RMSEA.Rd      |    2 
 man/GAIPE-package.Rd |   50 +++++-----
 man/GAIPE.RMSEA.Rd   |  128 ++++++++++++-------------
 man/PA.RMSEA.Rd      |  104 ++++++++++++--------
 13 files changed, 585 insertions(+), 335 deletions(-)

More information about GAIPE at CRAN
Permanent link

Package RcppAPT updated to version 0.0.9 with previous version 0.0.8 dated 2021-12-04

Title: 'Rcpp' Interface to the APT Package Manager
Description: The 'APT Package Management System' provides Debian and Debian-derived Linux systems with a powerful system to resolve package dependencies. This package offers access directly from R. This can only work on a system with a suitable 'libapt-pkg-dev' installation so functionality is curtailed if such a library is not found.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppAPT versions 0.0.8 dated 2021-12-04 and 0.0.9 dated 2022-05-25

 ChangeLog                     |   26 +
 DESCRIPTION                   |    8 
 MD5                           |   28 -
 build/vignette.rds            |binary
 cleanup                       |    2 
 inst/NEWS.Rd                  |    7 
 inst/doc/binnmuAfterR340.html |  863 +++++++++++++++++++++---------------------
 inst/doc/binnmuAfterR340.md   |    2 
 inst/scripts/configure.bash   |    4 
 src/Makevars.in               |    2 
 src/buildDepends.cpp          |   23 -
 src/getPackages.cpp           |    6 
 src/hasPackage.cpp            |   10 
 src/reverseDepends.cpp        |    7 
 vignettes/binnmuAfterR340.md  |    2 
 15 files changed, 509 insertions(+), 481 deletions(-)

More information about RcppAPT at CRAN
Permanent link

Package monotone updated to version 0.1.2 with previous version 0.1.1 dated 2022-05-25

Title: Performs Monotone Regression
Description: The monotone package contains a fast up-and-down-blocks implementation for the pool-adjacent-violators algorithm for simple linear ordered monotone regression, including two spin-off functions for unimodal and bivariate monotone regression (see <doi:10.18637/jss.v102.c01>).
Author: Frank Busing [aut, cre], Juan Claramunt Gonzalez [aut]
Maintainer: Frank Busing <busing@fsw.leidenuniv.nl>

Diff between monotone versions 0.1.1 dated 2022-05-25 and 0.1.2 dated 2022-05-25

 DESCRIPTION     |    6 +++---
 MD5             |   10 +++++-----
 R/legacy.R      |    2 +-
 R/monotone.R    |    2 +-
 man/legacy.Rd   |    2 +-
 man/monotone.Rd |    2 +-
 6 files changed, 12 insertions(+), 12 deletions(-)

More information about monotone at CRAN
Permanent link

Package MLGL updated to version 0.6.7 with previous version 0.6.5 dated 2020-11-28

Title: Multi-Layer Group-Lasso
Description: It implements a new procedure of variable selection in the context of redundancy between explanatory variables, which holds true with high dimensional data (Grimonprez et al. (2018) <https://hal.inria.fr/hal-01857242>).
Author: Quentin Grimonprez [aut, cre], Samuel Blanck [ctb], Alain Celisse [ths], Guillemette Marot [ths], Yi Yang [ctb], Hui Zou [ctb]
Maintainer: Quentin Grimonprez <quentingrim@yahoo.fr>

Diff between MLGL versions 0.6.5 dated 2020-11-28 and 0.6.7 dated 2022-05-25

 DESCRIPTION              |   10 +++----
 MD5                      |   64 +++++++++++++++++++++++------------------------
 NAMESPACE                |    6 ++--
 NEWS                     |    9 ++++++
 R/HMT.R                  |   12 +++++---
 R/MLGL-package.R         |   12 +++++---
 R/MLGL.R                 |   48 ++++++++++++++++++++++-------------
 R/cv.MLGL.R              |   12 +++++---
 R/fullProcess.R          |   30 ++++++++++++++--------
 R/hierarchicalFDR.R      |   23 ++++++++++------
 R/hierarchicalFWER.R     |   15 +++++------
 R/overlap.R              |    9 ++++--
 R/plot.R                 |    2 -
 R/predict.R              |   25 ++++++++++++++++--
 R/print.R                |   13 ++++-----
 R/simuBlockGaussian.R    |    3 +-
 R/stability.R            |   15 +++++++----
 R/uniqueGroupHclust.R    |    2 -
 R/utilities.R            |    6 ++--
 man/HMT.Rd               |    3 +-
 man/MLGL-package.Rd      |   12 +++++---
 man/MLGL.Rd              |   32 +++++++++++++++--------
 man/cv.MLGL.Rd           |    6 ++--
 man/fullProcess.Rd       |   23 +++++++++++-----
 man/hierarchicalFDR.Rd   |   11 +++++---
 man/hierarchicalFWER.Rd  |    8 +++--
 man/listToMatrix.Rd      |    6 ++--
 man/overlapgglasso.Rd    |    9 ++++--
 man/predict.MLGL.Rd      |   13 ++++++++-
 man/predict.cv.MLGL.Rd   |    3 +-
 man/selFDR.Rd            |    6 ++--
 man/simuBlockGaussian.Rd |    3 +-
 man/stability.MLGL.Rd    |    9 ++++--
 33 files changed, 296 insertions(+), 164 deletions(-)

More information about MLGL at CRAN
Permanent link

Package mlr3viz updated to version 0.5.9 with previous version 0.5.8 dated 2022-04-04

Title: Visualizations for 'mlr3'
Description: Provides visualizations for 'mlr3' objects such as tasks, predictions, resample results or benchmark results via the autoplot() generic of 'ggplot2'. The returned 'ggplot' objects are intended to provide sensible defaults, yet can easily be customized to create camera-ready figures. Visualizations include barplots, boxplots, histograms, ROC curves, and Precision-Recall curves.
Author: Michel Lang [cre, aut] , Patrick Schratz [aut] , Raphael Sonabend [aut] , Marc Becker [aut] , Jakob Richter [aut] , Damir Pulatov [ctb]
Maintainer: Michel Lang <michellang@gmail.com>

Diff between mlr3viz versions 0.5.8 dated 2022-04-04 and 0.5.9 dated 2022-05-25

 mlr3viz-0.5.8/mlr3viz/R/PredictionSurv.R                   |only
 mlr3viz-0.5.8/mlr3viz/R/TaskDens.R                         |only
 mlr3viz-0.5.8/mlr3viz/R/TaskSurv.R                         |only
 mlr3viz-0.5.8/mlr3viz/man/autoplot.PredictionSurv.Rd       |only
 mlr3viz-0.5.8/mlr3viz/man/autoplot.TaskDens.Rd             |only
 mlr3viz-0.5.8/mlr3viz/man/autoplot.TaskSurv.Rd             |only
 mlr3viz-0.5.8/mlr3viz/tests/testthat/_snaps/PredictionSurv |only
 mlr3viz-0.5.8/mlr3viz/tests/testthat/_snaps/TaskDens       |only
 mlr3viz-0.5.8/mlr3viz/tests/testthat/test_PredictionSurv.R |only
 mlr3viz-0.5.8/mlr3viz/tests/testthat/test_TaskDens.R       |only
 mlr3viz-0.5.8/mlr3viz/tests/testthat/test_TaskSurv.R       |only
 mlr3viz-0.5.9/mlr3viz/DESCRIPTION                          |   25 ++++------
 mlr3viz-0.5.9/mlr3viz/MD5                                  |   32 +++----------
 mlr3viz-0.5.9/mlr3viz/NAMESPACE                            |    5 --
 mlr3viz-0.5.9/mlr3viz/NEWS.md                              |    8 +++
 mlr3viz-0.5.9/mlr3viz/R/bibentries.R                       |   11 ----
 mlr3viz-0.5.9/mlr3viz/README.md                            |   10 ++--
 mlr3viz-0.5.9/mlr3viz/build/partial.rdb                    |binary
 mlr3viz-0.5.9/mlr3viz/man/figures/README-demo-1.png        |binary
 mlr3viz-0.5.9/mlr3viz/man/figures/README-demo-2.png        |binary
 20 files changed, 33 insertions(+), 58 deletions(-)

More information about mlr3viz at CRAN
Permanent link

Package mlr3learners updated to version 0.5.3 with previous version 0.5.2 dated 2022-01-22

Title: Recommended Learners for 'mlr3'
Description: Recommended Learners for 'mlr3'. Extends 'mlr3' with interfaces to essential machine learning packages on CRAN. This includes, but is not limited to: (penalized) linear and logistic regression, linear and quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support vector machines, and gradient boosting.
Author: Michel Lang [cre, aut] , Quay Au [aut] , Stefan Coors [aut] , Patrick Schratz [aut]
Maintainer: Michel Lang <michellang@gmail.com>

Diff between mlr3learners versions 0.5.2 dated 2022-01-22 and 0.5.3 dated 2022-05-25

 mlr3learners-0.5.2/mlr3learners/R/LearnerSurvCVGlmnet.R                        |only
 mlr3learners-0.5.2/mlr3learners/R/LearnerSurvGlmnet.R                          |only
 mlr3learners-0.5.2/mlr3learners/R/LearnerSurvRanger.R                          |only
 mlr3learners-0.5.2/mlr3learners/R/LearnerSurvXgboost.R                         |only
 mlr3learners-0.5.2/mlr3learners/inst/paramtest/test_paramtest_surv.cv_glmnet.R |only
 mlr3learners-0.5.2/mlr3learners/inst/paramtest/test_paramtest_surv.glmnet.R    |only
 mlr3learners-0.5.2/mlr3learners/inst/paramtest/test_paramtest_surv.ranger.R    |only
 mlr3learners-0.5.2/mlr3learners/inst/paramtest/test_paramtest_surv.xgboost.R   |only
 mlr3learners-0.5.2/mlr3learners/man/mlr_learners_surv.cv_glmnet.Rd             |only
 mlr3learners-0.5.2/mlr3learners/man/mlr_learners_surv.glmnet.Rd                |only
 mlr3learners-0.5.2/mlr3learners/man/mlr_learners_surv.ranger.Rd                |only
 mlr3learners-0.5.2/mlr3learners/man/mlr_learners_surv.xgboost.Rd               |only
 mlr3learners-0.5.2/mlr3learners/tests/testthat/test_surv_cv_glmnet.R           |only
 mlr3learners-0.5.2/mlr3learners/tests/testthat/test_surv_glmnet.R              |only
 mlr3learners-0.5.2/mlr3learners/tests/testthat/test_surv_ranger.R              |only
 mlr3learners-0.5.2/mlr3learners/tests/testthat/test_surv_xgboost.R             |only
 mlr3learners-0.5.3/mlr3learners/DESCRIPTION                                    |   16 -
 mlr3learners-0.5.3/mlr3learners/MD5                                            |   96 ++----
 mlr3learners-0.5.3/mlr3learners/NAMESPACE                                      |    4 
 mlr3learners-0.5.3/mlr3learners/NEWS.md                                        |    6 
 mlr3learners-0.5.3/mlr3learners/R/LearnerClassifGlmnet.R                       |    4 
 mlr3learners-0.5.3/mlr3learners/R/LearnerClassifKKNN.R                         |   22 +
 mlr3learners-0.5.3/mlr3learners/R/LearnerClassifMultinom.R                     |    5 
 mlr3learners-0.5.3/mlr3learners/R/LearnerClassifNnet.R                         |    7 
 mlr3learners-0.5.3/mlr3learners/R/LearnerClassifRanger.R                       |    6 
 mlr3learners-0.5.3/mlr3learners/R/LearnerClassifXgboost.R                      |    2 
 mlr3learners-0.5.3/mlr3learners/R/LearnerRegrKKNN.R                            |   22 +
 mlr3learners-0.5.3/mlr3learners/R/LearnerRegrRanger.R                          |    4 
 mlr3learners-0.5.3/mlr3learners/R/LearnerRegrXgboost.R                         |    2 
 mlr3learners-0.5.3/mlr3learners/R/zzz.R                                        |    6 
 mlr3learners-0.5.3/mlr3learners/README.md                                      |   11 
 mlr3learners-0.5.3/mlr3learners/build/partial.rdb                              |binary
 mlr3learners-0.5.3/mlr3learners/inst/paramtest/test_paramtest_classif.kknn.R   |    3 
 mlr3learners-0.5.3/mlr3learners/inst/paramtest/test_paramtest_regr.kknn.R      |    3 
 mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.cv_glmnet.Rd          |  116 ++------
 mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.glmnet.Rd             |  114 ++------
 mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.kknn.Rd               |   80 ++---
 mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.lda.Rd                |   71 ++---
 mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.log_reg.Rd            |   86 ++----
 mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.multinom.Rd           |   92 ++----
 mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.naive_bayes.Rd        |   67 ++--
 mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.nnet.Rd               |   80 ++---
 mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.qda.Rd                |   69 ++---
 mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.ranger.Rd             |  109 ++-----
 mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.svm.Rd                |   80 ++---
 mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.xgboost.Rd            |  138 ++--------
 mlr3learners-0.5.3/mlr3learners/man/mlr_learners_regr.cv_glmnet.Rd             |  117 ++------
 mlr3learners-0.5.3/mlr3learners/man/mlr_learners_regr.glmnet.Rd                |  119 ++------
 mlr3learners-0.5.3/mlr3learners/man/mlr_learners_regr.kknn.Rd                  |   80 ++---
 mlr3learners-0.5.3/mlr3learners/man/mlr_learners_regr.km.Rd                    |   92 ++----
 mlr3learners-0.5.3/mlr3learners/man/mlr_learners_regr.lm.Rd                    |   85 ++----
 mlr3learners-0.5.3/mlr3learners/man/mlr_learners_regr.ranger.Rd                |  109 ++-----
 mlr3learners-0.5.3/mlr3learners/man/mlr_learners_regr.svm.Rd                   |   78 ++---
 mlr3learners-0.5.3/mlr3learners/man/mlr_learners_regr.xgboost.Rd               |  138 ++--------
 mlr3learners-0.5.3/mlr3learners/tests/testthat/helper.R                        |    4 
 mlr3learners-0.5.3/mlr3learners/tests/testthat/test_classif_kknn.R             |    6 
 mlr3learners-0.5.3/mlr3learners/tests/testthat/test_regr_kknn.R                |    6 
 57 files changed, 760 insertions(+), 1395 deletions(-)

More information about mlr3learners at CRAN
Permanent link

New package africamonitor with initial version 0.1.2
Package: africamonitor
Title: Africa Macroeconomic Monitor Database API
Version: 0.1.2
Description: An R API providing access to a relational database with macroeconomic data for Africa. The database is maintained at the Kiel Institute for the World Economy. See <https://africamonitor.ifw-kiel.de/>.
URL: https://africamonitor.ifw-kiel.de/
License: GPL-3
Encoding: UTF-8
Imports: DBI, RMySQL, data.table, collapse
Depends: R (>= 3.3.0)
LazyData: true
NeedsCompilation: no
Packaged: 2022-05-24 21:19:17 UTC; sebastiankrantz
Author: Sebastian Krantz [aut, cre]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Repository: CRAN
Date/Publication: 2022-05-25 12:00:02 UTC

More information about africamonitor at CRAN
Permanent link

Package seqHMM updated to version 1.2.1-1 with previous version 1.2.0 dated 2021-10-18

Title: Mixture Hidden Markov Models for Social Sequence Data and Other Multivariate, Multichannel Categorical Time Series
Description: Designed for fitting hidden (latent) Markov models and mixture hidden Markov models for social sequence data and other categorical time series. Also some more restricted versions of these type of models are available: Markov models, mixture Markov models, and latent class models. The package supports models for one or multiple subjects with one or multiple parallel sequences (channels). External covariates can be added to explain cluster membership in mixture models. The package provides functions for evaluating and comparing models, as well as functions for visualizing of multichannel sequence data and hidden Markov models. Models are estimated using maximum likelihood via the EM algorithm and/or direct numerical maximization with analytical gradients. All main algorithms are written in C++ with support for parallel computation. Documentation is available via several vignettes in this page, and the paper by Helske and Helske (2019, <doi:10.18637/jss.v088.i03>).
Author: Jouni Helske [aut, cre] , Satu Helske [aut]
Maintainer: Jouni Helske <jouni.helske@iki.fi>

Diff between seqHMM versions 1.2.0 dated 2021-10-18 and 1.2.1-1 dated 2022-05-25

 seqHMM-1.2.0/seqHMM/NEWS                                     |only
 seqHMM-1.2.1-1/seqHMM/DESCRIPTION                            |   10 
 seqHMM-1.2.1-1/seqHMM/MD5                                    |  171 
 seqHMM-1.2.1-1/seqHMM/NEWS.md                                |only
 seqHMM-1.2.1-1/seqHMM/R/build_mm.R                           |   71 
 seqHMM-1.2.1-1/seqHMM/R/build_mmm.R                          |  500 
 seqHMM-1.2.1-1/seqHMM/R/check_deprecated_args.R              |    6 
 seqHMM-1.2.1-1/seqHMM/R/colorpalette.R                       |   58 
 seqHMM-1.2.1-1/seqHMM/R/estimate_coef.R                      |  126 
 seqHMM-1.2.1-1/seqHMM/R/fit_model.R                          |    4 
 seqHMM-1.2.1-1/seqHMM/R/gridplot.R                           | 1352 -
 seqHMM-1.2.1-1/seqHMM/R/hidden_paths.R                       |   21 
 seqHMM-1.2.1-1/seqHMM/R/mssplot.R                            |  789 
 seqHMM-1.2.1-1/seqHMM/R/plot.hmm.R                           | 1294 -
 seqHMM-1.2.1-1/seqHMM/R/plot.mhmm.R                          |  406 
 seqHMM-1.2.1-1/seqHMM/R/posterior_probs.R                    |   62 
 seqHMM-1.2.1-1/seqHMM/R/seqHMM-package.R                     |   76 
 seqHMM-1.2.1-1/seqHMM/R/simulate_hmm.R                       |  306 
 seqHMM-1.2.1-1/seqHMM/R/ssp.R                                | 1422 -
 seqHMM-1.2.1-1/seqHMM/R/ssplot.R                             |  499 
 seqHMM-1.2.1-1/seqHMM/R/zzz.R                                |   12 
 seqHMM-1.2.1-1/seqHMM/README.md                              |only
 seqHMM-1.2.1-1/seqHMM/build/vignette.rds                     |binary
 seqHMM-1.2.1-1/seqHMM/inst/CITATION                          |   56 
 seqHMM-1.2.1-1/seqHMM/inst/doc/seqHMM.R                      |   84 
 seqHMM-1.2.1-1/seqHMM/inst/doc/seqHMM.Rnw                    |   34 
 seqHMM-1.2.1-1/seqHMM/inst/doc/seqHMM.pdf                    | 4033 ++--
 seqHMM-1.2.1-1/seqHMM/inst/doc/seqHMM_algorithms.Rnw         |  446 
 seqHMM-1.2.1-1/seqHMM/inst/doc/seqHMM_algorithms.pdf         |binary
 seqHMM-1.2.1-1/seqHMM/inst/doc/seqHMM_estimation.Rnw         |  356 
 seqHMM-1.2.1-1/seqHMM/inst/doc/seqHMM_estimation.pdf         |binary
 seqHMM-1.2.1-1/seqHMM/inst/doc/seqHMM_visualization.Rnw      |  808 
 seqHMM-1.2.1-1/seqHMM/inst/doc/seqHMM_visualization.pdf      | 9038 +++++------
 seqHMM-1.2.1-1/seqHMM/man/TraMineR_imports.Rd                |   24 
 seqHMM-1.2.1-1/seqHMM/man/biofam3c.Rd                        |  176 
 seqHMM-1.2.1-1/seqHMM/man/build_hmm.Rd                       |  366 
 seqHMM-1.2.1-1/seqHMM/man/build_lcm.Rd                       |  332 
 seqHMM-1.2.1-1/seqHMM/man/build_mhmm.Rd                      |  502 
 seqHMM-1.2.1-1/seqHMM/man/build_mm.Rd                        |  123 
 seqHMM-1.2.1-1/seqHMM/man/build_mmm.Rd                       |  240 
 seqHMM-1.2.1-1/seqHMM/man/colorpalette.Rd                    |   66 
 seqHMM-1.2.1-1/seqHMM/man/estimate_coef.Rd                   |   36 
 seqHMM-1.2.1-1/seqHMM/man/forward_backward.Rd                |   88 
 seqHMM-1.2.1-1/seqHMM/man/gridplot.Rd                        |  300 
 seqHMM-1.2.1-1/seqHMM/man/hidden_paths.Rd                    |   92 
 seqHMM-1.2.1-1/seqHMM/man/hmm_biofam.Rd                      |  182 
 seqHMM-1.2.1-1/seqHMM/man/hmm_mvad.Rd                        |  134 
 seqHMM-1.2.1-1/seqHMM/man/logLik.hmm.Rd                      |   66 
 seqHMM-1.2.1-1/seqHMM/man/logLik.mhmm.Rd                     |   66 
 seqHMM-1.2.1-1/seqHMM/man/mc_to_sc.Rd                        |  102 
 seqHMM-1.2.1-1/seqHMM/man/mc_to_sc_data.Rd                   |  148 
 seqHMM-1.2.1-1/seqHMM/man/mhmm_biofam.Rd                     |  332 
 seqHMM-1.2.1-1/seqHMM/man/mhmm_mvad.Rd                       |  182 
 seqHMM-1.2.1-1/seqHMM/man/mssplot.Rd                         |  439 
 seqHMM-1.2.1-1/seqHMM/man/plot.hmm.Rd                        |  576 
 seqHMM-1.2.1-1/seqHMM/man/plot.mhmm.Rd                       |  474 
 seqHMM-1.2.1-1/seqHMM/man/plot.ssp.Rd                        |   92 
 seqHMM-1.2.1-1/seqHMM/man/plot_colors.Rd                     |   64 
 seqHMM-1.2.1-1/seqHMM/man/posterior_probs.Rd                 |   62 
 seqHMM-1.2.1-1/seqHMM/man/print.Rd                           |   58 
 seqHMM-1.2.1-1/seqHMM/man/separate_mhmm.Rd                   |   72 
 seqHMM-1.2.1-1/seqHMM/man/seqHMM-deprecated.Rd               |  300 
 seqHMM-1.2.1-1/seqHMM/man/seqHMM.Rd                          |   50 
 seqHMM-1.2.1-1/seqHMM/man/simulate_hmm.Rd                    |  112 
 seqHMM-1.2.1-1/seqHMM/man/simulate_mhmm.Rd                   |  230 
 seqHMM-1.2.1-1/seqHMM/man/simulate_pars.Rd                   |   82 
 seqHMM-1.2.1-1/seqHMM/man/ssp.Rd                             |  551 
 seqHMM-1.2.1-1/seqHMM/man/ssplot.Rd                          |  529 
 seqHMM-1.2.1-1/seqHMM/man/summary.mhmm.Rd                    |  136 
 seqHMM-1.2.1-1/seqHMM/man/trim_model.Rd                      |   96 
 seqHMM-1.2.1-1/seqHMM/man/vcov.mhmm.Rd                       |   78 
 seqHMM-1.2.1-1/seqHMM/src/EM.cpp                             |    2 
 seqHMM-1.2.1-1/seqHMM/src/EMx.cpp                            |    2 
 seqHMM-1.2.1-1/seqHMM/src/logSumExp.cpp                      |    2 
 seqHMM-1.2.1-1/seqHMM/src/log_EM.cpp                         |    2 
 seqHMM-1.2.1-1/seqHMM/src/log_EMx.cpp                        |    2 
 seqHMM-1.2.1-1/seqHMM/src/log_objectivex.cpp                 |    2 
 seqHMM-1.2.1-1/seqHMM/src/log_optCoef.cpp                    |    4 
 seqHMM-1.2.1-1/seqHMM/src/objectivex.cpp                     |    2 
 seqHMM-1.2.1-1/seqHMM/src/optCoef.cpp                        |    4 
 seqHMM-1.2.1-1/seqHMM/src/sa_opt_coef.cpp                    |    2 
 seqHMM-1.2.1-1/seqHMM/vignettes/mhmm.rds                     |only
 seqHMM-1.2.1-1/seqHMM/vignettes/references.bib               | 1172 -
 seqHMM-1.2.1-1/seqHMM/vignettes/references_for_vignettes.bib | 5842 +++----
 seqHMM-1.2.1-1/seqHMM/vignettes/sc_fit.rds                   |only
 seqHMM-1.2.1-1/seqHMM/vignettes/seqHMM.Rnw                   |   34 
 seqHMM-1.2.1-1/seqHMM/vignettes/seqHMM_algorithms.Rnw        |  446 
 seqHMM-1.2.1-1/seqHMM/vignettes/seqHMM_estimation.Rnw        |  356 
 seqHMM-1.2.1-1/seqHMM/vignettes/seqHMM_visualization.Rnw     |  808 
 89 files changed, 19476 insertions(+), 18804 deletions(-)

More information about seqHMM at CRAN
Permanent link

Package r2spss updated to version 0.3.2 with previous version 0.3.1 dated 2022-03-23

Title: Format R Output to Look Like SPSS
Description: Create plots and LaTeX tables that look like SPSS output for use in teaching materials. Rather than copying-and-pasting SPSS output into documents, R code that mocks up SPSS output can be integrated directly into dynamic LaTeX documents with tools such as knitr. Functionality includes statistical techniques that are typically covered in introductory statistics classes: descriptive statistics, common hypothesis tests, ANOVA, and linear regression, as well as box plots, histograms, scatter plots, and line plots (including profile plots).
Author: Andreas Alfons [aut, cre]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>

Diff between r2spss versions 0.3.1 dated 2022-03-23 and 0.3.2 dated 2022-05-25

 DESCRIPTION                |   10 +-
 MD5                        |   29 ++++---
 NEWS                       |    5 +
 R/Eredivisie.R             |only
 R/Exams.R                  |only
 R/r2spss-package.R         |only
 build/partial.rdb          |binary
 build/vignette.rds         |binary
 data/Eredivisie.RData      |binary
 data/Exams.RData           |binary
 inst/doc/r2spss-intro.Rnw  |    2 
 inst/doc/r2spss-intro.pdf  |binary
 man/Eredivisie.Rd          |   94 ++++++++++++-----------
 man/Exams.Rd               |   63 ++++++++-------
 man/r2spss-package.Rd      |   43 +++++-----
 vignettes/r2spss-intro.Rnw |    2 
 vignettes/r2spss.bib       |  178 ++++++++++++++++++++++-----------------------
 17 files changed, 219 insertions(+), 207 deletions(-)

More information about r2spss at CRAN
Permanent link

Package list updated to version 9.2.2 with previous version 9.2.1 dated 2022-05-10

Title: Statistical Methods for the Item Count Technique and List Experiment
Description: Allows researchers to conduct multivariate statistical analyses of survey data with list experiments. This survey methodology is also known as the item count technique or the unmatched count technique and is an alternative to the commonly used randomized response method. The package implements the methods developed by Imai (2011) <doi:10.1198/jasa.2011.ap10415>, Blair and Imai (2012) <doi:10.1093/pan/mpr048>, Blair, Imai, and Lyall (2013) <doi:10.1111/ajps.12086>, Imai, Park, and Greene (2014) <doi:10.1093/pan/mpu017>, Aronow, Coppock, Crawford, and Green (2015) <doi:10.1093/jssam/smu023>, Chou, Imai, and Rosenfeld (2017) <doi:10.1177/0049124117729711>, and Blair, Chou, and Imai (2018) <https://imai.fas.harvard.edu/research/files/listerror.pdf>. This includes a Bayesian MCMC implementation of regression for the standard and multiple sensitive item list experiment designs and a random effects setup, a Bayesian MCMC hierarchical regression model with up to three hierarchical groups, the combined list experiment and endorsement experiment regression model, a joint model of the list experiment that enables the analysis of the list experiment as a predictor in outcome regression models, a method for combining list experiments with direct questions, and methods for diagnosing and adjusting for response error. In addition, the package implements the statistical test that is designed to detect certain failures of list experiments, and a placebo test for the list experiment using data from direct questions.
Author: Graeme Blair [aut, cre], Winston Chou [aut], Kosuke Imai [aut], Bethany Park [ctb], Alexander Coppock [ctb]
Maintainer: Graeme Blair <graeme.blair@gmail.com>

Diff between list versions 9.2.1 dated 2022-05-10 and 9.2.2 dated 2022-05-25

 ChangeLog                             |    3 +
 DESCRIPTION                           |    8 ++--
 MD5                                   |   66 +++++++++++++++++-----------------
 R/ictreg.R                            |    8 +++-
 build/vignette.rds                    |binary
 inst/doc/combined-list.html           |    5 +-
 man/affirm.Rd                         |    6 ++-
 man/combinedListDirect.Rd             |    8 +++-
 man/combinedListExps.Rd               |    6 ++-
 man/comp.listEndorse.Rd               |   11 ++++-
 man/ict.hausman.test.Rd               |    2 -
 man/ict.test.Rd                       |   11 ++++-
 man/ictreg.Rd                         |   36 ++++++++++++++----
 man/ictreg.joint.Rd                   |   13 +++++-
 man/ictregBayes.Rd                    |   43 ++++++++++++++++++----
 man/ictregBayesHier.Rd                |   57 ++++++++++++++++++++++-------
 man/mexico.Rd                         |    6 ++-
 man/mis.Rd                            |    6 ++-
 man/multi.Rd                          |    6 ++-
 man/plot.predict.ictreg.Rd            |   17 ++++++--
 man/predict.ictreg.Rd                 |   19 ++++++++-
 man/predict.ictreg.joint.Rd           |   19 +++++++--
 man/predict.ictregBayes.Rd            |   14 +++++--
 man/predict.ictregBayesHier.Rd        |   12 ++++--
 man/race.Rd                           |    6 ++-
 man/summary.ictreg.Rd                 |    3 -
 src/combine.c                         |    2 -
 src/init.c                            |    4 +-
 tests/testthat/test-combined.R        |    1 
 tests/testthat/test-ict.test.R        |    1 
 tests/testthat/test-ictreg.R          |   21 +++++-----
 tests/testthat/test-ictreg.joint.R    |    1 
 tests/testthat/test-ictregBayes.R     |    3 -
 tests/testthat/test-ictregBayesHier.R |    4 --
 34 files changed, 294 insertions(+), 134 deletions(-)

More information about list at CRAN
Permanent link

Package GMSE updated to version 1.0.0.1 with previous version 0.7.0.0 dated 2021-08-02

Title: Generalised Management Strategy Evaluation Simulator
Description: Integrates game theory and ecological theory to construct social-ecological models that simulate the management of populations and stakeholder actions. These models build off of a previously developed management strategy evaluation (MSE) framework to simulate all aspects of management: population dynamics, manager observation of populations, manager decision making, and stakeholder responses to management decisions. The newly developed generalised management strategy evaluation (GMSE) framework uses genetic algorithms to mimic the decision-making process of managers and stakeholders under conditions of change, uncertainty, and conflict. Simulations can be run using gmse(), gmse_apply(), and gmse_gui() functions.
Author: A. Bradley Duthie [aut, cre] , Adrian Bach [aut], Nils Bunnefeld [aut, fnd] , Jeremy Cusack [ctb] , Isabel Jones [ctb] , Jeroen Minderman [aut] , Erlend Nilsen [ctb] , Ochoa Gabriela [aut] , Rocio Pozo [ctb] , Sarobidy Rakotonarivo [ctb] , Bram Van M [...truncated...]
Maintainer: A. Bradley Duthie <brad.duthie@gmail.com>

Diff between GMSE versions 0.7.0.0 dated 2021-08-02 and 1.0.0.1 dated 2022-05-25

 DESCRIPTION                              |   15 +
 MD5                                      |   44 ++---
 NEWS.md                                  |   13 +
 R/gmse.R                                 |   29 ++-
 R/gmse_apply.R                           |   92 ++++++++--
 R/gmse_apply_summary.R                   |    5 
 README.md                                |    2 
 build/vignette.rds                       |binary
 inst/doc/SI9.pdf                         |only
 inst/doc/SI9.pdf.asis                    |only
 man/gmse.Rd                              |   14 +
 src/game.c                               |  267 ++++++++++++++++++++++++++-----
 src/game.h                               |   19 +-
 src/landscape.c                          |   10 -
 src/manager.c                            |   56 +++---
 src/observation.c                        |   40 ++--
 src/resource.c                           |   20 +-
 src/user.c                               |   74 ++++----
 src/utilities.c                          |    2 
 tests/testthat/test-gmse_sim_annealing.R |only
 tests/testthat/test-manager.R            |    4 
 tests/testthat/test-observation.R        |    8 
 tests/testthat/test-resource.R           |    8 
 tests/testthat/test-user.R               |    6 
 vignettes/SI9.pdf.asis                   |only
 25 files changed, 529 insertions(+), 199 deletions(-)

More information about GMSE at CRAN
Permanent link

Package eurlex updated to version 0.4.2 with previous version 0.4.1 dated 2022-03-31

Title: Retrieve Data on European Union Law
Description: Access to data on European Union laws and court decisions made easy with pre-defined 'SPARQL' queries and 'GET' requests.
Author: Michal Ovadek [aut, cre, cph]
Maintainer: Michal Ovadek <michal.ovadek@gmail.com>

Diff between eurlex versions 0.4.1 dated 2022-03-31 and 0.4.2 dated 2022-05-25

 DESCRIPTION             |    6 +++---
 MD5                     |   12 ++++++------
 NEWS.md                 |   10 ++++++++++
 R/elx_make_query.R      |   31 +++++++++++++++++++++++++++----
 README.md               |    5 +++++
 inst/doc/eurlexpkg.html |   22 +++++++++++-----------
 man/elx_make_query.Rd   |    3 +++
 7 files changed, 65 insertions(+), 24 deletions(-)

More information about eurlex at CRAN
Permanent link

Package binGroup2 updated to version 1.2.4 with previous version 1.2.3 dated 2022-05-16

Title: Identification and Estimation using Group Testing
Description: Methods for the group testing identification problem: 1) Operating characteristics (e.g., expected number of tests) for commonly used hierarchical and array-based algorithms, and 2) Optimal testing configurations for these same algorithms. Methods for the group testing estimation problem: 1) Estimation and inference procedures for an overall prevalence, and 2) Regression modeling for commonly used hierarchical and array-based algorithms.
Author: Brianna Hitt [aut, cre] , Christopher Bilder [aut] , Frank Schaarschmidt [aut] , Brad Biggerstaff [aut] , Christopher McMahan [aut] , Joshua Tebbs [aut] , Boan Zhang [ctb], Michael Black [ctb], Peijie Hou [ctb], Peng Chen [ctb]
Maintainer: Brianna Hitt <brianna.hitt@afacademy.af.edu>

Diff between binGroup2 versions 1.2.3 dated 2022-05-16 and 1.2.4 dated 2022-05-25

 DESCRIPTION                   |   12 ++++++------
 MD5                           |   38 +++++++++++++++++++-------------------
 R/OTC1.R                      |   22 +++++++++++-----------
 R/OTC2.R                      |   18 +++++++++---------
 R/OTCMethodFunctions.R        |   40 ++++++++++++++++++++--------------------
 R/SupportingOTCFunctions.R    |   28 ++++++++++++++--------------
 R/binGroup2-package.R         |   12 ++++++------
 R/designFunctions.R           |    4 ++--
 R/gtReg.R                     |    4 +---
 R/opCharMethodFunctions.R     |    2 +-
 R/operatingCharacteristics2.R |    2 +-
 build/partial.rdb             |binary
 man/OTC1.Rd                   |   22 +++++++++++-----------
 man/OTC2.Rd                   |   16 ++++++++--------
 man/binGroup2.Rd              |   10 +++++-----
 man/designPower.Rd            |    4 ++--
 man/gtReg.Rd                  |    4 +---
 man/plot.OTC.Rd               |   18 +++++++++---------
 man/summary.OTC.Rd            |   22 +++++++++++-----------
 man/summary.opChar.Rd         |    2 +-
 20 files changed, 138 insertions(+), 142 deletions(-)

More information about binGroup2 at CRAN
Permanent link

Package monotone updated to version 0.1.1 with previous version 0.1.0 dated 2021-03-10

Title: Performs Monotone Regression
Description: The monotone package contains a fast up-and-down-blocks implementation for the pool-adjacent-violators algorithm for simple linear ordered monotone regression, including two spin-off functions for unimodal and bivariate monotone regression (see <doi:10.18637/jss.v102.c01>).
Author: Frank Busing [aut, cre], Juan Claramunt Gonzalez [aut]
Maintainer: Frank Busing <busing@fsw.leidenuniv.nl>

Diff between monotone versions 0.1.0 dated 2021-03-10 and 0.1.1 dated 2022-05-25

 DESCRIPTION        |   13 ++++++-------
 MD5                |   19 ++++++++++---------
 R/bimonotone.R     |    5 +++--
 R/legacy.R         |   12 +++++++-----
 R/monotone.R       |    6 ++++--
 R/unimonotone.R    |    5 +++--
 inst               |only
 man/bimonotone.Rd  |    5 +++--
 man/legacy.Rd      |   10 +++++-----
 man/monotone.Rd    |    6 ++++--
 man/unimonotone.Rd |    5 +++--
 11 files changed, 48 insertions(+), 38 deletions(-)

More information about monotone at CRAN
Permanent link

Package epiR updated to version 2.0.48 with previous version 2.0.46 dated 2022-03-31

Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> and Evan Sergeant <evansergeant@gmail.com> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>

Diff between epiR versions 2.0.46 dated 2022-03-31 and 2.0.48 dated 2022-05-25

 DESCRIPTION                                |    8 -
 MD5                                        |   22 ++--
 NEWS                                       |   18 +++
 R/epi.kappa.R                              |    8 -
 R/epi.prev.R                               |  143 +++++++++++++++++++----------
 inst/doc/epiR_descriptive.html             |   32 +++---
 inst/doc/epiR_measures_of_association.html |   52 +++++-----
 inst/doc/epiR_sample_size.html             |    4 
 inst/doc/epiR_surveillance.Rmd             |   20 ++--
 inst/doc/epiR_surveillance.html            |   84 ++++++++---------
 man/epi.prev.Rd                            |   18 ++-
 vignettes/epiR_surveillance.Rmd            |   20 ++--
 12 files changed, 253 insertions(+), 176 deletions(-)

More information about epiR at CRAN
Permanent link

Package SoilHyP updated to version 0.1.6 with previous version 0.1.5 dated 2021-01-08

Title: Soil Hydraulic Properties
Description: Provides functions for (1) soil water retention (SWC) and unsaturated hydraulic conductivity (Ku) (van Genuchten-Mualem (vGM or vG) [1, 2], Peters-Durner-Iden (PDI) [3, 4, 5], Brooks and Corey (bc) [8]), (2) fitting of parameter for SWC and/or Ku using Shuffled Complex Evolution (SCE) optimisation and (3) calculation of soil hydraulic properties (Ku and soil water contents) based on the simplified evaporation method (SEM) [6, 7]. Main references: [1] van Genuchten (1980) <doi:10.2136/sssaj1980.03615995004400050002x>, [2] Mualem (1976) <doi:10.1029/WR012i003p00513>, [3] Peters (2013) <doi:10.1002/wrcr.20548>, [4] Iden and Durner (2013) <doi:10.1002/2014WR015937>, [5] Peters (2014) <doi:10.1002/2014WR015937>, [6] Wind G. P. (1966), [7] Peters and Durner (2008) <doi:10.1016/j.jhydrol.2008.04.016> and [8] Brooks and Corey (1964).
Author: Ullrich Dettmann [aut, cre], Felix Andrews [ctb] which is not on r-cran . The SCEoptim function is adapted, and substantially revised from Brecht Donckels MATLAB code which is in turn adopted from Qingyun Duans MATLAB code), Brecht Donckels [ctb] , [...truncated...]
Maintainer: Ullrich Dettmann <ullrich.dettmann@thuenen.de>

Diff between SoilHyP versions 0.1.5 dated 2021-01-08 and 0.1.6 dated 2022-05-25

 DESCRIPTION         |   10 +++++-----
 MD5                 |   52 ++++++++++++++++++++++++++--------------------------
 R/DK_to_SWC.R       |   11 ++++++-----
 R/Kcap.R            |    2 +-
 R/Kfilm.R           |    2 +-
 R/Ku.R              |    4 ++--
 R/SEM.R             |    7 +++----
 R/SWC.R             |    5 +++--
 R/Sad.R             |    2 +-
 R/Sat.R             |    2 +-
 R/Sat_old.R         |    2 +-
 R/Scap.R            |    2 +-
 R/dataSEM.R         |    9 +++++----
 R/dataSHP.R         |    8 ++++----
 R/dataTestthat.R    |   18 +++++++++---------
 man/Kcap.Rd         |    2 +-
 man/Kfilm.Rd        |    2 +-
 man/Ku.Rd           |    4 ++--
 man/SEM.Rd          |    7 +++----
 man/SWC.Rd          |    4 ++--
 man/Sad.Rd          |    2 +-
 man/Sat.Rd          |    2 +-
 man/Sat_old.Rd      |    2 +-
 man/Scap.Rd         |    2 +-
 man/dataSEM.Rd      |    9 +++++----
 man/dataSHP.Rd      |    8 ++++----
 man/dataTestthat.Rd |   18 +++++++++---------
 27 files changed, 100 insertions(+), 98 deletions(-)

More information about SoilHyP at CRAN
Permanent link

Package SecDim updated to version 2.2 with previous version 1.3 dated 2022-05-02

Title: The Second Dimension of Spatial Association
Description: Most of the current methods explore spatial association using observations at sample locations, which are defined as the first dimension of spatial association (FDA). The proposed concept of the second dimension of spatial association (SDA) aims to extract in-depth information about the geographical environment from locations outside sample locations for exploring spatial association.
Author: Yongze Song [aut, cre]
Maintainer: Yongze Song <yongze.song@postgrad.curtin.edu.au>

Diff between SecDim versions 1.3 dated 2022-05-02 and 2.2 dated 2022-05-25

 DESCRIPTION              |   22 ++++++++++++----------
 MD5                      |   20 ++++++++++++++------
 NAMESPACE                |    1 +
 R/data.R                 |   13 +++++++++++++
 R/selectvarlm.R          |    5 ++++-
 R/selectvarsda.R         |    2 +-
 build                    |only
 data/sample_vars_fda.rda |only
 inst                     |only
 man/sample_vars_fda.Rd   |only
 man/selectvarsda.Rd      |    2 +-
 vignettes                |only
 12 files changed, 46 insertions(+), 19 deletions(-)

More information about SecDim at CRAN
Permanent link

Package radiant.model updated to version 1.4.4 with previous version 1.4.3 dated 2021-12-21

Title: Model Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Model menu includes interfaces for linear and logistic regression, naive Bayes, neural networks, classification and regression trees, model evaluation, collaborative filtering, decision analysis, and simulation. The application extends the functionality in 'radiant.data'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>

Diff between radiant.model versions 1.4.3 dated 2021-12-21 and 1.4.4 dated 2022-05-25

 DESCRIPTION              |   10 ++--
 MD5                      |   40 ++++++++--------
 NEWS.md                  |    4 +
 R/crtree.R               |    6 +-
 R/evalbin.R              |  113 +++++++++++++++++++++++------------------------
 R/gbt.R                  |    2 
 R/nn.R                   |  100 +++++++++++++++++++----------------------
 README.md                |    8 +--
 man/auc.Rd               |    1 
 man/confusion.Rd         |    1 
 man/evalbin.Rd           |    1 
 man/nn.Rd                |    1 
 man/plot.confusion.Rd    |    1 
 man/plot.evalbin.Rd      |    1 
 man/plot.nn.Rd           |    1 
 man/predict.nn.Rd        |    1 
 man/profit.Rd            |    1 
 man/rig.Rd               |    1 
 man/summary.confusion.Rd |    1 
 man/summary.evalbin.Rd   |    1 
 man/summary.nn.Rd        |    1 
 21 files changed, 142 insertions(+), 154 deletions(-)

More information about radiant.model at CRAN
Permanent link

Package radiant.data updated to version 1.4.2 with previous version 1.4.1 dated 2021-11-12

Title: Data Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Data menu includes interfaces for loading, saving, viewing, visualizing, summarizing, transforming, and combining data. It also contains functionality to generate reproducible reports of the analyses conducted in the application.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>

Diff between radiant.data versions 1.4.1 dated 2021-11-12 and 1.4.2 dated 2022-05-25

 DESCRIPTION                     |   16 ++---
 MD5                             |   26 ++++----
 NAMESPACE                       |    1 
 NEWS.md                         |    5 +
 R/aaa.R                         |    2 
 R/radiant.R                     |  124 +++++++++++++++++++++-------------------
 R/visualize.R                   |   18 +----
 README.md                       |   14 ++--
 inst/app/global.R               |    2 
 inst/app/radiant.R              |    4 -
 inst/app/tools/app/about.md     |    8 +-
 inst/app/tools/app/tutorials.md |   11 ---
 man/sshh.Rd                     |    2 
 man/sshhr.Rd                    |    2 
 14 files changed, 116 insertions(+), 119 deletions(-)

More information about radiant.data at CRAN
Permanent link

Package ORKM updated to version 0.1.1.1 with previous version 0.0.2.1 dated 2022-04-25

Title: The Online Regularized K-Means Clustering Algorithm
Description: Algorithm of online regularized k-means to deal with online multi(single) view data. The philosophy of the package is described in Guo G. (2020) <doi:10.1080/02331888.2020.1823979>.
Author: Guangbao Guo [aut, cre] , Miao Yu [aut], Haoyue Song [aut], Ruiling Niu [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>

Diff between ORKM versions 0.0.2.1 dated 2022-04-25 and 0.1.1.1 dated 2022-05-25

 DESCRIPTION        |    8 ++++----
 MD5                |   34 +++++++++++++++++++++-------------
 R/DMC.R            |   33 ++++++++++++++-------------------
 R/KMeans.R         |   26 +++++++++++++++-----------
 R/OGD.R            |    4 ++--
 R/OMU.R            |    5 ++---
 R/ORKMeans.R       |   23 +++++++++++------------
 R/PKMeans.R        |    4 ++--
 R/RKMeans.R        |   17 +++++++++--------
 data/QCM.rda       |only
 data/movie1.rda    |only
 data/movie2.rda    |only
 data/turelabel.rda |only
 man/DMC.Rd         |   10 +++++-----
 man/KMeans.Rd      |   10 +++++-----
 man/ORKMeans.Rd    |    2 +-
 man/PKMeans.Rd     |    2 +-
 man/QCM.Rd         |only
 man/RKMeans.Rd     |   10 +++++-----
 man/movie1.Rd      |only
 man/movie2.Rd      |only
 man/turelabel.Rd   |only
 22 files changed, 97 insertions(+), 91 deletions(-)

More information about ORKM at CRAN
Permanent link

Package MeTo updated to version 0.1.1 with previous version 0.1.0 dated 2019-01-11

Title: Meteorological Tools
Description: Meteorological Tools following the FAO56 irrigation paper of Allen et al. (1998) [1]. Functions for calculating: reference evapotranspiration (ETref), extraterrestrial radiation (Ra), net radiation (Rn), saturation vapor pressure (satVP), global radiation (Rs), soil heat flux (G), daylight hours, and more. [1] Allen, R. G., Pereira, L. S., Raes, D., & Smith, M. (1998). Crop evapotranspiration-Guidelines for computing crop water requirements-FAO Irrigation and drainage paper 56. FAO, Rome, 300(9).
Author: Ullrich Dettmann [aut, cre], R. Grima [aut]
Maintainer: Ullrich Dettmann <ullrich.dettmann@thuenen.de>

Diff between MeTo versions 0.1.0 dated 2019-01-11 and 0.1.1 dated 2022-05-25

 DESCRIPTION            |   13 ++++++-------
 MD5                    |   48 ++++++++++++++++++++++++------------------------
 R/ETref.R              |    1 +
 R/Ra.R                 |    4 ++--
 R/Rn.R                 |   10 +++++-----
 R/Rns.R                |    4 ++--
 R/Rso.R                |    8 ++++----
 R/estG.R               |   14 ++++++++------
 R/estP.r               |   12 ++++++------
 R/estRs.R              |    6 +++---
 R/w.R                  |    4 ++--
 man/ETref.Rd           |   25 +++++++++++++++++++++----
 man/Ra.Rd              |    7 +++----
 man/Rn.Rd              |   32 +++++++++++++++++++++++---------
 man/Rnl.Rd             |   20 +++++++++++++++++---
 man/Rns.Rd             |    4 ++--
 man/Rso.Rd             |   19 +++++++++++++------
 man/VP.Rd              |   16 +++++++++++++---
 man/constDefaults.Rd   |    6 ++++--
 man/controlDefaults.Rd |    6 ++++--
 man/estG.Rd            |   29 ++++++++++++++++++++---------
 man/estP.Rd            |   12 ++++++------
 man/estRs.Rd           |   16 +++++++++++-----
 man/satVP.Rd           |    9 +++++++--
 man/w.Rd               |    4 ++--
 25 files changed, 209 insertions(+), 120 deletions(-)

More information about MeTo at CRAN
Permanent link

Package basefun updated to version 1.1-3 with previous version 1.1-2 dated 2022-01-14

Title: Infrastructure for Computing with Basis Functions
Description: Some very simple infrastructure for basis functions.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between basefun versions 1.1-2 dated 2022-01-14 and 1.1-3 dated 2022-05-25

 DESCRIPTION      |    8 ++++----
 MD5              |    8 ++++----
 R/Bernstein.R    |    7 ++++++-
 inst/NEWS.Rd     |    7 +++++++
 tests/bases-Ex.R |   55 ++++++++++++++++++++++++++++++++++++-------------------
 5 files changed, 57 insertions(+), 28 deletions(-)

More information about basefun at CRAN
Permanent link

New package SynDI with initial version 0.1.0
Package: SynDI
Title: Synthetic Data Integration
Version: 0.1.0
Description: Regression inference for multiple populations by integrating summary-level data using stacked imputations. Gu, T., Taylor, J.M.G. and Mukherjee, B. (2021) A synthetic data integration framework to leverage external summary-level information from heterogeneous populations <arXiv:2106.06835>.
License: GPL-2
URL: https://github.com/umich-biostatistics/SynDI
BugReports: https://github.com/umich-biostatistics/SynDI/issues
Depends: R (>= 3.6.0)
Imports: mice, magrittr, dplyr, StackImpute, arm, boot, broom, mvtnorm, randomForest, MASS, knitr
Suggests: markdown
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2022-05-24 15:19:44 UTC; mk
Author: Tian Gu [aut], Jeremy M.G. Taylor [aut], Bhramar Mukherjee [aut], Michael Kleinsasser [cre]
Maintainer: Michael Kleinsasser <mkleinsa@umich.edu>
Repository: CRAN
Date/Publication: 2022-05-25 07:50:05 UTC

More information about SynDI at CRAN
Permanent link

Package shadowr updated to version 0.0.2 with previous version 0.0.1 dated 2022-04-22

Title: Selenium Plugin to Manage Multi Level Shadow Elements on Web Page
Description: Shadow Document Object Model is a web standard that offers component style and markup encapsulation. It is a critically important piece of the Web Components story as it ensures that a component will work in any environment even if other CSS or JavaScript is at play on the page. Custom HTML tags can't be directly identified with selenium tools, because Selenium doesn't provide any way to deal with shadow elements. Using this plugin you can handle any custom HTML tags.
Author: Ricardo Landolt [cre, aut], Sushil Gupta [ctb]
Maintainer: Ricardo Landolt <ricardo.landolt1@gmail.com>

Diff between shadowr versions 0.0.1 dated 2022-04-22 and 0.0.2 dated 2022-05-25

 DESCRIPTION                        |    6 
 MD5                                |   27 +-
 NAMESPACE                          |   60 +++---
 NEWS.md                            |    2 
 README.md                          |   11 -
 inst/figures                       |only
 inst/resources/test/button.html    |   34 +--
 inst/resources/test/index.html     |   24 +-
 inst/resources/test/script.js      |   28 +-
 inst/resources/test/style.css      |    6 
 man/convert_js_to_text.Rd          |   24 +-
 man/shadow-class.Rd                |  352 ++++++++++++++++++-------------------
 man/shadow.Rd                      |   42 ++--
 tests/testthat.R                   |    8 
 tests/testthat/test-check-output.R |  155 +++++-----------
 15 files changed, 366 insertions(+), 413 deletions(-)

More information about shadowr at CRAN
Permanent link

Package relliptical updated to version 1.2.0 with previous version 1.1.0 dated 2022-01-07

Title: The Truncated Elliptical Family of Distributions
Description: It offers random numbers generation from members of the truncated multivariate elliptical family of distribution such as the truncated versions of the Normal, Student-t, Pearson VII, Slash, Logistic, among others. Particular distributions can be provided by specifying the density generating function. It also computes the first two moments (covariance matrix as well) for some particular distributions. References used for this package: Galarza, C. E., Matos, L. A., Castro, L. M., & Lachos, V. H. (2022). Moments of the doubly truncated selection elliptical distributions with emphasis on the unified multivariate skew-t distribution. Journal of Multivariate Analysis, 189, 104944 <doi:10.1016/j.jmva.2021.104944>; Ho, H. J., Lin, T. I., Chen, H. Y., & Wang, W. L. (2012). Some results on the truncated multivariate t distribution. Journal of Statistical Planning and Inference, 142(1), 25-40 <doi:10.1016/j.jspi.2011.06.006>; Valeriano, K. A., Galarza, C. E., & Matos, L. A. (2021). Moments and random number generation for the truncated elliptical family of distributions. arXiv preprint <arXiv:2112.09319>.
Author: Katherine A. L. Valeriano [aut, cre] , Larissa Avila Matos [ctb] , Christian Galarza Morales [ctb]
Maintainer: Katherine A. L. Valeriano <katandreina@gmail.com>

Diff between relliptical versions 1.1.0 dated 2022-01-07 and 1.2.0 dated 2022-05-25

 DESCRIPTION          |   14 +--
 MD5                  |   21 ++--
 NAMESPACE            |    1 
 NEWS.md              |only
 R/Compute_Moments.R  |   21 ++--
 R/Random_Numbers.R   |   26 +++---
 README.md            |   39 +++++----
 build/partial.rdb    |binary
 inst/REFERENCES.bib  |   36 +++++---
 man/mvtelliptical.Rd |   20 ++--
 man/rtelliptical.Rd  |   16 ++-
 src/Functions.cpp    |  215 ++++++++++++---------------------------------------
 12 files changed, 169 insertions(+), 240 deletions(-)

More information about relliptical at CRAN
Permanent link

Package radiant updated to version 1.4.2 with previous version 1.4.1 dated 2021-11-22

Title: Business Analytics using R and Shiny
Description: A platform-independent browser-based interface for business analytics in R, based on the shiny package. The application combines the functionality of 'radiant.data', 'radiant.design', 'radiant.basics', 'radiant.model', and 'radiant.multivariate'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>

Diff between radiant versions 1.4.1 dated 2021-11-22 and 1.4.2 dated 2022-05-25

 DESCRIPTION               |   10 -
 MD5                       |   26 +--
 NEWS.md                   |    5 
 R/radiant.R               |   57 ++++++--
 README.md                 |    8 -
 build/vignette.rds        |binary
 inst/doc/programming.R    |    4 
 inst/doc/programming.Rmd  |    4 
 inst/doc/programming.html |  321 ++++++++++++++++++++++++++++++++++++++++------
 man/launcher.Rd           |    8 +
 man/lin_launcher.Rd       |   10 +
 man/mac_launcher.Rd       |   10 +
 man/win_launcher.Rd       |   10 +
 vignettes/programming.Rmd |    4 
 14 files changed, 390 insertions(+), 87 deletions(-)

More information about radiant at CRAN
Permanent link

New package OPTS with initial version 0.1
Package: OPTS
Title: Optimization via Subsampling (OPTS)
Version: 0.1
Date: 2022-05-20
Maintainer: Mihai Giurcanu <giurcanu@uchicago.edu>
Author: Mihai Giurcanu [aut, cre], Marinela Capanu [aut, ctb], Colin Begg [aut], Mithat Gonen [aut]
Imports: MASS, cvTools, changepoint
Description: Subsampling based variable selection for low dimensional generalized linear models. The methods repeatedly subsample the data minimizing an information criterion (AIC/BIC) over a sequence of nested models for each subsample. Marinela Capanu, Mihai Giurcanu, Colin B Begg, Mithat Gonen, Subsampling based variable selection for generalized linear models.
License: GPL-2
NeedsCompilation: no
Packaged: 2022-05-24 14:16:53 UTC; mgiurcanu
Repository: CRAN
Date/Publication: 2022-05-25 07:50:08 UTC

More information about OPTS at CRAN
Permanent link

New package nimbleNoBounds with initial version 1.0.1
Package: nimbleNoBounds
Title: Transformed Distributions for Improved MCMC Efficiency
Version: 1.0.1
Encoding: UTF-8
Date: 2022-05-24
Maintainer: David Pleydell <david.pleydell@inrae.fr>
Author: David Pleydell [aut, cre, cph]
URL: https://github.com/DRJP/nimbleNoBounds
Description: A collection of common univariate bounded probability distributions transformed to the unbounded real line, for the purpose of increased MCMC efficiency.
License: BSD_3_clause + file LICENSE
Copyright: See COPYRIGHTS file.
Depends: R (>= 3.1.2), nimble
Imports: methods
Suggests: knitr, rmarkdown, coda
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-24 14:27:37 UTC; pleydell
Repository: CRAN
Date/Publication: 2022-05-25 07:50:02 UTC

More information about nimbleNoBounds at CRAN
Permanent link

New package multifunc with initial version 0.9.4
Package: multifunc
Version: 0.9.4
Date: 2022-05-23
Title: Analysis of Ecological Drivers on Ecosystem Multifunctionality
Description: Methods for the analysis of how ecological drivers affect the multifunctionality of an ecosystem based on methods of Byrnes et al. 2016 <doi:10.1111/2041-210X.12143> and Byrnes et al. 2022 <doi:10.1101/2022.03.17.484802>. Most standard methods in the literature are implemented (see vignettes) in a tidy format.
URL: https://jebyrnes.github.io/multifunc/, https://github.com/jebyrnes/multifunc
BugReports: https://github.com/jebyrnes/multifunc/issues
Imports: stats, dplyr, purrr, broom, MASS, utils, magrittr
Suggests: ggplot2, forcats, tidyr, gridExtra, knitr, patchwork, car
License: MIT + file LICENSE
LazyData: true
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-23 16:01:35 UTC; jebyrnes
Author: Jarrett Byrnes [aut, cre, cph]
Maintainer: Jarrett Byrnes <jarrett.byrnes@umb.edu>
Repository: CRAN
Date/Publication: 2022-05-25 07:30:09 UTC

More information about multifunc at CRAN
Permanent link

Package meteospain updated to version 0.0.4 with previous version 0.0.3 dated 2021-11-05

Title: Access to Spanish Meteorological Stations Services
Description: Access to different Spanish meteorological stations data services and APIs (AEMET, SMC, MG, Meteoclimatic...).
Author: Victor Granda [aut, cre] , Miquel de Caceres [ctb] , Aitor Ameztegui [ctb]
Maintainer: Victor Granda <victorgrandagarcia@gmail.com>

Diff between meteospain versions 0.0.3 dated 2021-11-05 and 0.0.4 dated 2022-05-25

 DESCRIPTION                                        |   10 
 MD5                                                |  100 ++++----
 NEWS.md                                            |   12 
 R/aemet_helpers.R                                  |   11 
 R/get_data.R                                       |   17 +
 R/meteocat_helpers.R                               |    8 
 R/meteoclimatic_helpers.R                          |   33 +-
 R/meteogalicia_helpers.R                           |   14 -
 R/ria_helpers.R                                    |   13 -
 R/services_options.R                               |    4 
 R/utils.R                                          |   95 +++++++
 README.md                                          |   63 ++---
 build/vignette.rds                                 |binary
 inst/doc/aemet.R                                   |    3 
 inst/doc/aemet.Rmd                                 |    4 
 inst/doc/aemet.html                                |  245 ++++++++++++++++++-
 inst/doc/api_limits.R                              |    3 
 inst/doc/api_limits.Rmd                            |    3 
 inst/doc/api_limits.html                           |  254 +++++++++++++++++++-
 inst/doc/compatibility.R                           |    3 
 inst/doc/compatibility.Rmd                         |    3 
 inst/doc/compatibility.html                        |  228 +++++++++++++++++-
 inst/doc/meteocat.R                                |    3 
 inst/doc/meteocat.Rmd                              |    4 
 inst/doc/meteocat.html                             |  252 ++++++++++++++++++--
 inst/doc/meteoclimatic.R                           |    3 
 inst/doc/meteoclimatic.Rmd                         |    4 
 inst/doc/meteoclimatic.html                        |  216 ++++++++++++++++-
 inst/doc/meteogalicia.R                            |    3 
 inst/doc/meteogalicia.Rmd                          |   24 +
 inst/doc/meteogalicia.html                         |  261 ++++++++++++++++++---
 inst/doc/ria.R                                     |    3 
 inst/doc/ria.Rmd                                   |   24 +
 inst/doc/ria.html                                  |  261 +++++++++++++++++++--
 man/figures/README-plot_stations-1.png             |binary
 man/figures/README-plot_stations-2.png             |binary
 man/get_meteo_from.Rd                              |    1 
 man/get_stations_info_from.Rd                      |    1 
 tests/testthat/test-aemet.R                        |   22 +
 tests/testthat/test-concordance_between_services.R |    3 
 tests/testthat/test-meteocat.R                     |   77 ++++--
 tests/testthat/test-meteoclimatic.R                |    4 
 tests/testthat/test-meteogalicia.R                 |   37 ++
 tests/testthat/test-riaa.R                         |   13 -
 vignettes/aemet.Rmd                                |    4 
 vignettes/api_limits.Rmd                           |    3 
 vignettes/compatibility.Rmd                        |    3 
 vignettes/meteocat.Rmd                             |    4 
 vignettes/meteoclimatic.Rmd                        |    4 
 vignettes/meteogalicia.Rmd                         |   24 +
 vignettes/ria.Rmd                                  |   24 +
 51 files changed, 2099 insertions(+), 309 deletions(-)

More information about meteospain at CRAN
Permanent link

New package lacrmr with initial version 1.0.5
Package: lacrmr
Title: Connect to the 'Less Annoying CRM' API
Version: 1.0.5
Description: Connect to the 'Less Annoying CRM' API with ease to get your crm data in a clean and tidy format. 'Less Annoying CRM' is a simple CRM built for small businesses, more information is available on their website <https://www.lessannoyingcrm.com/>.
License: GPL-3
URL: https://ixpantia.github.io/lacrmr/
BugReports: https://github.com/ixpantia/lacrmr/issues
Encoding: UTF-8
Depends: R (>= 3.6), magrittr
Suggests: testthat (>= 2.1.0), knitr, rmarkdown, httptest, mockery
VignetteBuilder: knitr
Imports: dplyr, httr, jsonlite, janitor, sjmisc, stringr
NeedsCompilation: no
Packaged: 2022-05-25 00:23:47 UTC; frans
Author: ixpantia, family = SRL [cph], Ronny Hernandez Mora [aut] , Frans van Dunne [cre, aut]
Maintainer: Frans van Dunne <frans@ixpantia.com>
Repository: CRAN
Date/Publication: 2022-05-25 07:30:16 UTC

More information about lacrmr at CRAN
Permanent link

New package GeoModels with initial version 1.0.0
Package: GeoModels
Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large) Data Analysis
Version: 1.0.0
Date: 2022-05-01
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) simulation and inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Covariance functions for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. See the URL for the papers associated with this package, as for instance, Bevilacqua and Gaetan (2015) <doi:10.1007/s11222-014-9460-6>, Bevilacqua et al. (2016) <doi:10.1007/s13253-016-0256-3>, Vallejos et al. (2020) <doi:10.1007/978-3-030-56681-4>, Bevilacqua et al. (2022) <doi:10.1016/j.jmva.2022.104949>, Bevilacqua et al. (2022) <doi:10.1007/s11749-021-00797-5>, Blasi et al. (2022) <doi:10.1016/j.spasta.2022.100596>, Morales-Navarrete et al. (2022) <arXiv:2105.03734>, and a large class of examples and tutorials.
Depends: R (>= 4.1.0), GPvecchia,fields, mapproj, plot3D, shape
License: GPL (>= 3)
Encoding: UTF-8
Imports: methods, spam, scatterplot3d, dfoptim, dotCall64, optimParallel, parallel, plotrix, pracma, pbivnorm, zipfR, sn, nabor, numDeriv, hypergeo, ucminf, lamW, GpGp,VGAM, data.table
Suggests: actuar, GoFKernel, sphereplot
Repository: CRAN
URL: https://vmoprojs.github.io/GeoModels-page/
BugReports: https://github.com/vmoprojs/GeoModels/issues
NeedsCompilation: yes
Packaged: 2022-05-24 12:55:45 UTC; morenobevilacqua
Author: Moreno Bevilacqua [aut, cre] , Victor Morales-Onate [aut] , Christian Caamano-Carrillo [aut]
Date/Publication: 2022-05-25 07:40:05 UTC

More information about GeoModels at CRAN
Permanent link

Package ergm.count updated to version 4.1.1 with previous version 4.0.2 dated 2021-06-18

Title: Fit, Simulate and Diagnose Exponential-Family Models for Networks with Count Edges
Description: A set of extensions for the 'ergm' package to fit weighted networks whose edge weights are counts. See Krivitsky (2012) <doi:10.1214/12-EJS696> and Krivitsky, Hunter, Morris, and Klumb (2021) <arXiv:2106.04997>.
Author: Pavel N. Krivitsky [aut, cre] , Mark S. Handcock [ctb], David R. Hunter [ctb], Joyce Cheng [ctb]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>

Diff between ergm.count versions 4.0.2 dated 2021-06-18 and 4.1.1 dated 2022-05-25

 ergm.count-4.0.2/ergm.count/build/partial.rdb              |only
 ergm.count-4.0.2/ergm.count/man/ergm-references.Rd         |only
 ergm.count-4.0.2/ergm.count/man/ergm-terms.Rd              |only
 ergm.count-4.0.2/ergm.count/src/wtMHproposals.h            |only
 ergm.count-4.0.2/ergm.count/tests/testnet3d.RData          |only
 ergm.count-4.0.2/ergm.count/tests/valued_fit.R             |only
 ergm.count-4.0.2/ergm.count/tests/valued_sim.R             |only
 ergm.count-4.1.1/ergm.count/DESCRIPTION                    |   22 
 ergm.count-4.1.1/ergm.count/LICENSE                        |    2 
 ergm.count-4.1.1/ergm.count/MD5                            |   66 +-
 ergm.count-4.1.1/ergm.count/R/InitErgmReference.R          |   99 +++
 ergm.count-4.1.1/ergm.count/R/InitWtErgmProposal.R         |  113 ++--
 ergm.count-4.1.1/ergm.count/R/InitWtErgmTerm.R             |   49 +
 ergm.count-4.1.1/ergm.count/R/data.R                       |    6 
 ergm.count-4.1.1/ergm.count/R/ergm.count-package.R         |   36 +
 ergm.count-4.1.1/ergm.count/R/zzz.R                        |   13 
 ergm.count-4.1.1/ergm.count/build/ergm.count.pdf           |only
 ergm.count-4.1.1/ergm.count/build/vignette.rds             |binary
 ergm.count-4.1.1/ergm.count/inst/CITATION                  |   17 
 ergm.count-4.1.1/ergm.count/inst/NEWS.Rd                   |   51 +
 ergm.count-4.1.1/ergm.count/inst/doc/valued.R              |    7 
 ergm.count-4.1.1/ergm.count/inst/doc/valued.Rmd            |   10 
 ergm.count-4.1.1/ergm.count/inst/doc/valued.html           |  350 ++++++------
 ergm.count-4.1.1/ergm.count/man/Binomial-ergmReference.Rd  |only
 ergm.count-4.1.1/ergm.count/man/CMB-ergmTerm.Rd            |only
 ergm.count-4.1.1/ergm.count/man/CMP-ergmTerm.Rd            |only
 ergm.count-4.1.1/ergm.count/man/Disc-ergmProposal.Rd       |only
 ergm.count-4.1.1/ergm.count/man/DiscTNT-ergmProposal.Rd    |only
 ergm.count-4.1.1/ergm.count/man/Geometric-ergmReference.Rd |only
 ergm.count-4.1.1/ergm.count/man/Poisson-ergmReference.Rd   |only
 ergm.count-4.1.1/ergm.count/man/ZIPoisson-ergmProposal.Rd  |only
 ergm.count-4.1.1/ergm.count/man/ergm.count-package.Rd      |   39 +
 ergm.count-4.1.1/ergm.count/man/zach.Rd                    |    4 
 ergm.count-4.1.1/ergm.count/src/include_stubs.c            |    2 
 ergm.count-4.1.1/ergm.count/src/init.c                     |    2 
 ergm.count-4.1.1/ergm.count/src/wtMHproposals.c            |  366 ++++---------
 ergm.count-4.1.1/ergm.count/src/wtchangestats.c            |    2 
 ergm.count-4.1.1/ergm.count/src/wtchangestats.h            |    2 
 ergm.count-4.1.1/ergm.count/tests/testthat                 |only
 ergm.count-4.1.1/ergm.count/tests/testthat.R               |only
 ergm.count-4.1.1/ergm.count/vignettes/timings.csv          |only
 ergm.count-4.1.1/ergm.count/vignettes/valued.Rmd           |   10 
 ergm.count-4.1.1/ergm.count/vignettes/valued.bib           |  183 ++----
 43 files changed, 797 insertions(+), 654 deletions(-)

More information about ergm.count at CRAN
Permanent link

Package dycdtools updated to version 0.4.2 with previous version 0.4.1 dated 2022-05-08

Title: Tools for DYRESM-CAEDYM Model Development: Calibration Assistant and Post-Processing
Description: Tools for DYRESM-CAEDYM model development, including assisting with calibrating selected model parameters and visualising model output through time series plot, profile plot, contour plot, and scatter plot.
Author: Songyan Yu [aut, cre] , Christopher McBride [ctb], Marieke Frassl [ctb]
Maintainer: Songyan Yu <sunny.yu@griffith.edu.au>

Diff between dycdtools versions 0.4.1 dated 2022-05-08 and 0.4.2 dated 2022-05-25

 dycdtools-0.4.1/dycdtools/R/dycdtools.R                            |only
 dycdtools-0.4.2/dycdtools/DESCRIPTION                              |    7 
 dycdtools-0.4.2/dycdtools/MD5                                      |   69 +-
 dycdtools-0.4.2/dycdtools/NAMESPACE                                |    1 
 dycdtools-0.4.2/dycdtools/NEWS.md                                  |    5 
 dycdtools-0.4.2/dycdtools/R/Fun_Calib-assist.R                     |  261 ++++++----
 dycdtools-0.4.2/dycdtools/R/Fun_Change-input-file.R                |    8 
 dycdtools-0.4.2/dycdtools/R/Fun_Contour-plot_sim.R                 |  107 ++--
 dycdtools-0.4.2/dycdtools/R/Fun_Contour-plot_sim_obs.R             |  171 +++---
 dycdtools-0.4.2/dycdtools/R/Fun_Extract-simulation.R               |   64 +-
 dycdtools-0.4.2/dycdtools/R/Fun_Interpol.R                         |   48 +
 dycdtools-0.4.2/dycdtools/R/Fun_Objective-func.R                   |   44 +
 dycdtools-0.4.2/dycdtools/R/Fun_Profile-plot.R                     |   58 +-
 dycdtools-0.4.2/dycdtools/R/Fun_Run-iteration.R                    |   29 -
 dycdtools-0.4.2/dycdtools/R/Fun_Scatter-plot.R                     |   52 +
 dycdtools-0.4.2/dycdtools/R/Fun_TS-plot.R                          |  142 +++--
 dycdtools-0.4.2/dycdtools/R/obs_temp.R                             |    6 
 dycdtools-0.4.2/dycdtools/R/output_name.R                          |    5 
 dycdtools-0.4.2/dycdtools/README.md                                |  154 +++++
 dycdtools-0.4.2/dycdtools/man/calib_assist.Rd                      |  119 +++-
 dycdtools-0.4.2/dycdtools/man/change_input_file.Rd                 |   10 
 dycdtools-0.4.2/dycdtools/man/ext_output.Rd                        |   24 
 dycdtools-0.4.2/dycdtools/man/interpol.Rd                          |   30 -
 dycdtools-0.4.2/dycdtools/man/objective_fun.Rd                     |   33 -
 dycdtools-0.4.2/dycdtools/man/obs_temp.Rd                          |    6 
 dycdtools-0.4.2/dycdtools/man/output_name.Rd                       |    5 
 dycdtools-0.4.2/dycdtools/man/plot_cont.Rd                         |   49 -
 dycdtools-0.4.2/dycdtools/man/plot_cont_comp.Rd                    |   76 +-
 dycdtools-0.4.2/dycdtools/man/plot_prof.Rd                         |   40 -
 dycdtools-0.4.2/dycdtools/man/plot_scatter.Rd                      |   37 -
 dycdtools-0.4.2/dycdtools/man/plot_ts.Rd                           |   56 +-
 dycdtools-0.4.2/dycdtools/man/run_iteration.Rd                     |    9 
 dycdtools-0.4.2/dycdtools/tests/testthat/test-FUN-plot_cont_comp.R |only
 dycdtools-0.4.2/dycdtools/tests/testthat/test-FUN-plot_prof.R      |only
 dycdtools-0.4.2/dycdtools/tests/testthat/test-FUN-plot_scatter.R   |only
 dycdtools-0.4.2/dycdtools/tests/testthat/test-FUN-plot_ts.R        |only
 dycdtools-0.4.2/dycdtools/tests/testthat/test-Fun_Delete-space.R   |    2 
 dycdtools-0.4.2/dycdtools/tests/testthat/test-Fun_Height2Depth.R   |    2 
 38 files changed, 1136 insertions(+), 593 deletions(-)

More information about dycdtools at CRAN
Permanent link

New package ClusROC with initial version 1.0.1
Package: ClusROC
Title: ROC Analysis in Three-Class Classification Problems for Clustered Data
Date: 2022-05-12
Version: 1.0.1
Author: Duc-Khanh To [aut, cre] , with contributions from Gianfranco Adimari and Monica Chiogna
Maintainer: Duc-Khanh To <toduc@stat.unipd.it>
Description: Statistical methods for ROC surface analysis in three-class classification problems for clustered data and in presence of covariates. In particular, the package allows to obtain covariate-specific point and interval estimation for: (i) true class fractions (TCFs) at fixed pairs of thresholds; (ii) the ROC surface; (iii) the volume under ROC surface (VUS); (iv) the optimal pairs of thresholds. Methods considered in points (i), (ii) and (iv) are proposed and discussed in To et al. (2022) <doi:10.1177/09622802221089029>. Referring to point (iv), three different selection criteria are implemented: Generalized Youden Index (GYI), Closest to Perfection (CtP) and Maximum Volume (MV). Methods considered in point (iii) are proposed and discussed in Xiong et al. (2018) <doi:10.1177/0962280217742539>. Visualization tools are also provided. We refer readers to the articles cited above for all details.
License: GPL (>= 2)
Depends: R (>= 3.5.0), stats, utils, graphics, nlme
Imports: rgl, car, numDeriv, ggplot2, ggpubr, snow, doSNOW, foreach
Encoding: UTF-8
LazyData: true
LazyLoad: yes
ByteCompile: yes
URL: https://github.com/toduckhanh/ClusROC
BugReports: https://github.com/toduckhanh/ClusROC/issues
NeedsCompilation: no
Packaged: 2022-05-24 13:54:48 UTC; duckh
Repository: CRAN
Date/Publication: 2022-05-25 07:40:11 UTC

More information about ClusROC at CRAN
Permanent link

Package AlgDesign updated to version 1.2.1 with previous version 1.2.0 dated 2019-11-29

Title: Algorithmic Experimental Design
Description: Algorithmic experimental designs. Calculates exact and approximate theory experimental designs for D,A, and I criteria. Very large designs may be created. Experimental designs may be blocked or blocked designs created from a candidate list, using several criteria. The blocking can be done when whole and within plot factors interact.
Author: Bob Wheeler <bwheelerg@gmail.com>
Maintainer: Jerome Braun <jvbraun.statistics@gmail.com>

Diff between AlgDesign versions 1.2.0 dated 2019-11-29 and 1.2.1 dated 2022-05-25

 AlgDesign-1.2.0/AlgDesign/INDEX                   |only
 AlgDesign-1.2.1/AlgDesign/DESCRIPTION             |    6 +++---
 AlgDesign-1.2.1/AlgDesign/MD5                     |   15 +++++++--------
 AlgDesign-1.2.1/AlgDesign/NEWS                    |    5 +++++
 AlgDesign-1.2.1/AlgDesign/build/vignette.rds      |binary
 AlgDesign-1.2.1/AlgDesign/inst/doc/AlgDesign.Rnw  |    4 ++--
 AlgDesign-1.2.1/AlgDesign/inst/doc/AlgDesign.pdf  |binary
 AlgDesign-1.2.1/AlgDesign/src/FederovOpt.c        |    2 +-
 AlgDesign-1.2.1/AlgDesign/vignettes/AlgDesign.Rnw |    4 ++--
 9 files changed, 20 insertions(+), 16 deletions(-)

More information about AlgDesign at CRAN
Permanent link

New package tvmediation with initial version 1.1.0
Package: tvmediation
Date: 2022-05-13
Version: 1.1.0
Title: Time Varying Mediation Analysis
Description: Provides functions for estimating mediation effects that vary over time as described in Cai X, Coffman DL, Piper ME, Li R. Estimation and inference for the mediation effect in a time-varying mediation model. BMC Med Res Methodol. 2022;22(1):1-12.
Depends: R (>= 4.0.0)
Imports: stats (>= 4.0.2), dplyr (>= 1.0.2), ggplot2 (>= 3.3.2), locpol (>= 0.7-0)
Suggests: knitr, rmarkdown
License: GPL-3
URL: https://github.com/dcoffman/tvmediation/wiki
BugReports: https://github.com/dcoffman/tvmediation/issues
LazyData: true
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-21 15:38:02 UTC; yajna
Author: Donna Coffman [aut, cre] , Xizhen Cai [aut] , Yajnaseni Chakraborti [aut] , Harry Zobel [ctb]
Maintainer: Donna Coffman <dcoffman@temple.edu>
Repository: CRAN
Date/Publication: 2022-05-25 06:40:02 UTC

More information about tvmediation at CRAN
Permanent link

Package hibayes updated to version 1.1.0 with previous version 1.0.1 dated 2022-01-13

Title: Individual-Level, Summary-Level and Single-Step Bayesian Regression Model
Description: A user-friendly tool to fit Bayesian regression models. It can fit 3 types of Bayesian models using individual-level, summary-level, and individual plus pedigree-level (single-step) data for both Genomic prediction/selection (GS) and Genome-Wide Association Study (GWAS), it was designed to estimate joint effects and genetic parameters for a complex trait, including: (1) fixed effects and coefficients of covariates, (2) environmental random effects, and its corresponding variance, (3) genetic variance, (4) residual variance, (5) heritability, (6) genomic estimated breeding values (GEBV) for both genotyped and non-genotyped individuals, (7) SNP effect size, (8) phenotype/genetic variance explained (PVE) for single or multiple SNPs, (9) posterior probability of association of the genomic window (WPPA), (10) posterior inclusive probability (PIP). The functions are not limited, we will keep on going in enriching it with more features. References: Meuwissen et al. (2001) <doi:10.1093/genetics/157.4.1819>; Gustavo et al. (2013) <doi:10.1534/genetics.112.143313>; Habier et al. (2011) <doi:10.1186/1471-2105-12-186>; Yi et al. (2008) <doi:10.1534/genetics.107.085589>; Zhou et al. (2013) <doi:10.1371/journal.pgen.1003264>; Moser et al. (2015) <doi:10.1371/journal.pgen.1004969>; Lloyd-Jones et al. (2019) <doi:10.1038/s41467-019-12653-0>; Henderson (1976) <doi:10.2307/2529339>; Fernando et al. (2014) <doi:10.1186/1297-9686-46-50>.
Author: Lilin Yin [aut, cre, cph], Haohao Zhang [aut, cph], Xiaolei Liu [aut, cph]
Maintainer: Lilin Yin <ylilin@163.com>

Diff between hibayes versions 1.0.1 dated 2022-01-13 and 1.1.0 dated 2022-05-25

 DESCRIPTION     |   10 -
 MD5             |   24 +--
 R/bayes.r       |   42 ++++--
 R/ldm.r         |    3 
 R/sbayes.r      |   23 ++-
 R/ssbayes.r     |   58 +++++---
 man/bayes.Rd    |   26 ++-
 man/sbayes.Rd   |   19 +-
 man/ssbayes.Rd  |   30 +++-
 src/Bayes.cpp   |  372 ++++++++++++++++++++++++++++++--------------------------
 src/SBayesD.cpp |  176 +++++++++++++++-----------
 src/SBayesS.cpp |  174 +++++++++++++++-----------
 src/solver.cpp  |    2 
 13 files changed, 555 insertions(+), 404 deletions(-)

More information about hibayes at CRAN
Permanent link

Package AzureStor updated to version 3.7.0 with previous version 3.6.1 dated 2022-02-03

Title: Storage Management in 'Azure'
Description: Manage storage in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/en-us/product-categories/storage/>. On the admin side, 'AzureStor' includes features to create, modify and delete storage accounts. On the client side, it includes an interface to blob storage, file storage, and 'Azure Data Lake Storage Gen2': upload and download files and blobs; list containers and files/blobs; create containers; and so on. Authenticated access to storage is supported, via either a shared access key or a shared access signature (SAS). Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre], Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>

Diff between AzureStor versions 3.6.1 dated 2022-02-03 and 3.7.0 dated 2022-05-25

 DESCRIPTION                           |    6 +--
 MD5                                   |   44 ++++++++++++----------
 NAMESPACE                             |   15 +++++++
 NEWS.md                               |    9 ++++
 R/AzureStor.R                         |    2 -
 R/adls_client_funcs.R                 |    2 -
 R/az_storage.R                        |    4 +-
 R/blob_client_funcs.R                 |   24 +++++++++---
 R/blob_snapshot.R                     |only
 R/blob_transfer_internal.R            |   14 +++++--
 R/blob_version.R                      |only
 R/client_generics.R                   |   67 ++++++++++++++++++++++++++++++++--
 R/file_client_funcs.R                 |    2 -
 R/storage_metadata.R                  |   12 +++++-
 R/storage_properties.R                |   13 +++++-
 man/adls.Rd                           |    5 +-
 man/blob.Rd                           |   15 ++++---
 man/file.Rd                           |    5 +-
 man/generics.Rd                       |   39 ++++++++++++++++++-
 man/metadata.Rd                       |    4 +-
 man/properties.Rd                     |    6 ++-
 man/snapshot.Rd                       |only
 man/version.Rd                        |only
 tests/testthat/test02f_blobsnapshot.R |only
 tests/testthat/test02g_blobversion.R  |only
 tests/testthat/test10a_service_sas.R  |   15 +++++++
 26 files changed, 245 insertions(+), 58 deletions(-)

More information about AzureStor at CRAN
Permanent link

Package perARMA (with last version 1.6) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2016-02-25 1.6
2013-03-01 1.5
2013-02-26 1.4
2013-01-26 1.3
2013-01-11 1.2
2013-01-10 1.1

Permanent link
Package rHL7 (with last version 1.0.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2022-03-02 1.0.0

Permanent link
Package rwt (with last version 1.0.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-06-24 1.0.0
2013-10-14 0.9.4
2009-04-04 0.9.2
2005-06-25 0.9-1

Permanent link
Package nowcastDFM (with last version 1.0.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-12-01 1.0.0

Permanent link
Package nowcasting (with last version 1.1.4) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2019-08-01 1.1.4
2019-06-12 1.1.3
2019-06-04 1.1.2
2019-05-02 1.1.1
2019-04-24 1.1.0
2018-11-27 1.0.0
2018-04-25 0.1.3
2018-03-02 0.1.2
2017-11-06 0.1.1
2017-11-02 0.1
2017-09-19 0.0.90
2017-08-18 0.0.82

Permanent link
Package modesto (with last version 0.1.3) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-04-18 0.1.3
2019-01-04 0.1.2
2018-11-09 0.1.1
2018-11-03 0.1.0

Permanent link
Package RPS (with last version 1.0.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2018-07-27 1.0.1
2018-07-18 1.0.0

Permanent link
Package epca (with last version 1.0.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-06-26 1.0.0

Permanent link
Package Robocoap (with last version 0.1-1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2017-07-08 0.1-1

Permanent link
Package markovchain (with last version 0.8.6) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-05-17 0.8.6
2021-01-10 0.8.5-4
2020-12-06 0.8.5-3
2020-09-08 0.8.5-2
2020-05-21 0.8.5
2020-05-03 0.8.4.1
2020-03-12 0.8.4
2020-03-07 0.8.3
2020-01-10 0.8.2
2019-12-16 0.8.1
2019-09-14 0.8.0
2019-08-26 0.7.0
2019-07-22 0.6.9.16
2019-01-21 0.6.9.14
2018-08-23 0.6.9.12
2018-06-29 0.6.9.11
2018-06-02 0.6.9.10
2017-08-16 0.6.9.8-1
2017-07-09 0.6.9.6
2017-05-19 0.6.9.3
2017-04-05 0.6.9
2017-03-17 0.6.8.1
2017-01-23 0.6.6
2016-09-08 0.6.5.1
2016-08-29 0.6.5
2016-08-11 0.6
2016-07-07 0.5
2016-07-03 0.4.9.9
2016-05-12 0.4.4
2016-03-05 0.4.3.1
2015-11-26 0.4.3
2015-08-24 0.4.2
2015-08-03 0.4
2015-07-07 0.3.1
2015-06-19 0.3.0.1
2015-06-14 0.3
2015-05-12 0.2.1
2015-04-29 0.2
2015-02-21 0.1.1
2015-01-04 0.1.0
2014-06-20 0.0.9.5
2014-04-19 0.0.9
2014-02-10 0.0.8
2014-01-11 0.0.7
2013-12-31 0.0.5
2013-11-04 0.0.3
2013-09-09 0.0.2
2013-08-13 0.0.1

Permanent link
Package lifecontingencies (with last version 1.3.8) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2022-01-07 1.3.8
2021-03-21 1.3.7
2019-03-05 1.3.6
2018-09-18 1.3.5
2017-12-09 1.3.2
2017-09-29 1.3.1
2017-07-30 1.3
2017-07-17 1.2.5
2017-02-20 1.2.3
2016-07-07 1.2.1
2016-06-13 1.2
2016-05-12 1.1.12
2015-10-01 1.1.10
2015-07-10 1.1.9
2015-04-25 1.1.6
2015-01-03 1.1.5
2014-05-01 1.1
2014-02-25 1.0.6
2014-02-21 1.0.5
2013-11-02 1.0
2013-07-21 0.9.8.6
2013-06-10 0.9.8.5
2013-05-06 0.9.8
2013-03-07 0.9.7
2012-12-03 0.9.6
2012-11-06 0.9.5
2012-05-16 0.9.3
2012-04-09 0.9.2
2012-03-07 0.9.1
2012-03-05 0.9
2012-02-25 0.1.1
2012-01-02 0.1
2011-12-30 0.0.7
2011-11-05 0.0.6
2011-10-01 0.0.5
2011-09-17 0.0.4
2011-09-07 0.0.3
2011-08-17 0.0.2
2011-08-14 0.0.1

Permanent link
Package StVAR (with last version 1.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2017-02-11 1.1

Permanent link
Package asus (with last version 1.0.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2017-10-25 1.0.0

Permanent link
Package metScanR (with last version 1.2.3) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2019-10-16 1.2.3
2019-02-02 1.2.2
2019-01-30 1.2.1
2018-03-19 1.2.0

Permanent link
Package MultiHorizonSPA (with last version 1.0.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-04-06 1.0.0

Permanent link
Package liayson (with last version 1.0.4) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-06-21 1.0.4

Permanent link
Package NPC (with last version 1.1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2016-03-28 1.1.0
2015-10-21 1.0.2
2015-04-18 1.0.0

Permanent link
Package matlab (with last version 1.0.2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-06-24 1.0.2
2014-02-08 1.0.1
2011-09-30 0.8.9
2011-09-14 0.8.8
2011-07-23 0.8.7
2011-04-24 0.8.6
2009-10-13 0.8-3
2008-10-17 0.8-2
2006-10-04 0.8-1

Permanent link
Package SuperPCA (with last version 0.4.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-07-26 0.4.0

Permanent link
Package cwm (with last version 0.0.3) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-01-09 0.0.3
2013-03-28 0.0.2

Permanent link
Package babsim.hospital (with last version 11.8.4) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-11-10 11.8.4
2021-05-15 11.8.2
2021-03-18 11.7.14
2021-03-14 11.7.12
2020-12-14 11.5.14

Permanent link
Package fdcov (with last version 1.1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2017-12-21 1.1.0
2016-06-16 1.0.0

Permanent link
Package MIMSunit (with last version 0.11.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-11-19 0.11.1

Permanent link
Package FactorCopula (with last version 0.8) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-12-18 0.8
2020-09-11 0.5

Permanent link
Package CopulaREMADA (with last version 1.5) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2022-02-09 1.5
2019-03-25 1.3
2019-02-08 1.2
2018-06-22 1.1
2016-09-13 1.0
2015-06-12 0.9
2015-02-22 0.5-1

Permanent link
Package FAVAR (with last version 0.1.2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2022-03-13 0.1.2
2022-03-10 0.1.1

Permanent link
Package kedd (with last version 1.0.3) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2015-10-30 1.0.3
2015-01-28 1.0.2
2014-08-18 1.0.1
2013-08-14 1.0.0

Permanent link
Package splashr (with last version 0.6.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2019-02-26 0.6.0
2018-01-15 0.4.1
2017-08-29 0.4.0

Permanent link
Package cubble (with last version 0.1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2022-04-22 0.1.0

Permanent link
Package baggingbwsel (with last version 1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-07-12 1.0

Permanent link
Package effectFusion (with last version 1.1.3) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-10-13 1.1.3

Permanent link
Package rSQM (with last version 1.3.14) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2018-01-11 1.3.14
2017-09-25 1.2.42

Permanent link
Package tvmediation (with last version 1.0.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-03-09 1.0.0

Permanent link
Package getMet (with last version 0.3.2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2016-03-20 0.3.2
2015-11-13 0.2.1

Permanent link
Package EcoHydRology (with last version 0.4.12.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2018-09-24 0.4.12.1
2014-04-04 0.4.12
2013-10-19 0.4.11
2013-04-04 0.4.9
2013-01-16 0.4.7
2013-01-14 0.4.6
2012-08-01 0.4.5
2012-07-16 0.4.3
2012-05-23 0.4.1
2011-06-20 0.3.8
2011-06-17 0.3.7

Permanent link
Package CityWaterBalance (with last version 0.1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2017-06-16 0.1.0

Permanent link
Package DoE.multi.response (with last version 0.1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2019-08-22 0.1.0

Permanent link
Package advclust (with last version 0.4) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2016-09-04 0.4

Permanent link
Package HARtools (with last version 0.0.5) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2016-11-09 0.0.5

Permanent link
Package baggedcv (with last version 1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2019-07-26 1.0

Permanent link
Package SpaTimeClus (with last version 1.0.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-10-14 1.0.1
2016-12-21 1.0

Permanent link
Package Clustering (with last version 1.7.6) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2022-04-19 1.7.6
2021-12-14 1.7.5
2021-12-08 1.7.4
2021-09-22 1.7.3

Permanent link

Tue, 24 May 2022

Package timedeppar updated to version 1.0.2 with previous version 1.0.1 dated 2020-10-01

Title: Infer Constant and Stochastic, Time-Dependent Model Parameters
Description: Infer constant and stochastic, time-dependent parameters to consider intrinsic stochasticity of a dynamic model and/or to analyze model structure modifications that could reduce model deficits. The concept is based on inferring time-dependent parameters as stochastic processes in the form of Ornstein-Uhlenbeck processes jointly with inferring constant model parameters and parameters of the Ornstein-Uhlenbeck processes. The package also contains functions to sample from and calculate densities of Ornstein-Uhlenbeck processes. References: Tomassini, L., Reichert, P., Kuensch, H.-R. Buser, C., Knutti, R. and Borsuk, M.E. (2009), A smoothing algorithm for estimating stochastic, continuous-time model parameters and its application to a simple climate model, Journal of the Royal Statistical Society: Series C (Applied Statistics) 58, 679-704, <doi:10.1111/j.1467-9876.2009.00678.x> Reichert, P., and Mieleitner, J. (2009), Analyzing input and structural uncertainty of nonlinear dynamic models with stochastic, time-dependent parameters. Water Resources Research, 45, W10402, <doi:10.1029/2009WR007814> Reichert, P., Ammann, L. and Fenicia, F. (2021), Potential and challenges of investigating intrinsic uncertainty of hydrological models with time-dependent, stochastic parameters. Water Resources Research 57(8), e2020WR028311, <doi:10.1029/2020WR028311> Reichert, P. (2022), timedeppar: An R package for inferring stochastic, time-dependent model parameters, in preparation.
Author: Peter Reichert <peter.reichert@eawag.ch>
Maintainer: Peter Reichert <peter.reichert@eawag.ch>

Diff between timedeppar versions 1.0.1 dated 2020-10-01 and 1.0.2 dated 2022-05-24

 DESCRIPTION                    |   18 ++---
 MD5                            |   19 +++--
 R/calc.acceptfreq.timedeppar.R |    2 
 R/get.param.timedeppar.R       |    2 
 R/get.parsamp.timedeppar.R     |    2 
 R/infer.timedeppar.R           |  131 ++++++++++++++++++++++++++---------------
 R/plot.timedeppar.R            |    4 -
 R/readres.timedeppar.R         |    2 
 build                          |only
 inst/NEWS.md                   |    9 ++
 man/infer.timedeppar.Rd        |  107 ++++++++++++++++++++++-----------
 11 files changed, 190 insertions(+), 106 deletions(-)

More information about timedeppar at CRAN
Permanent link

Package sleev updated to version 1.0.2 with previous version 1.0.1 dated 2022-02-01

Title: Semiparametric Likelihood Estimation with Errors in Variables
Description: Efficient regression analysis under general two-phase sampling, where Phase I includes error-prone data and Phase II contains validated data on a subset.
Author: Sarah Lotspeich [aut], Ran Tao [aut, cre], Joey Sherrill [prg]
Maintainer: Ran Tao <r.tao@vanderbilt.edu>

Diff between sleev versions 1.0.1 dated 2022-02-01 and 1.0.2 dated 2022-05-24

 DESCRIPTION                       |   14 
 MD5                               |   23 -
 R/RcppExports.R                   |  238 ++++++------
 R/cv_observed_data_loglik.R       |  221 +++++------
 R/data.R                          |only
 R/logistic2ph.R                   |  706 +++++++++++---------------------------
 R/observed_data_loglik.R          |   91 +---
 R/profile_out.R                   |  200 +++-------
 build                             |only
 data                              |only
 inst                              |only
 man/logistic2ph.Rd                |   83 +---
 man/mock.vccc.Rd                  |only
 tests/testthat/test_logistic2ph.R |  657 +++++++++++++++++------------------
 vignettes                         |only
 15 files changed, 895 insertions(+), 1338 deletions(-)

More information about sleev at CRAN
Permanent link

Package omu updated to version 1.0.5 with previous version 1.0.4 dated 2020-05-18

Title: A Metabolomics Analysis Tool for Intuitive Figures and Convenient Metadata Collection
Description: Facilitates the creation of intuitive figures to describe metabolomics data by utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG) hierarchy data, and gathers functional orthology and gene data from the KEGG-REST API.
Author: Connor Tiffany [aut, cre]
Maintainer: Connor Tiffany <crtiffany@ucdavis.edu>

Diff between omu versions 1.0.4 dated 2020-05-18 and 1.0.5 dated 2022-05-24

 DESCRIPTION                       |   15 
 MD5                               |  100 +-
 NAMESPACE                         |  175 ++--
 R/Internal_Functions.R            |  242 +++--
 R/KEGG_gather.R                   |  231 ++---
 R/PCA_plot.R                      |  123 ++
 R/Pie_Chart.R                     |   90 +-
 R/assign_hierarchy.R              |  220 ++---
 R/check_zeros.R                   |only
 R/count_fold_changes.R            |  129 +--
 R/data.R                          |   32 
 R/get_seqs.R                      |only
 R/omu_anova.R                     |  593 +++++++++-----
 R/omu_summary.R                   |  483 +++++++----
 R/plate_omelette.R                |  261 ++++--
 R/plot_bar.R                      |  112 +-
 R/plot_boxplot.R                  |  214 +++--
 R/plot_heatmap.R                  |  260 +++---
 R/plot_volcano.R                  |  243 +++--
 R/ra_table.R                      |  102 +-
 R/random_forest.R                 |only
 R/read_metabo.R                   |   34 
 R/rf_plot_functions.R             |only
 R/transform_functions.R           |only
 build/vignette.rds                |binary
 inst/CITATION                     |   18 
 inst/doc/Omu_vignette.R           |   40 
 inst/doc/Omu_vignette.Rmd         |  121 --
 inst/doc/Omu_vignette.html        | 1581 ++------------------------------------
 inst/extdata/read_metabo_test.csv |    6 
 man/KEGG_gather.Rd                |   62 -
 man/PCA_plot.Rd                   |   69 +
 man/assign_hierarchy.Rd           |   50 -
 man/c57_nos2KO_mouse_countDF.Rd   |   34 
 man/c57_nos2KO_mouse_metadata.Rd  |   32 
 man/check_zeros.Rd                |only
 man/count_fold_changes.Rd         |   70 -
 man/get_seqs.Rd                   |only
 man/make_omelette.Rd              |   36 
 man/omu_anova.Rd                  |  102 +-
 man/omu_summary.Rd                |  106 +-
 man/pie_chart.Rd                  |   72 -
 man/plate_omelette.Rd             |   47 -
 man/plate_omelette_rxnko.Rd       |   34 
 man/plot_bar.Rd                   |   72 -
 man/plot_boxplot.Rd               |   88 +-
 man/plot_heatmap.Rd               |   92 +-
 man/plot_rf_PCA.Rd                |only
 man/plot_variable_importance.Rd   |only
 man/plot_volcano.Rd               |  127 +--
 man/ra_table.Rd                   |   58 -
 man/random_forest.Rd              |only
 man/read_metabo.Rd                |   38 
 man/transform_metabolites.Rd      |only
 man/transform_samples.Rd          |only
 vignettes/Omu_vignette.Rmd        |  121 --
 vignettes/vignettes               |  130 +--
 57 files changed, 3139 insertions(+), 3726 deletions(-)

More information about omu at CRAN
Permanent link

Package IFC updated to version 0.1.5 with previous version 0.1.2 dated 2021-10-13

Title: Tools for Imaging Flow Cytometry
Description: Contains several tools to treat imaging flow cytometry data from 'ImageStream®' and 'FlowSight®' cytometers ('Amnis®', part of 'Luminex®'). Provides an easy and simple way to read and write .fcs, .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved for each single cell. In addition, raw data such as images stored can also be accessed. Users, may hopefully increase their productivity thanks to dedicated functions to extract, visualize, manipulate and export 'IFC' data. Toy data example can be installed through the 'IFCdata' package of approximately 32 MB, which is available in a 'drat' repository <https://gitdemont.github.io/IFCdata/>. See file 'COPYRIGHTS' and file 'AUTHORS' for a list of copyright holders and authors.
Author: Yohann Demont [aut, cre], Gautier Stoll [ctb], Guido Kroemer [ldr], Jean-Pierre Marolleau [ldr], Loïc Garcon [ldr]
Maintainer: Yohann Demont <git.demont@gmail.com>

Diff between IFC versions 0.1.2 dated 2021-10-13 and 0.1.5 dated 2022-05-24

 IFC-0.1.2/IFC/R/gatingML.R                  |only
 IFC-0.1.2/IFC/man/convert_to_baseplot.Rd    |only
 IFC-0.1.5/IFC/DESCRIPTION                   |    8 
 IFC-0.1.5/IFC/MD5                           |  204 +++---
 IFC-0.1.5/IFC/NAMESPACE                     |    5 
 IFC-0.1.5/IFC/R/ExportToDAF.R               |   34 -
 IFC-0.1.5/IFC/R/ExportToReport.R            |  343 +++++++---
 IFC-0.1.5/IFC/R/ExtractFromDAF.R            |    6 
 IFC-0.1.5/IFC/R/ExtractFromXIF.R            |    4 
 IFC-0.1.5/IFC/R/GatingML.R                  |only
 IFC-0.1.5/IFC/R/RcppExports.R               |  332 ++++++++++
 IFC-0.1.5/IFC/R/applyGatingStrategy.R       |   27 
 IFC-0.1.5/IFC/R/autoplot.R                  |    5 
 IFC-0.1.5/IFC/R/buildBatch.R                |    6 
 IFC-0.1.5/IFC/R/buildGraph.R                |   47 -
 IFC-0.1.5/IFC/R/checksumDAF.R               |    2 
 IFC-0.1.5/IFC/R/data_add_features.R         |    6 
 IFC-0.1.5/IFC/R/data_add_pop_sample.R       |only
 IFC-0.1.5/IFC/R/data_add_pops.R             |   10 
 IFC-0.1.5/IFC/R/data_to_DAF.R               |    4 
 IFC-0.1.5/IFC/R/fastAny.R                   |only
 IFC-0.1.5/IFC/R/fastCbind.R                 |only
 IFC-0.1.5/IFC/R/fcs.R                       |  841 ++++++++++++++++++--------
 IFC-0.1.5/IFC/R/getFullTag.R                |    2 
 IFC-0.1.5/IFC/R/getIFD.R                    |    2 
 IFC-0.1.5/IFC/R/getInfo.R                   |    2 
 IFC-0.1.5/IFC/R/getOffsets.R                |    2 
 IFC-0.1.5/IFC/R/graphs_utils.R              |  888 +++++++++++++++++++++++-----
 IFC-0.1.5/IFC/R/group.R                     |only
 IFC-0.1.5/IFC/R/plotGraph.R                 |  382 ++----------
 IFC-0.1.5/IFC/R/popsRetrieveGraph.R         |    3 
 IFC-0.1.5/IFC/R/popsWithin.R                |    6 
 IFC-0.1.5/IFC/R/rasterplot.R                |only
 IFC-0.1.5/IFC/R/readGatingStrategy.R        |    6 
 IFC-0.1.5/IFC/R/strings_utils.R             |   38 +
 IFC-0.1.5/IFC/R/toXML2_graphs.R             |   15 
 IFC-0.1.5/IFC/R/trans_utils.R               |   23 
 IFC-0.1.5/IFC/R/whoami.R                    |  332 +++++-----
 IFC-0.1.5/IFC/R/writeGatingStrategy.R       |    4 
 IFC-0.1.5/IFC/R/writeIFC.R                  |  140 ++--
 IFC-0.1.5/IFC/R/xml_utils.R                 |    3 
 IFC-0.1.5/IFC/build                         |only
 IFC-0.1.5/IFC/inst/AUTHORS                  |    4 
 IFC-0.1.5/IFC/inst/CITATION                 |    6 
 IFC-0.1.5/IFC/inst/COPYRIGHTS               |   12 
 IFC-0.1.5/IFC/inst/include/align.hpp        |    6 
 IFC-0.1.5/IFC/inst/include/cbind.hpp        |only
 IFC-0.1.5/IFC/inst/include/decomp.hpp       |    3 
 IFC-0.1.5/IFC/inst/include/extract.hpp      |    3 
 IFC-0.1.5/IFC/inst/include/group.hpp        |only
 IFC-0.1.5/IFC/inst/include/plot.hpp         |only
 IFC-0.1.5/IFC/inst/include/scan.hpp         |    6 
 IFC-0.1.5/IFC/inst/include/tiff.hpp         |   61 -
 IFC-0.1.5/IFC/inst/include/trans.hpp        |   34 +
 IFC-0.1.5/IFC/inst/include/utils.hpp        |  187 +++++
 IFC-0.1.5/IFC/man/BatchReport.Rd            |   30 
 IFC-0.1.5/IFC/man/CreateGraphReport.Rd      |   12 
 IFC-0.1.5/IFC/man/ExportToFCS.Rd            |    6 
 IFC-0.1.5/IFC/man/ExportToReport.Rd         |   12 
 IFC-0.1.5/IFC/man/ExtractFromFCS.Rd         |    5 
 IFC-0.1.5/IFC/man/FCS_merge_dataset.Rd      |only
 IFC-0.1.5/IFC/man/FCS_merge_sample.Rd       |only
 IFC-0.1.5/IFC/man/FCS_to_data.Rd            |only
 IFC-0.1.5/IFC/man/applyGatingStrategy.Rd    |   15 
 IFC-0.1.5/IFC/man/applyTrans.Rd             |    2 
 IFC-0.1.5/IFC/man/buildGraph.Rd             |   23 
 IFC-0.1.5/IFC/man/convert_spillover.Rd      |only
 IFC-0.1.5/IFC/man/coord_to_px.Rd            |only
 IFC-0.1.5/IFC/man/cpp_align.Rd              |    2 
 IFC-0.1.5/IFC/man/cpp_as_nativeRaster.Rd    |only
 IFC-0.1.5/IFC/man/cpp_checkTIFF.Rd          |    2 
 IFC-0.1.5/IFC/man/cpp_checksum.Rd           |    2 
 IFC-0.1.5/IFC/man/cpp_coord_to_px.Rd        |only
 IFC-0.1.5/IFC/man/cpp_draw.Rd               |only
 IFC-0.1.5/IFC/man/cpp_fastTAGS.Rd           |    2 
 IFC-0.1.5/IFC/man/cpp_fast_cbind_DF_DF.Rd   |only
 IFC-0.1.5/IFC/man/cpp_fast_cbind_DF_L.Rd    |only
 IFC-0.1.5/IFC/man/cpp_fast_cbind_DF_M.Rd    |only
 IFC-0.1.5/IFC/man/cpp_fast_cbind_L_DF.Rd    |only
 IFC-0.1.5/IFC/man/cpp_fast_cbind_M_DF.Rd    |only
 IFC-0.1.5/IFC/man/cpp_fast_cbind_M_M.Rd     |only
 IFC-0.1.5/IFC/man/cpp_fast_factor.Rd        |only
 IFC-0.1.5/IFC/man/cpp_fast_listAny.Rd       |only
 IFC-0.1.5/IFC/man/cpp_fast_range.Rd         |only
 IFC-0.1.5/IFC/man/cpp_fast_rowAny.Rd        |only
 IFC-0.1.5/IFC/man/cpp_fast_sample.Rd        |only
 IFC-0.1.5/IFC/man/cpp_getTAGS.Rd            |    2 
 IFC-0.1.5/IFC/man/cpp_get_bytes_order.Rd    |only
 IFC-0.1.5/IFC/man/cpp_getoffsets_noid.Rd    |    2 
 IFC-0.1.5/IFC/man/cpp_getoffsets_wid.Rd     |    2 
 IFC-0.1.5/IFC/man/cpp_group_df.Rd           |only
 IFC-0.1.5/IFC/man/cpp_raster.Rd             |only
 IFC-0.1.5/IFC/man/cpp_replace_non_finite.Rd |only
 IFC-0.1.5/IFC/man/cpp_scanFirst.Rd          |    2 
 IFC-0.1.5/IFC/man/cpp_v_int32_to_uint32.Rd  |only
 IFC-0.1.5/IFC/man/cpp_v_int64_to_uint64.Rd  |only
 IFC-0.1.5/IFC/man/data_add_pop_sample.Rd    |only
 IFC-0.1.5/IFC/man/densCols.Rd               |    2 
 IFC-0.1.5/IFC/man/fastAny.Rd                |only
 IFC-0.1.5/IFC/man/fastCbind.Rd              |only
 IFC-0.1.5/IFC/man/fromXML2_gating.Rd        |    2 
 IFC-0.1.5/IFC/man/getFullTag.Rd             |    2 
 IFC-0.1.5/IFC/man/getIFD.Rd                 |    2 
 IFC-0.1.5/IFC/man/getOffsets.Rd             |    2 
 IFC-0.1.5/IFC/man/get_coordmap_adjusted.Rd  |only
 IFC-0.1.5/IFC/man/get_coordmap_raw.Rd       |only
 IFC-0.1.5/IFC/man/group.Rd                  |only
 IFC-0.1.5/IFC/man/layoutReport.Rd           |only
 IFC-0.1.5/IFC/man/parseFCSname.Rd           |only
 IFC-0.1.5/IFC/man/plotGraph.Rd              |    8 
 IFC-0.1.5/IFC/man/plot_base.Rd              |only
 IFC-0.1.5/IFC/man/plot_lattice.Rd           |only
 IFC-0.1.5/IFC/man/plot_raster.Rd            |only
 IFC-0.1.5/IFC/man/plot_stats.Rd             |only
 IFC-0.1.5/IFC/man/pow2.Rd                   |only
 IFC-0.1.5/IFC/man/rasterplot.Rd             |only
 IFC-0.1.5/IFC/man/readFCS.Rd                |   17 
 IFC-0.1.5/IFC/man/readGatingML.Rd           |    2 
 IFC-0.1.5/IFC/man/remove_ext.Rd             |    4 
 IFC-0.1.5/IFC/man/rev_string.Rd             |only
 IFC-0.1.5/IFC/man/toXML2_boolpop_gs.Rd      |    2 
 IFC-0.1.5/IFC/man/toXML2_graphpop_gs.Rd     |    2 
 IFC-0.1.5/IFC/man/toXML2_graphs_gs.Rd       |    2 
 IFC-0.1.5/IFC/man/toXML2_spillover_gs.Rd    |    2 
 IFC-0.1.5/IFC/man/trunc_string.Rd           |    2 
 IFC-0.1.5/IFC/man/writeGatingStrategy.Rd    |    2 
 IFC-0.1.5/IFC/man/writeIFC.Rd               |    5 
 IFC-0.1.5/IFC/src/RcppExports.cpp           |  277 ++++++++
 IFC-0.1.5/IFC/src/ifc.cpp                   |  376 +++++++++++
 129 files changed, 3545 insertions(+), 1341 deletions(-)

More information about IFC at CRAN
Permanent link

Package gtfstools updated to version 1.1.0 with previous version 1.0.0 dated 2021-11-16

Title: General Transit Feed Specification (GTFS) Editing and Analysing Tools
Description: Utility functions to read, manipulate, analyse and write transit feeds in the General Transit Feed Specification (GTFS) data format.
Author: Daniel Herszenhut [aut, cre] , Rafael H. M. Pereira [aut] , Pedro R. Andrade [aut] , Joao Bazzo [aut] , Mark Padgham [ctb], Marcus Saraiva [ctb] , Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Daniel Herszenhut <dhersz@gmail.com>

Diff between gtfstools versions 1.0.0 dated 2021-11-16 and 1.1.0 dated 2022-05-24

 gtfstools-1.0.0/gtfstools/man/polygon_from_bbox.Rd                        |only
 gtfstools-1.1.0/gtfstools/DESCRIPTION                                     |   18 
 gtfstools-1.1.0/gtfstools/MD5                                             |  195 ++++----
 gtfstools-1.1.0/gtfstools/NAMESPACE                                       |   12 
 gtfstools-1.1.0/gtfstools/NEWS.md                                         |   29 +
 gtfstools-1.1.0/gtfstools/R/convert_shapes_to_sf.R                        |   30 -
 gtfstools-1.1.0/gtfstools/R/convert_stops_to_sf.R                         |    6 
 gtfstools-1.1.0/gtfstools/R/convert_time_to_seconds.R                     |only
 gtfstools-1.1.0/gtfstools/R/filter_by_agency_id.R                         |only
 gtfstools-1.1.0/gtfstools/R/filter_by_route_id.R                          |   11 
 gtfstools-1.1.0/gtfstools/R/filter_by_route_type.R                        |    7 
 gtfstools-1.1.0/gtfstools/R/filter_by_service_id.R                        |only
 gtfstools-1.1.0/gtfstools/R/filter_by_sf.R                                |   33 -
 gtfstools-1.1.0/gtfstools/R/filter_by_shape_id.R                          |   11 
 gtfstools-1.1.0/gtfstools/R/filter_by_stop_id.R                           |    7 
 gtfstools-1.1.0/gtfstools/R/filter_by_time_of_day.R                       |only
 gtfstools-1.1.0/gtfstools/R/filter_by_trip_id.R                           |   11 
 gtfstools-1.1.0/gtfstools/R/filter_by_weekday.R                           |only
 gtfstools-1.1.0/gtfstools/R/frequencies_to_stop_times.R                   |only
 gtfstools-1.1.0/gtfstools/R/get_children_stops.R                          |only
 gtfstools-1.1.0/gtfstools/R/get_parent_station.R                          |   74 +--
 gtfstools-1.1.0/gtfstools/R/get_stop_times_patterns.R                     |only
 gtfstools-1.1.0/gtfstools/R/get_trip_duration.R                           |   91 ++-
 gtfstools-1.1.0/gtfstools/R/get_trip_geometry.R                           |   85 +--
 gtfstools-1.1.0/gtfstools/R/get_trip_length.R                             |only
 gtfstools-1.1.0/gtfstools/R/get_trip_segment_duration.R                   |  116 ++--
 gtfstools-1.1.0/gtfstools/R/get_trip_speed.R                              |   82 +--
 gtfstools-1.1.0/gtfstools/R/gtfstools.R                                   |   31 +
 gtfstools-1.1.0/gtfstools/R/merge_gtfs.R                                  |  164 ++++--
 gtfstools-1.1.0/gtfstools/R/read_gtfs.R                                   |   34 -
 gtfstools-1.1.0/gtfstools/R/remove_duplicates.R                           |    2 
 gtfstools-1.1.0/gtfstools/R/set_trip_speed.R                              |   95 +--
 gtfstools-1.1.0/gtfstools/R/standards.R                                   |    4 
 gtfstools-1.1.0/gtfstools/R/utils.R                                       |   13 
 gtfstools-1.1.0/gtfstools/R/validate_gtfs.R                               |    2 
 gtfstools-1.1.0/gtfstools/R/write_gtfs.R                                  |   40 -
 gtfstools-1.1.0/gtfstools/README.md                                       |   22 
 gtfstools-1.1.0/gtfstools/build/vignette.rds                              |binary
 gtfstools-1.1.0/gtfstools/inst/CITATION                                   |   14 
 gtfstools-1.1.0/gtfstools/inst/doc/filtering.R                            |   80 +++
 gtfstools-1.1.0/gtfstools/inst/doc/filtering.Rmd                          |  135 ++++-
 gtfstools-1.1.0/gtfstools/inst/doc/filtering.html                         |  239 ++++++++--
 gtfstools-1.1.0/gtfstools/inst/doc/gtfstools.R                            |    8 
 gtfstools-1.1.0/gtfstools/inst/doc/gtfstools.Rmd                          |   14 
 gtfstools-1.1.0/gtfstools/inst/doc/gtfstools.html                         |   35 -
 gtfstools-1.1.0/gtfstools/man/convert_from_standard.Rd                    |    2 
 gtfstools-1.1.0/gtfstools/man/convert_shapes_to_sf.Rd                     |    2 
 gtfstools-1.1.0/gtfstools/man/convert_stops_to_sf.Rd                      |    2 
 gtfstools-1.1.0/gtfstools/man/convert_time_to_seconds.Rd                  |only
 gtfstools-1.1.0/gtfstools/man/convert_to_standard.Rd                      |    2 
 gtfstools-1.1.0/gtfstools/man/copy_gtfs_diff_field_class.Rd               |    2 
 gtfstools-1.1.0/gtfstools/man/copy_gtfs_without_field.Rd                  |    2 
 gtfstools-1.1.0/gtfstools/man/copy_gtfs_without_file.Rd                   |    2 
 gtfstools-1.1.0/gtfstools/man/figures/gtfstools_hex_black.png             |only
 gtfstools-1.1.0/gtfstools/man/figures/logo.png                            |only
 gtfstools-1.1.0/gtfstools/man/filter_by_agency_id.Rd                      |only
 gtfstools-1.1.0/gtfstools/man/filter_by_route_id.Rd                       |    8 
 gtfstools-1.1.0/gtfstools/man/filter_by_route_type.Rd                     |    8 
 gtfstools-1.1.0/gtfstools/man/filter_by_service_id.Rd                     |only
 gtfstools-1.1.0/gtfstools/man/filter_by_sf.Rd                             |    8 
 gtfstools-1.1.0/gtfstools/man/filter_by_shape_id.Rd                       |    8 
 gtfstools-1.1.0/gtfstools/man/filter_by_stop_id.Rd                        |    8 
 gtfstools-1.1.0/gtfstools/man/filter_by_time_of_day.Rd                    |only
 gtfstools-1.1.0/gtfstools/man/filter_by_trip_id.Rd                        |    8 
 gtfstools-1.1.0/gtfstools/man/filter_by_weekday.Rd                        |only
 gtfstools-1.1.0/gtfstools/man/frequencies_to_stop_times.Rd                |only
 gtfstools-1.1.0/gtfstools/man/get_children_stops.Rd                       |only
 gtfstools-1.1.0/gtfstools/man/get_parent_station.Rd                       |   23 
 gtfstools-1.1.0/gtfstools/man/get_stop_times_patterns.Rd                  |only
 gtfstools-1.1.0/gtfstools/man/get_trip_duration.Rd                        |   14 
 gtfstools-1.1.0/gtfstools/man/get_trip_geometry.Rd                        |    2 
 gtfstools-1.1.0/gtfstools/man/get_trip_length.Rd                          |only
 gtfstools-1.1.0/gtfstools/man/get_trip_segment_duration.Rd                |   11 
 gtfstools-1.1.0/gtfstools/man/get_trip_speed.Rd                           |   35 -
 gtfstools-1.1.0/gtfstools/man/gtfstools.Rd                                |    8 
 gtfstools-1.1.0/gtfstools/man/merge_gtfs.Rd                               |   48 +-
 gtfstools-1.1.0/gtfstools/man/read_gtfs.Rd                                |    9 
 gtfstools-1.1.0/gtfstools/man/remove_duplicates.Rd                        |    2 
 gtfstools-1.1.0/gtfstools/man/roxygen                                     |only
 gtfstools-1.1.0/gtfstools/man/set_trip_speed.Rd                           |   59 +-
 gtfstools-1.1.0/gtfstools/man/validate_gtfs.Rd                            |    2 
 gtfstools-1.1.0/gtfstools/man/write_gtfs.Rd                               |   15 
 gtfstools-1.1.0/gtfstools/src/convert-time.cpp                            |   45 +
 gtfstools-1.1.0/gtfstools/src/convert-time.h                              |   10 
 gtfstools-1.1.0/gtfstools/src/cpp11.cpp                                   |    2 
 gtfstools-1.1.0/gtfstools/tests/testthat/test-convert_shapes_to_sf.R      |   16 
 gtfstools-1.1.0/gtfstools/tests/testthat/test-convert_stops_to_sf.R       |    7 
 gtfstools-1.1.0/gtfstools/tests/testthat/test-convert_time_to_seconds.R   |only
 gtfstools-1.1.0/gtfstools/tests/testthat/test-filter_by_agency_id.R       |only
 gtfstools-1.1.0/gtfstools/tests/testthat/test-filter_by_route_id.R        |   35 +
 gtfstools-1.1.0/gtfstools/tests/testthat/test-filter_by_route_type.R      |    2 
 gtfstools-1.1.0/gtfstools/tests/testthat/test-filter_by_service_id.R      |only
 gtfstools-1.1.0/gtfstools/tests/testthat/test-filter_by_sf.R              |   10 
 gtfstools-1.1.0/gtfstools/tests/testthat/test-filter_by_shape_id.R        |   35 +
 gtfstools-1.1.0/gtfstools/tests/testthat/test-filter_by_stop_id.R         |    8 
 gtfstools-1.1.0/gtfstools/tests/testthat/test-filter_by_time_of_day.R     |only
 gtfstools-1.1.0/gtfstools/tests/testthat/test-filter_by_trip_id.R         |   35 +
 gtfstools-1.1.0/gtfstools/tests/testthat/test-filter_by_weekday.R         |only
 gtfstools-1.1.0/gtfstools/tests/testthat/test-frequencies_to_stop_times.R |only
 gtfstools-1.1.0/gtfstools/tests/testthat/test-get_children_stops.R        |only
 gtfstools-1.1.0/gtfstools/tests/testthat/test-get_parent_station.R        |   85 +--
 gtfstools-1.1.0/gtfstools/tests/testthat/test-get_stop_times_patterns.R   |only
 gtfstools-1.1.0/gtfstools/tests/testthat/test-get_trip_duration.R         |  134 ++---
 gtfstools-1.1.0/gtfstools/tests/testthat/test-get_trip_geometry.R         |  220 +++------
 gtfstools-1.1.0/gtfstools/tests/testthat/test-get_trip_length.R           |only
 gtfstools-1.1.0/gtfstools/tests/testthat/test-get_trip_segment_duration.R |  124 ++---
 gtfstools-1.1.0/gtfstools/tests/testthat/test-get_trip_speed.R            |  214 +++++---
 gtfstools-1.1.0/gtfstools/tests/testthat/test-merge_gtfs.R                |   72 ++-
 gtfstools-1.1.0/gtfstools/tests/testthat/test-read_gtfs.R                 |   10 
 gtfstools-1.1.0/gtfstools/tests/testthat/test-set_trip_speed.R            |   41 -
 gtfstools-1.1.0/gtfstools/tests/testthat/test-utils.R                     |    3 
 gtfstools-1.1.0/gtfstools/tests/testthat/test-write_gtfs.R                |   19 
 gtfstools-1.1.0/gtfstools/vignettes/filtering.Rmd                         |  135 ++++-
 gtfstools-1.1.0/gtfstools/vignettes/gtfstools.Rmd                         |   14 
 114 files changed, 1891 insertions(+), 1425 deletions(-)

More information about gtfstools at CRAN
Permanent link

Package GeoWeightedModel updated to version 1.0.2 with previous version 1.0.0 dated 2022-05-11

Title: User-Friendly Interface for Geographically-Weighted Models
Description: Contains the development of a tool that provides a web-based graphical user interface (GUI) to perform Techniques from a subset of spatial statistics known as geographically weighted (GW) models. Contains methods described by Brunsdon et al., 1996 <doi:10.1111/j.1538-4632.1996.tb00936.x>, Brunsdon et al., 2002 <doi:10.1016/s0198-9715(01)00009-6>, Harris et al., 2011 <doi:10.1080/13658816.2011.554838>, Brunsdon et al., 2007 <doi:10.1111/j.1538-4632.2007.00709.x>.
Author: Javier De La Hoz Maestre [cre, aut] , Maria Jose Fernandez Gomez [aut] , Susana Mendez [aut]
Maintainer: Javier De La Hoz Maestre <jdelahozmaestre@gmail.com>

Diff between GeoWeightedModel versions 1.0.0 dated 2022-05-11 and 1.0.2 dated 2022-05-24

 DESCRIPTION                                            |    6 
 MD5                                                    |   22 -
 inst/GeoWeightedModelApp/server.R                      |   73 ++--
 inst/GeoWeightedModelApp/ui.R                          |   27 -
 inst/GeoWeightedModelApp/www/Distance_Matrix.html      |  261 +++++++++++++-
 inst/GeoWeightedModelApp/www/Help_Autocorrelation.html |   94 ++---
 inst/GeoWeightedModelApp/www/Help_bw.html              |  309 +++++++++++++++--
 inst/GeoWeightedModelApp/www/Help_gwda.html            |  301 ++++++++++++++--
 inst/GeoWeightedModelApp/www/Help_gwpca.html           |  293 ++++++++++++++--
 inst/GeoWeightedModelApp/www/Help_gwss.html            |  300 ++++++++++++++--
 inst/GeoWeightedModelApp/www/Upload-data.html          |  233 ++++++++++++
 inst/GeoWeightedModelApp/www/help_gwr.html             |  157 +++++---
 12 files changed, 1721 insertions(+), 355 deletions(-)

More information about GeoWeightedModel at CRAN
Permanent link

Package composits updated to version 0.1.1 with previous version 0.1.0 dated 2020-09-30

Title: Compositional, Multivariate and Univariate Time Series Outlier Ensemble
Description: A compositional, multivariate and univariate time series outlier ensemble. It uses the four R packages 'forecast', 'tsoutliers', 'otsad' and 'anomalize' to detect time series outliers (Kandanaarachchi, Menendez 2020) <doi:10.13140/RG.2.2.32217.95845>.
Author: Sevvandi Kandanaarachchi [aut, cre] , Patricia Menendez [aut] , Ursula Laa [aut] , Ruben Loaiza-Maya [aut]
Maintainer: Sevvandi Kandanaarachchi <sevvandik@gmail.com>

Diff between composits versions 0.1.0 dated 2020-09-30 and 0.1.1 dated 2022-05-24

 DESCRIPTION                       |   16 
 MD5                               |   54 -
 R/apportion_scores_comp.R         |    2 
 R/apportion_scores_multivariate.R |    2 
 R/composite_tsout_ensemble.R      |    2 
 R/dimred_methods_tsout_ensemble.R |    2 
 R/draw_table.R                    |    8 
 R/multivariate_tsout_ensemble.R   |    3 
 R/plot_decomposed.R               |   13 
 R/univariate_tsout_ensemble.R     |    4 
 R/utils.R                         |    1 
 README.md                         |   44 -
 build/vignette.rds                |binary
 inst/doc/composits.R              |   44 -
 inst/doc/composits.Rmd            |   12 
 inst/doc/composits.html           | 1548 ++++++++++++++++++++++----------------
 man/apportion_scores_comp.Rd      |    2 
 man/apportion_scores_mv.Rd        |    2 
 man/comp_tsout_ens.Rd             |    2 
 man/draw_table.Rd                 |    6 
 man/draw_table_html.Rd            |    6 
 man/mv_tsout_ens.Rd               |    3 
 man/plot_biplot.Rd                |    3 
 man/plot_decomposed.Rd            |    3 
 man/plot_decomposed_all.Rd        |    3 
 man/spanish_morte.Rd              |   40 
 man/uv_tsout_ens.Rd               |    2 
 vignettes/composits.Rmd           |   12 
 28 files changed, 1042 insertions(+), 797 deletions(-)

More information about composits at CRAN
Permanent link

Package clusterSim updated to version 0.50-1 with previous version 0.49-2 dated 2021-01-06

Title: Searching for Optimal Clustering Procedure for a Data Set
Description: Distance measures (GDM1, GDM2, Sokal-Michener, Bray-Curtis, for symbolic interval-valued data), cluster quality indices (Calinski-Harabasz, Baker-Hubert, Hubert-Levine, Silhouette, Krzanowski-Lai, Hartigan, Gap, Davies-Bouldin), data normalization formulas (metric data, interval-valued symbolic data), data generation (typical and non-typical data), HINoV method, replication analysis, linear ordering methods, spectral clustering, agreement indices between two partitions, plot functions (for categorical and symbolic interval-valued data). (MILLIGAN, G.W., COOPER, M.C. (1985) <doi:10.1007/BF02294245>, HUBERT, L., ARABIE, P. (1985) <doi:10.1007%2FBF01908075>, RAND, W.M. (1971) <doi:10.1080/01621459.1971.10482356>, JAJUGA, K., WALESIAK, M. (2000) <doi:10.1007/978-3-642-57280-7_11>, MILLIGAN, G.W., COOPER, M.C. (1988) <doi:10.1007/BF01897163>, JAJUGA, K., WALESIAK, M., BAK, A. (2003) <doi:10.1007/978-3-642-55721-7_12>, DAVIES, D.L., BOULDIN, D.W. (1979) <doi:10.1109/TPAMI.1979.4766909>, CALINSKI, T., HARABASZ, J. (1974) <doi:10.1080/03610927408827101>, HUBERT, L. (1974) <doi:10.1080/01621459.1974.10480191>, TIBSHIRANI, R., WALTHER, G., HASTIE, T. (2001) <doi:10.1111/1467-9868.00293>, BRECKENRIDGE, J.N. (2000) <doi:10.1207/S15327906MBR3502_5>, WALESIAK, M., DUDEK, A. (2008) <doi:10.1007/978-3-540-78246-9_11>).
Author: Marek Walesiak <marek.walesiak@ue.wroc.pl>, Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Maintainer: Andrzej Dudek <andrzej.dudek@ue.wroc.pl>

Diff between clusterSim versions 0.49-2 dated 2021-01-06 and 0.50-1 dated 2022-05-24

 clusterSim-0.49-2/clusterSim/man/plotCategorial3d.rd                  |only
 clusterSim-0.50-1/clusterSim/DESCRIPTION                              |   10 -
 clusterSim-0.50-1/clusterSim/MD5                                      |   76 +++++-----
 clusterSim-0.50-1/clusterSim/NAMESPACE                                |    1 
 clusterSim-0.50-1/clusterSim/R/reszta.r                               |   52 ------
 clusterSim-0.50-1/clusterSim/R/shapes.r                               |   19 --
 clusterSim-0.50-1/clusterSim/build/partial.rdb                        |binary
 clusterSim-0.50-1/clusterSim/data/data_binary.rda                     |binary
 clusterSim-0.50-1/clusterSim/data/data_interval.rda                   |binary
 clusterSim-0.50-1/clusterSim/data/data_mixed.rda                      |binary
 clusterSim-0.50-1/clusterSim/data/data_nominal.rda                    |binary
 clusterSim-0.50-1/clusterSim/data/data_ordinal.rda                    |binary
 clusterSim-0.50-1/clusterSim/data/data_ratio.rda                      |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/HINoVMod_details.pdf            |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/HINoVSymbolic_details.pdf       |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/IndexGap_details.pdf            |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/clusterGen_details.pdf          |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/clusterSim_details.pdf          |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/comparingPartitions_details.pdf |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/dataNormalization_details.pdf   |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/distBC_details.pdf              |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/distGDM_details.pdf             |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/distSM_details.pdf              |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/distSymbolic_details.pdf        |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/indexC_details.pdf              |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/indexDB_details.pdf             |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/indexG1_details.pdf             |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/indexG2_details.pdf             |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/indexG3_details.pdf             |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/indexH_details.pdf              |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/indexKL_details.pdf             |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/indexS_details.pdf              |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/ordinalToMetric_details.pdf     |only
 clusterSim-0.50-1/clusterSim/inst/pdf/patternGDM1_details.pdf         |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/patternGDM2_details.pdf         |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/replicationMod_details.pdf      |binary
 clusterSim-0.50-1/clusterSim/inst/pdf/speccl_details.pdf              |binary
 clusterSim-0.50-1/clusterSim/man/plotCategorial.rd                    |    2 
 clusterSim-0.50-1/clusterSim/man/plotInterval.rd                      |    2 
 clusterSim-0.50-1/clusterSim/man/shapes.blocks3d.rd                   |    4 
 40 files changed, 49 insertions(+), 117 deletions(-)

More information about clusterSim at CRAN
Permanent link

Package bcdata updated to version 0.3.1 with previous version 0.3.0 dated 2021-10-28

Title: Search and Retrieve Data from the BC Data Catalogue
Description: Search, query, and download tabular and 'geospatial' data from the British Columbia Data Catalogue (<https://catalogue.data.gov.bc.ca/>). Search catalogue data records based on keywords, data licence, sector, data format, and B.C. government organization. View metadata directly in R, download many data formats, and query 'geospatial' data available via the B.C. government Web Feature Service ('WFS') using 'dplyr' syntax.
Author: Andy Teucher [aut, cre] , Sam Albers [aut, ctb] , Stephanie Hazlitt [aut, ctb] , Province of British Columbia [cph]
Maintainer: Andy Teucher <andy.teucher@gov.bc.ca>

Diff between bcdata versions 0.3.0 dated 2021-10-28 and 0.3.1 dated 2022-05-24

 bcdata-0.3.0/bcdata/man/make_url.Rd                                                       |only
 bcdata-0.3.1/bcdata/DESCRIPTION                                                           |   12 
 bcdata-0.3.1/bcdata/MD5                                                                   |   40 +-
 bcdata-0.3.1/bcdata/NAMESPACE                                                             |    5 
 bcdata-0.3.1/bcdata/NEWS.md                                                               |    7 
 bcdata-0.3.1/bcdata/R/bcdc-get-citation.R                                                 |only
 bcdata-0.3.1/bcdata/R/bcdc-web-services.R                                                 |    6 
 bcdata-0.3.1/bcdata/R/bcdc_browse.R                                                       |    1 
 bcdata-0.3.1/bcdata/R/cql-translator.R                                                    |    6 
 bcdata-0.3.1/bcdata/R/get_data.R                                                          |    5 
 bcdata-0.3.1/bcdata/R/utils-classes.R                                                     |   17 -
 bcdata-0.3.1/bcdata/R/utils.R                                                             |    1 
 bcdata-0.3.1/bcdata/build/vignette.rds                                                    |binary
 bcdata-0.3.1/bcdata/inst/doc/bcdata.html                                                  |   97 ++++-
 bcdata-0.3.1/bcdata/inst/doc/efficiently-query-spatial-data-in-the-bc-data-catalogue.html |  162 ++++++++--
 bcdata-0.3.1/bcdata/inst/doc/explore-silviculture-data-using-bcdata.html                  |  108 +++++-
 bcdata-0.3.1/bcdata/inst/doc/service_documentation.html                                   |   23 +
 bcdata-0.3.1/bcdata/man/bcdata-package.Rd                                                 |    4 
 bcdata-0.3.1/bcdata/man/bcdc_get_citation.Rd                                              |only
 bcdata-0.3.1/bcdata/tests/testthat/test-bcdc-get-citation.R                               |only
 bcdata-0.3.1/bcdata/tests/testthat/test-edge-cases.R                                      |    5 
 bcdata-0.3.1/bcdata/tests/testthat/test-get-data.R                                        |   10 
 bcdata-0.3.1/bcdata/tests/testthat/test-search.R                                          |   13 
 23 files changed, 408 insertions(+), 114 deletions(-)

More information about bcdata at CRAN
Permanent link

Package BayesMallows updated to version 1.2.0 with previous version 1.1.2 dated 2022-04-11

Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model (Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>; Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>). Both Metropolis-Hastings and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule, Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the posterior distributions of parameters are provided. The package also provides functions for estimating the partition function (normalizing constant) of the Mallows rank model, both with the importance sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm (Mukherjee, Annals of Statistics, 2016 <doi:10.1214/15-AOS1389>).
Author: Oystein Sorensen [aut, cre] , Valeria Vitelli [aut] , Marta Crispino [aut], Qinghua Liu [aut], Cristina Mollica [aut], Luca Tardella [aut], Anja Stein [aut], Waldir Leoncio [ctr]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>

Diff between BayesMallows versions 1.1.2 dated 2022-04-11 and 1.2.0 dated 2022-05-24

 BayesMallows-1.1.2/BayesMallows/R/lik_db_mix.R                                            |only
 BayesMallows-1.1.2/BayesMallows/R/misc_likelihood.R                                       |only
 BayesMallows-1.1.2/BayesMallows/inst/examples/lik_db_mix_example.R                        |only
 BayesMallows-1.1.2/BayesMallows/man/lik_db_mix.Rd                                         |only
 BayesMallows-1.1.2/BayesMallows/man/metropolis_hastings_aug_ranking_pseudo.Rd             |only
 BayesMallows-1.1.2/BayesMallows/man/smc_mallows_new_item_rank_alpha_fixed.Rd              |only
 BayesMallows-1.1.2/BayesMallows/man/smc_mallows_new_users_complete.Rd                     |only
 BayesMallows-1.1.2/BayesMallows/man/smc_mallows_new_users_partial.Rd                      |only
 BayesMallows-1.1.2/BayesMallows/man/smc_mallows_new_users_partial_alpha_fixed.Rd          |only
 BayesMallows-1.1.2/BayesMallows/src/smc_calculate_backward_probability.cpp                |only
 BayesMallows-1.1.2/BayesMallows/src/smc_calculate_forward_probability.cpp                 |only
 BayesMallows-1.1.2/BayesMallows/src/smc_get_mallows_loglik.cpp                            |only
 BayesMallows-1.1.2/BayesMallows/src/smc_mallows_new_item_rank_alpha_fixed.cpp             |only
 BayesMallows-1.1.2/BayesMallows/src/smc_mallows_new_users_complete.cpp                    |only
 BayesMallows-1.1.2/BayesMallows/src/smc_mallows_new_users_partial.cpp                     |only
 BayesMallows-1.1.2/BayesMallows/src/smc_mallows_new_users_partial_alpha_fixed.cpp         |only
 BayesMallows-1.1.2/BayesMallows/src/smc_metropolis_hastings_aug_ranking_pseudo.cpp        |only
 BayesMallows-1.1.2/BayesMallows/tests/testthat/test-lik_db_mix.R                          |only
 BayesMallows-1.1.2/BayesMallows/tests/testthat/test-misc_cpp.R                            |only
 BayesMallows-1.2.0/BayesMallows/DESCRIPTION                                               |   20 
 BayesMallows-1.2.0/BayesMallows/MD5                                                       |  284 +++----
 BayesMallows-1.2.0/BayesMallows/NAMESPACE                                                 |    5 
 BayesMallows-1.2.0/BayesMallows/NEWS.md                                                   |   25 
 BayesMallows-1.2.0/BayesMallows/R/RcppExports.R                                           |  173 ----
 BayesMallows-1.2.0/BayesMallows/R/all_topological_sorts.R                                 |   11 
 BayesMallows-1.2.0/BayesMallows/R/assess_convergence.R                                    |   61 -
 BayesMallows-1.2.0/BayesMallows/R/assign_cluster.R                                        |   57 -
 BayesMallows-1.2.0/BayesMallows/R/catch-routine-registration.R                            |only
 BayesMallows-1.2.0/BayesMallows/R/compute_consensus.R                                     |  278 ++-----
 BayesMallows-1.2.0/BayesMallows/R/compute_mallows.R                                       |   84 +-
 BayesMallows-1.2.0/BayesMallows/R/compute_mallows_mixtures.R                              |    1 
 BayesMallows-1.2.0/BayesMallows/R/compute_posterior_intervals.R                           |  191 +----
 BayesMallows-1.2.0/BayesMallows/R/estimate_partition_function.R                           |   32 
 BayesMallows-1.2.0/BayesMallows/R/expected_dist.R                                         |   18 
 BayesMallows-1.2.0/BayesMallows/R/generate_constraints.R                                  |   21 
 BayesMallows-1.2.0/BayesMallows/R/generate_initial_ranking.R                              |   54 -
 BayesMallows-1.2.0/BayesMallows/R/generate_transitive_closure.R                           |   20 
 BayesMallows-1.2.0/BayesMallows/R/get_mallows_loglik.R                                    |only
 BayesMallows-1.2.0/BayesMallows/R/misc.R                                                  |   47 -
 BayesMallows-1.2.0/BayesMallows/R/misc_expected_dist.R                                    |   76 +-
 BayesMallows-1.2.0/BayesMallows/R/plot.BayesMallows.R                                     |   30 
 BayesMallows-1.2.0/BayesMallows/R/plot_elbow.R                                            |    9 
 BayesMallows-1.2.0/BayesMallows/R/plot_top_k.R                                            |   23 
 BayesMallows-1.2.0/BayesMallows/R/predict_top_k.R                                         |   47 -
 BayesMallows-1.2.0/BayesMallows/R/print.BayesMallowsMixtures.R                            |    6 
 BayesMallows-1.2.0/BayesMallows/R/rank_conversion.R                                       |    1 
 BayesMallows-1.2.0/BayesMallows/R/rank_distance.R                                         |    8 
 BayesMallows-1.2.0/BayesMallows/R/rank_freq_distr.R                                       |    2 
 BayesMallows-1.2.0/BayesMallows/R/sample_mallows.R                                        |   48 -
 BayesMallows-1.2.0/BayesMallows/R/smc_mallows_deprecated.R                                |only
 BayesMallows-1.2.0/BayesMallows/R/smc_post_processing_functions.R                         |   26 
 BayesMallows-1.2.0/BayesMallows/R/sysdata.rda                                             |binary
 BayesMallows-1.2.0/BayesMallows/R/tidy_mcmc.R                                             |   53 -
 BayesMallows-1.2.0/BayesMallows/build/partial.rdb                                         |binary
 BayesMallows-1.2.0/BayesMallows/build/vignette.rds                                        |binary
 BayesMallows-1.2.0/BayesMallows/data/beach_preferences.rda                                |binary
 BayesMallows-1.2.0/BayesMallows/inst/REFERENCES.bib                                       |   48 -
 BayesMallows-1.2.0/BayesMallows/inst/doc/SMC-Mallows.R                                    |   14 
 BayesMallows-1.2.0/BayesMallows/inst/doc/SMC-Mallows.Rmd                                  |   72 +
 BayesMallows-1.2.0/BayesMallows/inst/doc/SMC-Mallows.html                                 |  274 +++----
 BayesMallows-1.2.0/BayesMallows/inst/examples/compute_consensus_example.R                 |   10 
 BayesMallows-1.2.0/BayesMallows/inst/examples/compute_mallows_example.R                   |    4 
 BayesMallows-1.2.0/BayesMallows/inst/examples/compute_mallows_mixtures_example.R          |   17 
 BayesMallows-1.2.0/BayesMallows/inst/examples/estimate_partition_function_example.R       |   25 
 BayesMallows-1.2.0/BayesMallows/inst/examples/generate_transitive_closure_example.R       |   29 
 BayesMallows-1.2.0/BayesMallows/inst/examples/get_mallows_loglik_example.R                |only
 BayesMallows-1.2.0/BayesMallows/inst/examples/label_switching_example.R                   |   15 
 BayesMallows-1.2.0/BayesMallows/inst/examples/obs_freq_example.R                          |   22 
 BayesMallows-1.2.0/BayesMallows/inst/examples/plot_top_k_example.R                        |    4 
 BayesMallows-1.2.0/BayesMallows/inst/examples/smc_mallows_new_users_complete_example.R    |   44 -
 BayesMallows-1.2.0/BayesMallows/man/beach_preferences.Rd                                  |    2 
 BayesMallows-1.2.0/BayesMallows/man/compute_consensus.Rd                                  |   10 
 BayesMallows-1.2.0/BayesMallows/man/compute_mallows.Rd                                    |    4 
 BayesMallows-1.2.0/BayesMallows/man/compute_mallows_mixtures.Rd                           |   17 
 BayesMallows-1.2.0/BayesMallows/man/estimate_partition_function.Rd                        |   25 
 BayesMallows-1.2.0/BayesMallows/man/figures/README-unnamed-chunk-5-1.png                  |binary
 BayesMallows-1.2.0/BayesMallows/man/figures/README-unnamed-chunk-6-1.png                  |binary
 BayesMallows-1.2.0/BayesMallows/man/generate_transitive_closure.Rd                        |   29 
 BayesMallows-1.2.0/BayesMallows/man/get_exponent_sum.Rd                                   |only
 BayesMallows-1.2.0/BayesMallows/man/get_mallows_loglik.Rd                                 |  121 ++-
 BayesMallows-1.2.0/BayesMallows/man/label_switching.Rd                                    |   15 
 BayesMallows-1.2.0/BayesMallows/man/leap_and_shift_probs.Rd                               |    7 
 BayesMallows-1.2.0/BayesMallows/man/metropolis_hastings_aug_ranking.Rd                    |   22 
 BayesMallows-1.2.0/BayesMallows/man/obs_freq.Rd                                           |   22 
 BayesMallows-1.2.0/BayesMallows/man/plot_elbow.Rd                                         |   17 
 BayesMallows-1.2.0/BayesMallows/man/plot_top_k.Rd                                         |    4 
 BayesMallows-1.2.0/BayesMallows/man/predict_top_k.Rd                                      |   21 
 BayesMallows-1.2.0/BayesMallows/man/smc_mallows_new_item_rank.Rd                          |   34 
 BayesMallows-1.2.0/BayesMallows/man/smc_mallows_new_users.Rd                              |only
 BayesMallows-1.2.0/BayesMallows/src/RcppExports.cpp                                       |  181 ----
 BayesMallows-1.2.0/BayesMallows/src/distances.cpp                                         |   38 -
 BayesMallows-1.2.0/BayesMallows/src/distances.h                                           |    3 
 BayesMallows-1.2.0/BayesMallows/src/importance_sampling.cpp                               |   42 -
 BayesMallows-1.2.0/BayesMallows/src/leapandshift.cpp                                      |   60 -
 BayesMallows-1.2.0/BayesMallows/src/leapandshift.h                                        |    4 
 BayesMallows-1.2.0/BayesMallows/src/misc.cpp                                              |  154 ----
 BayesMallows-1.2.0/BayesMallows/src/misc.h                                                |   13 
 BayesMallows-1.2.0/BayesMallows/src/missing_data.cpp                                      |   45 -
 BayesMallows-1.2.0/BayesMallows/src/missing_data.h                                        |    3 
 BayesMallows-1.2.0/BayesMallows/src/mixtures.cpp                                          |   64 -
 BayesMallows-1.2.0/BayesMallows/src/mixtures.h                                            |    1 
 BayesMallows-1.2.0/BayesMallows/src/pairwise_comparisons.cpp                              |   89 +-
 BayesMallows-1.2.0/BayesMallows/src/pairwise_comparisons.h                                |    4 
 BayesMallows-1.2.0/BayesMallows/src/parameterupdates.cpp                                  |   48 -
 BayesMallows-1.2.0/BayesMallows/src/parameterupdates.h                                    |    7 
 BayesMallows-1.2.0/BayesMallows/src/partitionfuns.cpp                                     |   73 -
 BayesMallows-1.2.0/BayesMallows/src/partitionfuns.h                                       |    4 
 BayesMallows-1.2.0/BayesMallows/src/rmallows.cpp                                          |   16 
 BayesMallows-1.2.0/BayesMallows/src/run_mcmc.cpp                                          |   68 -
 BayesMallows-1.2.0/BayesMallows/src/sample.cpp                                            |only
 BayesMallows-1.2.0/BayesMallows/src/sample.h                                              |only
 BayesMallows-1.2.0/BayesMallows/src/setdiff.h                                             |only
 BayesMallows-1.2.0/BayesMallows/src/smc.h                                                 |    8 
 BayesMallows-1.2.0/BayesMallows/src/smc_calculate_probability.cpp                         |only
 BayesMallows-1.2.0/BayesMallows/src/smc_correction_kernel.cpp                             |    9 
 BayesMallows-1.2.0/BayesMallows/src/smc_correction_kernel_pseudo.cpp                      |   43 -
 BayesMallows-1.2.0/BayesMallows/src/smc_get_exponent_sum.cpp                              |only
 BayesMallows-1.2.0/BayesMallows/src/smc_get_sample_probabilities.cpp                      |   17 
 BayesMallows-1.2.0/BayesMallows/src/smc_leap_and_shift_probs.cpp                          |   80 --
 BayesMallows-1.2.0/BayesMallows/src/smc_mallows_new_item_rank.cpp                         |  283 +++----
 BayesMallows-1.2.0/BayesMallows/src/smc_mallows_new_users.cpp                             |only
 BayesMallows-1.2.0/BayesMallows/src/smc_mallows_new_users.h                               |only
 BayesMallows-1.2.0/BayesMallows/src/smc_mallows_new_users_funs.cpp                        |only
 BayesMallows-1.2.0/BayesMallows/src/smc_metropolis_hastings_alpha.cpp                     |   12 
 BayesMallows-1.2.0/BayesMallows/src/smc_metropolis_hastings_aug_ranking.cpp               |  102 +-
 BayesMallows-1.2.0/BayesMallows/src/smc_metropolis_hastings_rho.cpp                       |   30 
 BayesMallows-1.2.0/BayesMallows/src/subset.cpp                                            |    6 
 BayesMallows-1.2.0/BayesMallows/src/subset.h                                              |    8 
 BayesMallows-1.2.0/BayesMallows/src/test-leapandshift.cpp                                 |only
 BayesMallows-1.2.0/BayesMallows/src/test-runner.cpp                                       |only
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-assess_convergence.R                  |   39 -
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-assign_cluster.R                      |   72 -
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-classes_compute_consensus_posterior.R |   28 
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-compute_consensus.R                   |  253 ++++--
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-compute_mallows.R                     |  223 +++--
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-compute_mallows_mixtures.R            |  119 +--
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-compute_posterior_intervals.R         |   86 +-
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-cpp.R                                 |only
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-distance_function.R                   |   55 -
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-estimate_partition_function.R         |   44 -
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-expected_dist.R                       |   23 
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-generate_ranking.R                    |   63 -
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-generate_transitive_closure.R         |only
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-get_mallows_loglik.R                  |only
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-mcmc_function.R                       |   23 
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-misc_functions.R                      |   12 
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-partition_function.R                  |  122 +--
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-plot_elbow.R                          |   12 
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-plot_top_k.R                          |   73 +
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-print.R                               |   18 
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-random_number_seed.R                  |   58 -
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-rank_freq_distr.R                     |   96 +-
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-sample_mallows.R                      |   34 
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-smc_compute_rho_consensus.R           |    8 
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-smc_individual_functions.R            |   77 +-
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-smc_mallows_complete_rankings.R       |  376 +++++-----
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-smc_mallows_new_item_rank.R           |   71 +
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-smc_mallows_partial_rankings.R        |  151 +++-
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-smc_pseudolikelihood.R                |   15 
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-smc_uniform.R                         |   18 
 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-transitive_closure.R                  |   60 -
 BayesMallows-1.2.0/BayesMallows/vignettes/SMC-Mallows.Rmd                                 |   72 +
 162 files changed, 3190 insertions(+), 3265 deletions(-)

More information about BayesMallows at CRAN
Permanent link

Package nanostringr updated to version 0.3.0 with previous version 0.2.0 dated 2021-02-06

Title: Performs Quality Control, Data Normalization, and Batch Effect Correction for 'NanoString nCounter' Data
Description: Provides quality control (QC), normalization, and batch effect correction operations for 'NanoString nCounter' data, Talhouk et al. (2016) <doi:10.1371/journal.pone.0153844>. Various metrics are used to determine which samples passed or failed QC. Gene expression should first be normalized to housekeeping genes, before a reference-based approach is used to adjust for batch effects. Raw NanoString data can be imported in the form of Reporter Code Count (RCC) files.
Author: Derek Chiu [aut, cre], Aline Talhouk [aut], Samuel Leung [aut]
Maintainer: Derek Chiu <dchiu@bccrc.ca>

Diff between nanostringr versions 0.2.0 dated 2021-02-06 and 0.3.0 dated 2022-05-24

 DESCRIPTION                        |    8 
 LICENSE                            |    4 
 MD5                                |   63 +-
 NAMESPACE                          |   42 -
 NEWS.md                            |  100 +--
 R/CCplot.R                         |  218 +++----
 R/HKnorm.R                         |   66 +-
 R/NanoStringQC.R                   |  146 ++--
 R/check.R                          |   90 +-
 R/data.R                           |  116 +--
 R/nanostringr-package.R            |    8 
 R/read_rcc.R                       |  194 +++---
 R/refMethod.R                      |   54 -
 R/utils.R                          |    4 
 build/partial.rdb                  |only
 build/vignette.rds                 |binary
 inst/CITATION                      |   38 -
 inst/doc/Overview.R                |  298 ++++-----
 inst/doc/Overview.Rmd              |  688 +++++++++++-----------
 inst/doc/Overview.html             | 1131 ++++++++++++++++++++++---------------
 man/CCplot.Rd                      |  170 ++---
 man/cohort.Rd                      |  136 ++--
 man/expQC.Rd                       |   36 -
 man/nanostringr-package.Rd         |   68 --
 man/rcc.Rd                         |  124 ++--
 tests/testthat.R                   |    8 
 tests/testthat/test-CCplot.R       |   48 -
 tests/testthat/test-HKnorm.R       |   20 
 tests/testthat/test-NanoStringQC.R |   88 +-
 tests/testthat/test-order.R        |   28 
 tests/testthat/test-parse.R        |   50 -
 tests/testthat/test-ratioMethod.R  |   50 -
 vignettes/Overview.Rmd             |  688 +++++++++++-----------
 33 files changed, 2507 insertions(+), 2275 deletions(-)

More information about nanostringr at CRAN
Permanent link

Package TBEST updated to version 5.2 with previous version 5.0 dated 2014-12-29

Title: Tree Branches Evaluated Statistically for Tightness
Description: Our method introduces mathematically well-defined measures for tightness of branches in a hierarchical tree. Statistical significance of the findings is determined, for all branches of the tree, by performing permutation tests, optionally with generalized Pareto p-value estimation.
Author: Guoli Sun, Alex Krasnitz
Maintainer: Guoli Sun <guolisun87@gmail.com>

Diff between TBEST versions 5.0 dated 2014-12-29 and 5.2 dated 2022-05-24

 DESCRIPTION     |   10 +--
 MD5             |    6 +-
 NAMESPACE       |   10 ++-
 R/LeafContent.R |  148 ++++++++++++++++++++++++++++----------------------------
 4 files changed, 89 insertions(+), 85 deletions(-)

More information about TBEST at CRAN
Permanent link

Package ZetaSuite updated to version 1.0.1 with previous version 1.0.0 dated 2022-03-31

Title: Analyze High-Dimensional High-Throughput Dataset and Quality Control Single-Cell RNA-Seq
Description: The advent of genomic technologies has enabled the generation of two-dimensional or even multi-dimensional high-throughput data, e.g., monitoring multiple changes in gene expression in genome-wide siRNA screens across many different cell types (E Robert McDonald 3rd (2017) <doi: 10.1016/j.cell.2017.07.005> and Tsherniak A (2017) <doi: 10.1016/j.cell.2017.06.010>) or single cell transcriptomics under different experimental conditions. We found that simple computational methods based on a single statistical criterion is no longer adequate for analyzing such multi-dimensional data. We herein introduce 'ZetaSuite', a statistical package initially designed to score hits from two-dimensional RNAi screens.We also illustrate a unique utility of 'ZetaSuite' in analyzing single cell transcriptomics to differentiate rare cells from damaged ones (Vento-Tormo R (2018) <doi: 10.1038/s41586-018-0698-6>). In 'ZetaSuite', we have the following steps: QC of input datasets, normalization using Z-transformation, Zeta score calculation and hits selection based on defined Screen Strength.
Author: Yajing Hao [aut] , Shuyang Zhang [ctb] , Junhui Li [cre], Guofeng Zhao [ctb], Xiang-Dong Fu [cph, fnd]
Maintainer: Junhui Li <ljh.biostat@gmail.com>

Diff between ZetaSuite versions 1.0.0 dated 2022-03-31 and 1.0.1 dated 2022-05-24

 DESCRIPTION             |   10 ++---
 MD5                     |   10 ++---
 NAMESPACE               |    1 
 R/FDRcutoff.R           |   14 ++++----
 R/QC.R                  |    2 -
 inst/doc/ZetaSuite.html |   82 ++++++++++++++----------------------------------
 6 files changed, 43 insertions(+), 76 deletions(-)

More information about ZetaSuite at CRAN
Permanent link

Package wTO updated to version 2.0.1 with previous version 2.0 dated 2022-05-10

Title: Computing Weighted Topological Overlaps (wTO) & Consensus wTO Network
Description: Computes the Weighted Topological Overlap with positive and negative signs (wTO) networks given a data frame containing the mRNA count/ expression/ abundance per sample, and a vector containing the interested nodes of interaction (a subset of the elements of the full data frame). It also computes the cut-off threshold or p-value based on the individuals bootstrap or the values reshuffle per individual. It also allows the construction of a consensus network, based on multiple wTO networks. The package includes a visualization tool for the networks. More about the methodology can be found at <arXiv:1711.04702>.
Author: Deisy Morselli Gysi, Andre Voigt, Tiago Miranda Fragoso, Eivind Almaas and Katja Nowick.
Maintainer: Deisy Morselli Gysi <deisy.ccnr@gmail.com>

Diff between wTO versions 2.0 dated 2022-05-10 and 2.0.1 dated 2022-05-24

 DESCRIPTION  |    6 +++---
 MD5          |    4 ++--
 R/Cut.off2.R |    2 +-
 3 files changed, 6 insertions(+), 6 deletions(-)

More information about wTO at CRAN
Permanent link

Package VineCopula updated to version 2.4.4 with previous version 2.4.3 dated 2021-10-07

Title: Statistical Inference of Vine Copulas
Description: Provides tools for the statistical analysis of regular vine copula models, see Aas et al. (2009) <doi:10.1016/j.insmatheco.2007.02.001> and Dissman et al. (2013) <doi:10.1016/j.csda.2012.08.010>. The package includes tools for parameter estimation, model selection, simulation, goodness-of-fit tests, and visualization. Tools for estimation, selection and exploratory data analysis of bivariate copula models are also provided.
Author: Thomas Nagler [aut, cre], Ulf Schepsmeier [aut], Jakob Stoeber [aut], Eike Christian Brechmann [aut], Benedikt Graeler [aut], Tobias Erhardt [aut], Carlos Almeida [ctb], Aleksey Min [ctb, ths], Claudia Czado [ctb, ths], Mathias Hofmann [ctb], Matthia [...truncated...]
Maintainer: Thomas Nagler <mail@tnagler.com>

Diff between VineCopula versions 2.4.3 dated 2021-10-07 and 2.4.4 dated 2022-05-24

 DESCRIPTION       |    8 ++---
 MD5               |   20 ++++++-------
 NAMESPACE         |    1 
 NEWS.md           |   80 +++++++++++++++++++++++++++++++-----------------------
 R/BiCopLambda.R   |   10 +++---
 R/BiCopPar2Tau.R  |    2 -
 R/RVineMLE.R      |   14 +++++----
 R/RVineMatrix.R   |    4 --
 R/preprocessors.R |    2 -
 README.md         |    2 -
 build/partial.rdb |binary
 11 files changed, 79 insertions(+), 64 deletions(-)

More information about VineCopula at CRAN
Permanent link

Package TreeTools updated to version 1.7.2 with previous version 1.7.1 dated 2022-03-25

Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) <doi:10.1371/journal.pone.0212942>; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2021) <doi:10.1093/sysbio/syab072>, and of tree balance (Mir et al. 2013) <doi:10.1016/j.mbs.2012.10.005>; artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <http://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph] , Emmanuel Paradis [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>

Diff between TreeTools versions 1.7.1 dated 2022-03-25 and 1.7.2 dated 2022-05-24

 TreeTools-1.7.1/TreeTools/build/TreeTools.pdf                    |only
 TreeTools-1.7.2/TreeTools/DESCRIPTION                            |   13 
 TreeTools-1.7.2/TreeTools/MD5                                    |   80 +-
 TreeTools-1.7.2/TreeTools/NAMESPACE                              |    7 
 TreeTools-1.7.2/TreeTools/NEWS.md                                |   10 
 TreeTools-1.7.2/TreeTools/R/ClusterTable.R                       |only
 TreeTools-1.7.2/TreeTools/R/RcppExports.R                        |   12 
 TreeTools-1.7.2/TreeTools/R/tree_display.R                       |    9 
 TreeTools-1.7.2/TreeTools/R/tree_numbering.R                     |   73 +-
 TreeTools-1.7.2/TreeTools/R/tree_properties.R                    |    5 
 TreeTools-1.7.2/TreeTools/R/tree_rearrangement.R                 |    2 
 TreeTools-1.7.2/TreeTools/build/partial.rdb                      |binary
 TreeTools-1.7.2/TreeTools/build/vignette.rds                     |binary
 TreeTools-1.7.2/TreeTools/inst/doc/filesystem-navigation.html    |  219 +++++++
 TreeTools-1.7.2/TreeTools/inst/doc/load-data.html                |  286 +++++++++-
 TreeTools-1.7.2/TreeTools/inst/doc/load-trees.html               |  275 ++++++++-
 TreeTools-1.7.2/TreeTools/inst/include/TreeTools/ClusterTable.h  |   36 -
 TreeTools-1.7.2/TreeTools/inst/include/TreeTools/SplitList.h     |    6 
 TreeTools-1.7.2/TreeTools/inst/include/TreeTools/keep_tip.h      |    2 
 TreeTools-1.7.2/TreeTools/inst/include/TreeTools/renumber_tree.h |   12 
 TreeTools-1.7.2/TreeTools/inst/include/TreeTools/root_tree.h     |    8 
 TreeTools-1.7.2/TreeTools/inst/include/TreeTools/types.h         |   10 
 TreeTools-1.7.2/TreeTools/man/ClusterTable-methods.Rd            |only
 TreeTools-1.7.2/TreeTools/man/ClusterTable.Rd                    |only
 TreeTools-1.7.2/TreeTools/man/ConstrainedNJ.Rd                   |    5 
 TreeTools-1.7.2/TreeTools/man/RenumberTips.Rd                    |    2 
 TreeTools-1.7.2/TreeTools/man/Reorder.Rd                         |   15 
 TreeTools-1.7.2/TreeTools/man/SortTree.Rd                        |    3 
 TreeTools-1.7.2/TreeTools/man/SplitInformation.Rd                |    4 
 TreeTools-1.7.2/TreeTools/man/TreeNumber.Rd                      |   18 
 TreeTools-1.7.2/TreeTools/src/ClusterTable.cpp                   |only
 TreeTools-1.7.2/TreeTools/src/RcppExports-manual.cpp             |    1 
 TreeTools-1.7.2/TreeTools/src/RcppExports.cpp                    |   33 +
 TreeTools-1.7.2/TreeTools/src/TreeTools-init.c                   |    6 
 TreeTools-1.7.2/TreeTools/src/as_newick.cpp                      |    2 
 TreeTools-1.7.2/TreeTools/src/consensus.cpp                      |    5 
 TreeTools-1.7.2/TreeTools/src/int_to_tree.cpp                    |   12 
 TreeTools-1.7.2/TreeTools/src/splits.cpp                         |   16 
 TreeTools-1.7.2/TreeTools/src/tips_in_splits.cpp                 |    8 
 TreeTools-1.7.2/TreeTools/src/tree_shape.cpp                     |   14 
 TreeTools-1.7.2/TreeTools/tests/testthat/test-ClusterTable.R     |only
 TreeTools-1.7.2/TreeTools/tests/testthat/test-root_tree.h.R      |    6 
 TreeTools-1.7.2/TreeTools/tests/testthat/test-tree_numbering.R   |   60 +-
 TreeTools-1.7.2/TreeTools/tests/testthat/test-tree_properties.R  |    3 
 44 files changed, 1042 insertions(+), 236 deletions(-)

More information about TreeTools at CRAN
Permanent link

Package shinyFiles updated to version 0.9.2 with previous version 0.9.1 dated 2021-11-10

Title: A Server-Side File System Viewer for Shiny
Description: Provides functionality for client-side navigation of the server side file system in shiny apps. In case the app is running locally this gives the user direct access to the file system without the need to "download" files to a temporary location. Both file and folder selection as well as file saving is available.
Author: Thomas Lin Pedersen [cre, aut] , Vincent Nijs [aut], Thomas Schaffner [aut], Eric Nantz [aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>

Diff between shinyFiles versions 0.9.1 dated 2021-11-10 and 0.9.2 dated 2022-05-24

 DESCRIPTION               |    8 
 MD5                       |   20 -
 NEWS.md                   |    6 
 R/aaa.R                   |   25 +
 R/dirchoose.R             |  694 +++++++++++++++++++++++-----------------------
 R/filechoose.R            |   16 -
 R/filesave.R              |   66 +---
 inst/example/ui.R         |    8 
 inst/www/shinyFiles.js    |    3 
 inst/www/styles.css       |    2 
 man/shinyFiles-buttons.Rd |   16 -
 11 files changed, 449 insertions(+), 415 deletions(-)

More information about shinyFiles at CRAN
Permanent link

Package Rdsdp updated to version 1.0.5.2 with previous version 1.0.5.1 dated 2021-11-02

Title: R Interface to DSDP Semidefinite Programming Library
Description: R interface to DSDP semidefinite programming library. The DSDP software is a free open source implementation of an interior-point method for semidefinite programming. It provides primal and dual solutions, exploits low-rank structure and sparsity in the data, and has relatively low memory requirements for an interior-point method.
Author: Zhisu Zhu, Yinyu Ye
Maintainer: Zhisu Zhu <zhuzhisu@alumni.stanford.edu>

Diff between Rdsdp versions 1.0.5.1 dated 2021-11-02 and 1.0.5.2 dated 2022-05-24

 DESCRIPTION                       |    6 +++---
 MD5                               |    6 +++---
 src/dsdp/src/solver/dsdprescone.c |    2 +-
 src/dsdp/src/solver/dsdpvec.h     |    6 +++---
 4 files changed, 10 insertions(+), 10 deletions(-)

More information about Rdsdp at CRAN
Permanent link

Package RcppXPtrUtils updated to version 0.1.2 with previous version 0.1.1 dated 2019-01-21

Title: XPtr Add-Ons for 'Rcpp'
Description: Provides the means to compile user-supplied C++ functions with 'Rcpp' and retrieve an 'XPtr' that can be passed to other C++ components.
Author: Inaki Ucar [aut, cph, cre]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>

Diff between RcppXPtrUtils versions 0.1.1 dated 2019-01-21 and 0.1.2 dated 2022-05-24

 DESCRIPTION      |   10 +++++-----
 LICENSE          |    2 +-
 MD5              |   14 +++++++-------
 NEWS.md          |    4 ++++
 R/check.R        |    2 +-
 README.md        |   27 +++++++++++++--------------
 man/checkXPtr.Rd |    2 +-
 man/cppXPtr.Rd   |   12 +++++++++---
 8 files changed, 41 insertions(+), 32 deletions(-)

More information about RcppXPtrUtils at CRAN
Permanent link

Package parameters updated to version 0.18.0 with previous version 0.17.0 dated 2022-03-10

Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various statistical models. Beyond computing p values, CIs, and other indices for a wide variety of models (see list of supported models using the function 'insight::supported_models()'), this package implements features like bootstrapping or simulating of parameters and models, feature reduction (feature extraction and variable selection) as well as functions to describe data and variable characteristics (e.g. skewness, kurtosis, smoothness or distribution).
Author: Daniel Luedecke [aut, cre] , Dominique Makowski [aut] , Mattan S. Ben-Shachar [aut] , Indrajeet Patil [aut] , Soeren Hoejsgaard [aut], Brenton M. Wiernik [aut] , Zen J. Lau [ctb], Vincent Arel-Bundock [ctb] , Jeffrey Girard [ctb] , Christina Maimone [re [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>

Diff between parameters versions 0.17.0 dated 2022-03-10 and 0.18.0 dated 2022-05-24

 parameters-0.17.0/parameters/R/select_parameters.stanreg.R                      |only
 parameters-0.17.0/parameters/man/dot-factor_to_numeric.Rd                       |only
 parameters-0.18.0/parameters/DESCRIPTION                                        |   31 
 parameters-0.18.0/parameters/MD5                                                |  348 +++++-----
 parameters-0.18.0/parameters/NAMESPACE                                          |   45 -
 parameters-0.18.0/parameters/NEWS.md                                            |  202 +----
 parameters-0.18.0/parameters/R/1_model_parameters.R                             |   73 +-
 parameters-0.18.0/parameters/R/2_ci.R                                           |   23 
 parameters-0.18.0/parameters/R/3_p_value.R                                      |   31 
 parameters-0.18.0/parameters/R/4_standard_error.R                               |  142 ----
 parameters-0.18.0/parameters/R/5_simulate_model.R                               |   48 +
 parameters-0.18.0/parameters/R/bootstrap_parameters.R                           |    6 
 parameters-0.18.0/parameters/R/check_factorstructure.R                          |    6 
 parameters-0.18.0/parameters/R/check_heterogeneity.R                            |   12 
 parameters-0.18.0/parameters/R/ci_generic.R                                     |   20 
 parameters-0.18.0/parameters/R/ci_profile_boot.R                                |    2 
 parameters-0.18.0/parameters/R/cluster_analysis.R                               |   22 
 parameters-0.18.0/parameters/R/cluster_meta.R                                   |    2 
 parameters-0.18.0/parameters/R/compare_parameters.R                             |   35 -
 parameters-0.18.0/parameters/R/convert_efa_to_cfa.R                             |    2 
 parameters-0.18.0/parameters/R/display.R                                        |    5 
 parameters-0.18.0/parameters/R/dof_betwithin.R                                  |    2 
 parameters-0.18.0/parameters/R/dof_ml1.R                                        |    2 
 parameters-0.18.0/parameters/R/equivalence_test.R                               |    6 
 parameters-0.18.0/parameters/R/extract_parameters.R                             |   99 +-
 parameters-0.18.0/parameters/R/extract_parameters_anova.R                       |   13 
 parameters-0.18.0/parameters/R/extract_random_variances.R                       |  189 +++++
 parameters-0.18.0/parameters/R/factor_analysis.R                                |    6 
 parameters-0.18.0/parameters/R/format.R                                         |  105 ---
 parameters-0.18.0/parameters/R/format_order.R                                   |    2 
 parameters-0.18.0/parameters/R/format_p_adjust.R                                |   10 
 parameters-0.18.0/parameters/R/format_parameters.R                              |    2 
 parameters-0.18.0/parameters/R/methods_BayesFM.R                                |    6 
 parameters-0.18.0/parameters/R/methods_BayesFactor.R                            |    9 
 parameters-0.18.0/parameters/R/methods_DirichletReg.R                           |    5 
 parameters-0.18.0/parameters/R/methods_MCMCglmm.R                               |    2 
 parameters-0.18.0/parameters/R/methods_aov.R                                    |   10 
 parameters-0.18.0/parameters/R/methods_averaging.R                              |    5 
 parameters-0.18.0/parameters/R/methods_bamlss.R                                 |    2 
 parameters-0.18.0/parameters/R/methods_base.R                                   |   56 -
 parameters-0.18.0/parameters/R/methods_bayesQR.R                                |    2 
 parameters-0.18.0/parameters/R/methods_betareg.R                                |   56 +
 parameters-0.18.0/parameters/R/methods_bfsl.R                                   |    1 
 parameters-0.18.0/parameters/R/methods_brglm2.R                                 |   50 +
 parameters-0.18.0/parameters/R/methods_brms.R                                   |    6 
 parameters-0.18.0/parameters/R/methods_car.R                                    |only
 parameters-0.18.0/parameters/R/methods_cgam.R                                   |    8 
 parameters-0.18.0/parameters/R/methods_cplm.R                                   |    4 
 parameters-0.18.0/parameters/R/methods_effect_size.R                            |    6 
 parameters-0.18.0/parameters/R/methods_emmeans.R                                |    2 
 parameters-0.18.0/parameters/R/methods_gam.R                                    |    6 
 parameters-0.18.0/parameters/R/methods_ggeffects.R                              |    2 
 parameters-0.18.0/parameters/R/methods_glm.R                                    |    1 
 parameters-0.18.0/parameters/R/methods_glmmTMB.R                                |   71 +-
 parameters-0.18.0/parameters/R/methods_glmx.R                                   |    2 
 parameters-0.18.0/parameters/R/methods_htest.R                                  |   36 +
 parameters-0.18.0/parameters/R/methods_lavaan.R                                 |    4 
 parameters-0.18.0/parameters/R/methods_lme4.R                                   |   47 -
 parameters-0.18.0/parameters/R/methods_marginaleffects.R                        |only
 parameters-0.18.0/parameters/R/methods_mediate.R                                |    2 
 parameters-0.18.0/parameters/R/methods_metafor.R                                |    4 
 parameters-0.18.0/parameters/R/methods_metaplus.R                               |   18 
 parameters-0.18.0/parameters/R/methods_mfx.R                                    |   12 
 parameters-0.18.0/parameters/R/methods_mhurdle.R                                |    2 
 parameters-0.18.0/parameters/R/methods_mixmod.R                                 |    9 
 parameters-0.18.0/parameters/R/methods_mixor.R                                  |    3 
 parameters-0.18.0/parameters/R/methods_mlm.R                                    |  119 ++-
 parameters-0.18.0/parameters/R/methods_multcomp.R                               |    4 
 parameters-0.18.0/parameters/R/methods_mvord.R                                  |    6 
 parameters-0.18.0/parameters/R/methods_nlme.R                                   |   40 -
 parameters-0.18.0/parameters/R/methods_ordinal.R                                |    7 
 parameters-0.18.0/parameters/R/methods_posterior.R                              |only
 parameters-0.18.0/parameters/R/methods_pscl.R                                   |   32 
 parameters-0.18.0/parameters/R/methods_psych.R                                  |    6 
 parameters-0.18.0/parameters/R/methods_rstan.R                                  |    2 
 parameters-0.18.0/parameters/R/methods_rstanarm.R                               |   15 
 parameters-0.18.0/parameters/R/methods_selection.R                              |    2 
 parameters-0.18.0/parameters/R/methods_survey.R                                 |    2 
 parameters-0.18.0/parameters/R/methods_survival.R                               |    2 
 parameters-0.18.0/parameters/R/methods_varest.R                                 |    2 
 parameters-0.18.0/parameters/R/methods_wrs2.R                                   |    6 
 parameters-0.18.0/parameters/R/n_clusters.R                                     |   43 -
 parameters-0.18.0/parameters/R/n_clusters_easystats.R                           |    2 
 parameters-0.18.0/parameters/R/n_factors.R                                      |    2 
 parameters-0.18.0/parameters/R/p_value_kenward.R                                |   10 
 parameters-0.18.0/parameters/R/parameters_type.R                                |    2 
 parameters-0.18.0/parameters/R/pool_parameters.R                                |   16 
 parameters-0.18.0/parameters/R/principal_components.R                           |   13 
 parameters-0.18.0/parameters/R/random_parameters.R                              |   10 
 parameters-0.18.0/parameters/R/reduce_parameters.R                              |   22 
 parameters-0.18.0/parameters/R/reexports.R                                      |   23 
 parameters-0.18.0/parameters/R/reshape_loadings.R                               |   15 
 parameters-0.18.0/parameters/R/robust_estimation.R                              |   14 
 parameters-0.18.0/parameters/R/select_parameters.R                              |   26 
 parameters-0.18.0/parameters/R/simulate_parameters.R                            |   13 
 parameters-0.18.0/parameters/R/sort_parameters.R                                |only
 parameters-0.18.0/parameters/R/standardize_info.R                               |only
 parameters-0.18.0/parameters/R/standardize_parameters.R                         |only
 parameters-0.18.0/parameters/R/standardize_posteriors.R                         |only
 parameters-0.18.0/parameters/R/utils.R                                          |   46 -
 parameters-0.18.0/parameters/R/utils_cleaners.R                                 |   12 
 parameters-0.18.0/parameters/R/utils_clustering.R                               |   46 -
 parameters-0.18.0/parameters/R/utils_format.R                                   |   53 -
 parameters-0.18.0/parameters/R/utils_model_parameters.R                         |  101 +-
 parameters-0.18.0/parameters/README.md                                          |   64 -
 parameters-0.18.0/parameters/build/partial.rdb                                  |binary
 parameters-0.18.0/parameters/build/vignette.rds                                 |binary
 parameters-0.18.0/parameters/inst/WORDLIST                                      |    5 
 parameters-0.18.0/parameters/man/bootstrap_parameters.Rd                        |    9 
 parameters-0.18.0/parameters/man/check_kmo.Rd                                   |    2 
 parameters-0.18.0/parameters/man/check_sphericity_bartlett.Rd                   |    4 
 parameters-0.18.0/parameters/man/ci.default.Rd                                  |    4 
 parameters-0.18.0/parameters/man/ci_robust.Rd                                   |    8 
 parameters-0.18.0/parameters/man/cluster_analysis.Rd                            |    6 
 parameters-0.18.0/parameters/man/cluster_meta.Rd                                |    2 
 parameters-0.18.0/parameters/man/compare_parameters.Rd                          |    8 
 parameters-0.18.0/parameters/man/equivalence_test.lm.Rd                         |    2 
 parameters-0.18.0/parameters/man/format_order.Rd                                |    2 
 parameters-0.18.0/parameters/man/model_parameters.BFBayesFactor.Rd              |   11 
 parameters-0.18.0/parameters/man/model_parameters.Rd                            |   30 
 parameters-0.18.0/parameters/man/model_parameters.averaging.Rd                  |   12 
 parameters-0.18.0/parameters/man/model_parameters.befa.Rd                       |   11 
 parameters-0.18.0/parameters/man/model_parameters.cgam.Rd                       |    6 
 parameters-0.18.0/parameters/man/model_parameters.default.Rd                    |   31 
 parameters-0.18.0/parameters/man/model_parameters.glht.Rd                       |    4 
 parameters-0.18.0/parameters/man/model_parameters.lavaan.Rd                     |    2 
 parameters-0.18.0/parameters/man/model_parameters.merMod.Rd                     |   50 -
 parameters-0.18.0/parameters/man/model_parameters.mira.Rd                       |    2 
 parameters-0.18.0/parameters/man/model_parameters.mlm.Rd                        |   35 -
 parameters-0.18.0/parameters/man/model_parameters.principal.Rd                  |    6 
 parameters-0.18.0/parameters/man/model_parameters.rma.Rd                        |    4 
 parameters-0.18.0/parameters/man/model_parameters.stanreg.Rd                    |  103 +-
 parameters-0.18.0/parameters/man/model_parameters.zcpglm.Rd                     |   16 
 parameters-0.18.0/parameters/man/n_clusters.Rd                                  |    4 
 parameters-0.18.0/parameters/man/n_factors.Rd                                   |    2 
 parameters-0.18.0/parameters/man/p_value.DirichletRegModel.Rd                   |    9 
 parameters-0.18.0/parameters/man/p_value.Rd                                     |  189 +++++
 parameters-0.18.0/parameters/man/p_value.poissonmfx.Rd                          |    2 
 parameters-0.18.0/parameters/man/p_value.zcpglm.Rd                              |   15 
 parameters-0.18.0/parameters/man/p_value_robust.Rd                              |   23 
 parameters-0.18.0/parameters/man/pool_parameters.Rd                             |    6 
 parameters-0.18.0/parameters/man/principal_components.Rd                        |   13 
 parameters-0.18.0/parameters/man/print.parameters_model.Rd                      |    2 
 parameters-0.18.0/parameters/man/random_parameters.Rd                           |    8 
 parameters-0.18.0/parameters/man/reduce_parameters.Rd                           |   18 
 parameters-0.18.0/parameters/man/reexports.Rd                                   |   10 
 parameters-0.18.0/parameters/man/reshape_loadings.Rd                            |   13 
 parameters-0.18.0/parameters/man/select_parameters.Rd                           |   37 -
 parameters-0.18.0/parameters/man/simulate_model.Rd                              |   13 
 parameters-0.18.0/parameters/man/simulate_parameters.Rd                         |   18 
 parameters-0.18.0/parameters/man/sort_parameters.Rd                             |only
 parameters-0.18.0/parameters/man/standard_error.Rd                              |  108 ---
 parameters-0.18.0/parameters/man/standard_error_robust.Rd                       |   12 
 parameters-0.18.0/parameters/man/standardize_info.Rd                            |only
 parameters-0.18.0/parameters/man/standardize_parameters.Rd                      |only
 parameters-0.18.0/parameters/tests/testthat/test-base.R                         |only
 parameters-0.18.0/parameters/tests/testthat/test-betareg.R                      |    7 
 parameters-0.18.0/parameters/tests/testthat/test-bracl.R                        |    6 
 parameters-0.18.0/parameters/tests/testthat/test-car.R                          |only
 parameters-0.18.0/parameters/tests/testthat/test-ci.R                           |    1 
 parameters-0.18.0/parameters/tests/testthat/test-cluster_analysis.R             |only
 parameters-0.18.0/parameters/tests/testthat/test-format_parameters.R            |   11 
 parameters-0.18.0/parameters/tests/testthat/test-gamm.R                         |    3 
 parameters-0.18.0/parameters/tests/testthat/test-glmer.R                        |   38 +
 parameters-0.18.0/parameters/tests/testthat/test-glmmTMB.R                      |   53 +
 parameters-0.18.0/parameters/tests/testthat/test-lme.R                          |  190 +++--
 parameters-0.18.0/parameters/tests/testthat/test-marginaleffects.R              |only
 parameters-0.18.0/parameters/tests/testthat/test-mlm.R                          |   36 +
 parameters-0.18.0/parameters/tests/testthat/test-model_parameters.anova.R       |   26 
 parameters-0.18.0/parameters/tests/testthat/test-model_parameters.blmerMod.R    |    2 
 parameters-0.18.0/parameters/tests/testthat/test-model_parameters.fixest.R      |   39 -
 parameters-0.18.0/parameters/tests/testthat/test-model_parameters.htest.R       |    2 
 parameters-0.18.0/parameters/tests/testthat/test-model_parameters.metaBMA.R     |    9 
 parameters-0.18.0/parameters/tests/testthat/test-model_parameters.mixed.R       |   15 
 parameters-0.18.0/parameters/tests/testthat/test-model_parameters_random_pars.R |only
 parameters-0.18.0/parameters/tests/testthat/test-model_parameters_robust.R      |    5 
 parameters-0.18.0/parameters/tests/testthat/test-model_parameters_std_mixed.R   |   16 
 parameters-0.18.0/parameters/tests/testthat/test-p_value.R                      |   14 
 parameters-0.18.0/parameters/tests/testthat/test-panelr.R                       |    7 
 parameters-0.18.0/parameters/tests/testthat/test-posterior.R                    |only
 parameters-0.18.0/parameters/tests/testthat/test-robust.R                       |   18 
 parameters-0.18.0/parameters/tests/testthat/test-sort_parameters.R              |only
 parameters-0.18.0/parameters/tests/testthat/test-standardize_info.R             |only
 parameters-0.18.0/parameters/tests/testthat/test-standardize_parameters.R       |only
 parameters-0.18.0/parameters/tests/testthat/test-svytable.R                     |only
 parameters-0.18.0/parameters/tests/testthat/test-zeroinfl.R                     |    3 
 186 files changed, 2308 insertions(+), 1788 deletions(-)

More information about parameters at CRAN
Permanent link

Package openssl updated to version 2.0.2 with previous version 2.0.1 dated 2022-05-14

Title: Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers. Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] , Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between openssl versions 2.0.1 dated 2022-05-14 and 2.0.2 dated 2022-05-24

 DESCRIPTION                  |    6 ++---
 MD5                          |   18 ++++++++--------
 NEWS                         |    3 ++
 R/cert.R                     |    4 ++-
 inst/doc/bignum.html         |   32 ++++++++++++++--------------
 inst/doc/crypto_hashing.html |    4 +--
 inst/doc/keys.html           |   48 +++++++++++++++++++++----------------------
 inst/doc/secure_rng.html     |   18 ++++++++--------
 man/certificates.Rd          |    2 +
 tests/testthat/test_google.R |    3 ++
 10 files changed, 74 insertions(+), 64 deletions(-)

More information about openssl at CRAN
Permanent link

Package dexter updated to version 1.2.1 with previous version 1.1.5 dated 2022-02-19

Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Author: Gunter Maris [aut], Timo Bechger [aut], Jesse Koops [aut, cre], Ivailo Partchev [aut]
Maintainer: Jesse Koops <jesse.koops@cito.nl>

Diff between dexter versions 1.1.5 dated 2022-02-19 and 1.2.1 dated 2022-05-24

 DESCRIPTION                               |    6 
 MD5                                       |   42 +-
 NAMESPACE                                 |    2 
 NEWS                                      |   11 
 R/dexter.R                                |  408 ++++++++++++++++------
 R/enorm.R                                 |    2 
 R/individual_differences.R                |    2 
 R/plots.R                                 |   76 +++-
 R/predicates.R                            |   21 -
 R/reparam.R                               |    3 
 R/resp_data.R                             |   44 --
 build/vignette.rds                        |binary
 inst/doc/DIF_vignette.html                |  262 +++++++++++++-
 inst/doc/Equating.html                    |  433 ++++++++++++++++++++---
 inst/doc/Plausible_Values.html            |  325 ++++++++++++++++-
 inst/doc/Test_Individual_differences.html |  277 +++++++++++++--
 inst/doc/dexter.html                      |  550 +++++++++++++++++++++++++-----
 inst/doc/profile-plots.html               |  322 +++++++++++++++--
 man/add_booklet.Rd                        |   30 -
 man/coef.prms.Rd                          |    2 
 man/profile_plot.Rd                       |    3 
 tests/testthat/test_data_selection.R      |    4 
 22 files changed, 2383 insertions(+), 442 deletions(-)

More information about dexter at CRAN
Permanent link

Package Andromeda updated to version 0.6.1 with previous version 0.6.0 dated 2022-01-25

Title: Asynchronous Disk-Based Representation of Massive Data
Description: Storing very large data objects on a local drive, while still making it possible to manipulate the data in an efficient manner.
Author: Adam Black [aut, cre], Martijn Schuemie [aut], Marc A. Suchard [aut], Observational Health Data Science and Informatics [cph]
Maintainer: Adam Black <black@ohdsi.org>

Diff between Andromeda versions 0.6.0 dated 2022-01-25 and 0.6.1 dated 2022-05-24

 DESCRIPTION                 |    8 ++++----
 MD5                         |   12 ++++++------
 NEWS.md                     |    6 ++++++
 R/Operations.R              |    6 +++---
 build/vignette.rds          |binary
 inst/doc/UsingAndromeda.pdf |binary
 man/Andromeda-package.Rd    |    1 -
 7 files changed, 19 insertions(+), 14 deletions(-)

More information about Andromeda at CRAN
Permanent link

Package HostSwitch updated to version 0.1.1 with previous version 0.1.0 dated 2021-09-27

Title: Simulate the Extent of Host Switching by Consumers
Description: Using a simulation-based approach, the 'HostSwitch' package provides functions to investigate host switches by consumers. The individual-based model is based on the concept of ecological fitting. The mockup model is published by Araujo et al. 2015. Understanding Host-Switching by Ecological Fitting (<doi:10.1371/journal.pone.0139225>). The package provides an R-friendly and modified version of this model which can be applied to different consumer-resource scenarios.
Author: Valeria Trivellone [aut], Sabrina B.L. Araujo [aut], Bernd Panassiti [cre, aut]
Maintainer: Bernd Panassiti <bernd.panassiti@gmail.com>

Diff between HostSwitch versions 0.1.0 dated 2021-09-27 and 0.1.1 dated 2022-05-24

 DESCRIPTION              |   10 +++++-----
 MD5                      |   12 ++++++------
 NEWS.md                  |    7 +++++++
 R/HostSwitch.R           |   16 ++++++++--------
 build/vignette.rds       |binary
 inst/doc/HostSwitch.html |   14 +++++++-------
 man/simHostSwitch.Rd     |   16 ++++++++--------
 7 files changed, 41 insertions(+), 34 deletions(-)

More information about HostSwitch at CRAN
Permanent link

Package GaussSuppression updated to version 0.3.0 with previous version 0.2.0 dated 2022-04-05

Title: Tabular Data Suppression using Gaussian Elimination
Description: A statistical disclosure control tool to protect tables by suppression using the Gaussian elimination secondary suppression algorithm. Primary suppression functions for the minimum frequency rule, the dominance rule and a directly-disclosive rule are included. General primary suppression functions can be supplied as input. Suppressed frequencies can be replaced by synthetic decimal numbers as described in Langsrud (2019) <doi:10.1007/s11222-018-9848-9>.
Author: Oyvind Langsrud [aut, cre], Daniel Lupp [aut], Hege Boevelstad [ctb]
Maintainer: Oyvind Langsrud <oyl@ssb.no>

Diff between GaussSuppression versions 0.2.0 dated 2022-04-05 and 0.3.0 dated 2022-05-24

 DESCRIPTION                            |    8 ++++----
 MD5                                    |    9 +++++----
 R/GaussSuppressDec.R                   |   29 +++++++++++++++++++++++------
 R/GaussSuppressionFromData.R           |    4 ++++
 R/SuppressDec.R                        |    4 +++-
 tests/testthat/test-GaussSuppressDec.R |only
 6 files changed, 39 insertions(+), 15 deletions(-)

More information about GaussSuppression at CRAN
Permanent link

Package campfin updated to version 1.0.9 with previous version 1.0.8 dated 2021-09-02

Title: Wrangle Campaign Finance Data
Description: Explore and normalize American campaign finance data. Created by the Investigative Reporting Workshop to facilitate work on The Accountability Project, an effort to collect public data into a central, standard database that is more easily searched: <https://publicaccountability.org/>.
Author: Kiernan Nicholls [aut, cre, cph], Investigative Reporting Workshop [cph], Yanqi Xu [aut], Schuyler Erle [cph]
Maintainer: Kiernan Nicholls <kiernann@protonmail.com>

Diff between campfin versions 1.0.8 dated 2021-09-02 and 1.0.9 dated 2022-05-24

 DESCRIPTION                        |    8 
 MD5                                |   42 ++-
 NAMESPACE                          |    2 
 NEWS.md                            |    9 
 R/col-stats.R                      |    4 
 R/file-age.R                       |only
 R/guess-delims.R                   |    4 
 R/normal-address.R                 |   29 +-
 R/normal-state.R                   |   15 -
 R/str-normal.R                     |   12 -
 R/use-diary.R                      |    7 
 README.md                          |   69 ++----
 build/vignette.rds                 |binary
 inst/doc/normalize-geography.html  |  400 +++++++++++++++++++++++++++++++------
 inst/templates/template_diary.Rmd  |  221 +++++++++++---------
 man/file_age.Rd                    |only
 man/guess_delim.Rd                 |    4 
 man/normal_address.Rd              |   18 +
 man/str_normal.Rd                  |    7 
 man/use_diary.Rd                   |    5 
 tests/testthat/test-check-city.R   |    2 
 tests/testthat/test-diary.R        |    2 
 tests/testthat/test-normal-state.R |    6 
 23 files changed, 592 insertions(+), 274 deletions(-)

More information about campfin at CRAN
Permanent link

Package POSetR updated to version 1.1.0 with previous version 1.0.4 dated 2021-11-24

Title: Partially Ordered Sets in R
Description: Provides a set of basic tools for generating, analyzing, summarizing and visualizing finite partially ordered sets. In particular, it implements flexible and very efficient algorithms for the extraction of linear extensions and for the computation of mutual ranking probabilities and other user-defined functionals, over them. The package is meant as a computationally efficient "engine", for the implementation of data analysis procedures, on systems of multidimensional ordinal indicators and partially ordered data, in the spirit of Fattore, M. (2016) "Partially ordered sets and the measurement of multidimensional ordinal deprivation", Social Indicators Research <DOI:10.1007/s11205-015-1059-6>, and Fattore M. and Arcagni, A. (2018) "A reduced posetic approach to the measurement of multidimensional ordinal deprivation", Social Indicators Research <DOI:10.1007/s11205-016-1501-4>.
Author: Alberto Arcagni [aut, cre], Alessandro Avellone [aut], Marco Fattore [aut]
Maintainer: Alberto Arcagni <alberto.arcagni@uniroma1.it>

Diff between POSetR versions 1.0.4 dated 2021-11-24 and 1.1.0 dated 2022-05-24

 POSetR-1.0.4/POSetR/R/plot.Rcpp_POSet.R         |only
 POSetR-1.0.4/POSetR/R/print.Rcpp_POSet.R        |only
 POSetR-1.0.4/POSetR/R/summary.Rcpp_POSet.R      |only
 POSetR-1.0.4/POSetR/man/plot.Rcpp_POSet.Rd      |only
 POSetR-1.0.4/POSetR/man/print.Rcpp_POSet.Rd     |only
 POSetR-1.0.4/POSetR/man/summary.Rcpp_POSet.Rd   |only
 POSetR-1.1.0/POSetR/DESCRIPTION                 |   10 +--
 POSetR-1.1.0/POSetR/MD5                         |   64 ++++++++++++------------
 POSetR-1.1.0/POSetR/NAMESPACE                   |   14 +++--
 POSetR-1.1.0/POSetR/R/LEapply.R                 |   42 ++++++++-------
 POSetR-1.1.0/POSetR/R/POSetR-package.R          |    1 
 POSetR-1.1.0/POSetR/R/antiChain.R               |    2 
 POSetR-1.1.0/POSetR/R/chain.R                   |    2 
 POSetR-1.1.0/POSetR/R/intersection.R            |    8 +--
 POSetR-1.1.0/POSetR/R/plot.poset.R              |only
 POSetR-1.1.0/POSetR/R/poset.R                   |   28 +++++++---
 POSetR-1.1.0/POSetR/R/poset_from_igraph.R       |    4 -
 POSetR-1.1.0/POSetR/R/poset_from_incidence.R    |    2 
 POSetR-1.1.0/POSetR/R/print.poset.R             |only
 POSetR-1.1.0/POSetR/R/print.summary_poset.R     |    2 
 POSetR-1.1.0/POSetR/R/productOrder.R            |   18 ++++--
 POSetR-1.1.0/POSetR/R/summary.poset.R           |only
 POSetR-1.1.0/POSetR/R/utilities.R               |   26 +++++----
 POSetR-1.1.0/POSetR/build/partial.rdb           |binary
 POSetR-1.1.0/POSetR/man/LEapply.Rd              |    8 +--
 POSetR-1.1.0/POSetR/man/antiChain.Rd            |    2 
 POSetR-1.1.0/POSetR/man/chain.Rd                |    2 
 POSetR-1.1.0/POSetR/man/coverMatrix.Rd          |    6 +-
 POSetR-1.1.0/POSetR/man/incidenceMatrix.Rd      |    6 +-
 POSetR-1.1.0/POSetR/man/plot.poset.Rd           |only
 POSetR-1.1.0/POSetR/man/poset.Rd                |    4 +
 POSetR-1.1.0/POSetR/man/poset_from_igraph.Rd    |    2 
 POSetR-1.1.0/POSetR/man/poset_from_incidence.Rd |    2 
 POSetR-1.1.0/POSetR/man/print.poset.Rd          |only
 POSetR-1.1.0/POSetR/man/print.summary_poset.Rd  |    2 
 POSetR-1.1.0/POSetR/man/productOrder.Rd         |    6 +-
 POSetR-1.1.0/POSetR/man/summary.poset.Rd        |only
 POSetR-1.1.0/POSetR/src/RMod.cpp                |    3 -
 POSetR-1.1.0/POSetR/src/RMod.h                  |    2 
 39 files changed, 150 insertions(+), 118 deletions(-)

More information about POSetR at CRAN
Permanent link

Package audubon updated to version 0.2.0 with previous version 0.1.2 dated 2022-04-02

Title: Japanese Text Processing Tools
Description: A collection of Japanese text processing tools for filling Japanese iteration marks, Japanese character type conversions, segmentation by phrase, and text normalization which is based on rules for the 'Sudachi' morphological analyzer and the 'NEologd' (Neologism dictionary for 'MeCab'). These features are specific to Japanese and are not implemented in 'ICU' (International Components for Unicode).
Author: Akiru Kato [cre, aut], Koki Takahashi [cph] , Shuhei Iitsuka [cph] , Taku Kudo [cph]
Maintainer: Akiru Kato <paithiov909@gmail.com>

Diff between audubon versions 0.1.2 dated 2022-04-02 and 0.2.0 dated 2022-05-24

 DESCRIPTION                                     |   15 ++++---
 LICENSE.note                                    |    4 +-
 MD5                                             |   32 ++++++++--------
 NAMESPACE                                       |    1 
 NEWS.md                                         |   33 +++++++++-------
 R/pack.R                                        |   32 ++++------------
 R/strj-fill.R                                   |    2 -
 R/strj-normalize.R                              |    5 +-
 R/strj-rewrite.R                                |    2 -
 R/strj-segment.R                                |    4 --
 R/strj-tinyseg.R                                |only
 R/strj-tokenize.R                               |    4 --
 inst/WORDLIST                                   |    1 
 inst/packer/audubon.bundle.js                   |    2 -
 man/audubon-package.Rd                          |    3 +
 man/ngram_tokenizer.Rd                          |    6 ---
 man/strj_tinyseg.Rd                             |only
 tests/testthat/test_strj-tokenize-and-segment.R |   47 ++++++++++++++----------
 18 files changed, 97 insertions(+), 96 deletions(-)

More information about audubon at CRAN
Permanent link

New package nlmixr2 with initial version 2.0.6
Package: nlmixr2
Title: Nonlinear Mixed Effects Models in Population PK/PD
Version: 2.0.6
Description: Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
License: GPL (>= 3)
Encoding: UTF-8
Imports: nlmixr2est, nlmixr2extra, rxode2, nlmixr2plot, magrittr
Depends: nlmixr2data
Suggests: rmarkdown, knitr, devtools, withr, ggplot2, testthat
VignetteBuilder: knitr
BugReports: https://github.com/nlmixr2/nlmixr2/issues/
URL: https://nlmixr2.github.io/nlmixr2/, https://github.com/nlmixr2/nlmixr2/
NeedsCompilation: no
Packaged: 2022-05-23 15:42:00 UTC; matt
Author: Matthew Fidler [aut, cre] , Yuan Xiong [ctb], Rik Schoemaker [ctb] , Justin Wilkins [ctb] , Wenping Wang [aut], Mirjam Trame [ctb], Huijuan Xu [ctb], John Harrold [ctb], Bill Denney [ctb] , Theodoros Papathanasiou [ctb], Teun Post [ctb], Richard Hooi [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-24 15:50:02 UTC

More information about nlmixr2 at CRAN
Permanent link

New package ggisotonic with initial version 0.1.2
Package: ggisotonic
Title: 'ggplot2' Friendly Isotonic or Monotonic Regression Curves
Version: 0.1.2
Description: Provides stat_isotonic() to add weighted univariate isotonic regression curves.
License: GPL-3
Encoding: UTF-8
Imports: ggplot2 (>= 3.0.0), dplyr (>= 1.0.0), fdrtool (>= 1.2.17),
URL: https://github.com/talegari/ggisotonic
BugReports: https://github.com/talegari/ggisotonic/issues
NeedsCompilation: no
Packaged: 2022-05-23 16:29:35 UTC; dattachidambara
Author: Komala Sheshachala Srikanth [aut, cre]
Maintainer: Komala Sheshachala Srikanth <sri.teach@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-24 15:50:06 UTC

More information about ggisotonic at CRAN
Permanent link

New package FuzzyClass with initial version 0.1.0
Package: FuzzyClass
Title: Fuzzy and Non-Fuzzy Classifiers
Version: 0.1.0
Description: Provides classifiers that can be used for discrete variables and for continuous variables based on the idea of Naive Bayes and Fuzzy Naive Bayes considering some statistical distributions of articles published in the literature developed in the LabTEVE and LEAPIG research laboratories. Among the proposed classification methods is a with the Gamma distribution, proposed by Moraes, Soares and Machado (2018) <doi:10.1142/9789813273238_0088>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: caTools, datasets, doParallel, e1071, EnvStats, foreach, MASS, mlbench, parallel, Rdpack, rootSolve, trapezoid
Depends: R (>= 2.10)
Suggests: testthat (>= 3.0.0)
URL: https://github.com/Jodavid/FuzzyClass
BugReports: https://github.com/Jodavid/FuzzyClass/issues
NeedsCompilation: no
Packaged: 2022-05-23 14:48:09 UTC; hartbjf
Author: Jodavid Ferreira [aut, cre] , Ronei Moraes [ctb] , Arthur Ricardo [ctb]
Maintainer: Jodavid Ferreira <jodavid@protonmail.com>
Repository: CRAN
Date/Publication: 2022-05-24 15:40:01 UTC

More information about FuzzyClass at CRAN
Permanent link

Package Keyboard (with last version 0.1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-07-07 0.1.0

Permanent link
Package EntropyExplorer (with last version 1.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2015-06-11 1.1
2015-03-17 1.0

Permanent link
Package ri2 (with last version 0.2.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-12-07 0.2.0
2019-01-24 0.1.2

Permanent link
Package spcov (with last version 1.01) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2012-09-13 1.01
2012-02-19 1.0

Permanent link
Package WeightedPortTest (with last version 1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2012-05-24 1.0

Permanent link
Package EvaluateCore (with last version 0.1.2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-06-12 0.1.2
2020-06-03 0.1.1

Permanent link
Package ConnectednessApproach (with last version 1.0.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2022-03-22 1.0.0

Permanent link
Package RepeatedHighDim (with last version 2.0.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2013-08-21 2.0.0
2013-03-11 1.01
2011-03-14 1.0

Permanent link
Package KOBT (with last version 0.1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-02-20 0.1.0

Permanent link
Package mpathsenser updated to version 1.0.2 with previous version 1.0.1 dated 2022-05-19

Title: Process and Analyse Data from m-Path Sense
Description: Overcomes one of the major challenges in mobile (passive) sensing, namely being able to pre-process the raw data that comes from a mobile sensing app, specifically "m-Path Sense" <https://m-path.io>. The main task of 'mpathsenser' is therefore to read "m-Path Sense" JSON files into a database and provide several convenience functions to aid in data processing.
Author: Koen Niemeijer [aut, cre]
Maintainer: Koen Niemeijer <koen.niemeijer@kuleuven.be>

Diff between mpathsenser versions 1.0.1 dated 2022-05-19 and 1.0.2 dated 2022-05-24

 mpathsenser-1.0.1/mpathsenser/inst/testdata/broken/backup            |only
 mpathsenser-1.0.2/mpathsenser/DESCRIPTION                            |    6 
 mpathsenser-1.0.2/mpathsenser/MD5                                    |   23 
 mpathsenser-1.0.2/mpathsenser/R/database.R                           |    6 
 mpathsenser-1.0.2/mpathsenser/R/utils.R                              |   59 
 mpathsenser-1.0.2/mpathsenser/tests/testthat/test-database.R         |  410 +-
 mpathsenser-1.0.2/mpathsenser/tests/testthat/test-functions.R        |   13 
 mpathsenser-1.0.2/mpathsenser/tests/testthat/test-import-functions.R | 1815 +++++-----
 mpathsenser-1.0.2/mpathsenser/tests/testthat/test-utils.R            |  102 
 9 files changed, 1252 insertions(+), 1182 deletions(-)

More information about mpathsenser at CRAN
Permanent link

New package tidyterra with initial version 0.1.0
Package: tidyterra
Title: 'tidyverse' Methods and 'ggplot2' Utils for 'terra' Objects
Version: 0.1.0
Description: Extension of the 'tidyverse' for 'SpatRaster' and 'SpatVector' objects of the 'terra' package. It includes also new 'geom_' functions that provide a convenient way of visualizing 'terra' objects with 'ggplot2'.
License: MIT + file LICENSE
URL: https://dieghernan.github.io/tidyterra/, https://github.com/dieghernan/tidyterra
BugReports: https://github.com/dieghernan/tidyterra/issues
Depends: R (>= 3.6.0)
Imports: cli (>= 3.0.0), crayon, data.table, dplyr, ggplot2 (>= 3.1.0), magrittr, rlang, scales, sf (>= 1.0.0), terra (>= 1.5-12), tibble, tidyr
Suggests: isoband, knitr, lifecycle, maptiles, rmarkdown, s2, testthat (>= 3.0.0), vdiffr
VignetteBuilder: knitr
Config/testthat/parallel: true
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-23 14:34:35 UTC; diego
Author: Diego Hernangomez [aut, cre, cph] , Dewey Dunnington [ctb]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-24 11:00:02 UTC

More information about tidyterra at CRAN
Permanent link

New package subscore with initial version 3.3
Package: subscore
Title: Computing Subscores in Classical Test Theory and Item Response Theory
Version: 3.3
Author: Shenghai Dai [aut, cre], Xiaolin Wang [aut], Dubravka Svetina [aut]
Maintainer: Shenghai Dai <s.dai@wsu.edu>
Description: Functions for computing test subscores using different methods in both classical test theory (CTT) and item response theory (IRT). This package enables three types of subscoring methods within the framework of CTT and IRT, including (1) Wainer's augmentation method (Wainer et. al., 2001) <doi:10.4324/9781410604729>, (2) Haberman's subscoring methods (Haberman, 2008) <doi:10.3102/1076998607302636>, and (3) Yen's objective performance index (OPI; Yen, 1987) <https://www.ets.org/research/policy_research_reports/publications/paper/1987/hrap>. It also includes functions to compute Proportional Reduction of Mean Squared Errors (PRMSEs) in Haberman's methods which are used to examine whether test subscores are of added value. In addition, the package includes a function to assess the local independence assumption of IRT with Yen's Q3 statistic (Yen, 1984 <doi:10.1177/014662168400800201>; Yen, 1993 <doi:10.1111/j.1745-3984.1993.tb00423.x>).
Depends: R (>= 3.4.0), CTT, stats, irtoys, sirt, ltm
Imports: cocor, boot
NeedsCompilation: no
LazyData: true
Encoding: UTF-8
License: GPL (>= 2)
Packaged: 2022-05-20 15:33:36 UTC; daish
Repository: CRAN
Date/Publication: 2022-05-24 11:00:07 UTC

More information about subscore at CRAN
Permanent link

New package spNNGP with initial version 0.1.8
Package: spNNGP
Title: Spatial Regression Models for Large Datasets using Nearest Neighbor Gaussian Processes
Version: 0.1.8
Date: 2022-05-19
Maintainer: Andrew Finley <finleya@msu.edu>
Author: Andrew Finley [aut, cre], Abhirup Datta [aut], Sudipto Banerjee [aut]
Depends: R (>= 3.5.0), coda, Formula, RANN
Description: Fits univariate Bayesian spatial regression models for large datasets using Nearest Neighbor Gaussian Processes (NNGP) detailed in Finley, Datta, Banerjee (2020) <arXiv:2001.09111>, and Finley, Datta, Cook, Morton, Andersen, and Banerjee (2019) <doi:10.1080/10618600.2018.1537924> and Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091>.
License: GPL (>= 2)
Encoding: UTF-8
URL: https://www.finley-lab.com/
Repository: CRAN
NeedsCompilation: yes
Packaged: 2022-05-19 13:39:04 UTC; andy
Date/Publication: 2022-05-24 11:00:09 UTC
Imports: methods

More information about spNNGP at CRAN
Permanent link

New package SDLfilter with initial version 2.2.1
Package: SDLfilter
Title: Filtering and Assessing the Sample Size of Tracking Data
Version: 2.2.1
Date: 2022-05-15
Author: Takahiro Shimada
Maintainer: Takahiro Shimada <taka.shimada@gmail.com>
Description: Functions to filter GPS/Argos locations, as well as assessing the sample size for the analysis of animal distributions. The filters remove temporal and spatial duplicates, fixes located at a given height from estimated high tide line, and locations with high error as described in Shimada et al. (2012) <doi:10.3354/meps09747> and Shimada et al. (2016) <doi:10.1007/s00227-015-2771-0>. Sample size for the analysis of animal distributions can be assessed by the conventional area-based approach or the alternative probability-based approach as described in Shimada et al. (2021) <doi:10.1111/2041-210X.13506>.
Depends: R (>= 3.5.0), ggplot2
Imports: geosphere, data.table, gridExtra, ggsn, ggmap, maps, pracma, lubridate, dplyr, emmeans, utils, sf, stars
License: GPL-2 | file LICENSE
URL: https://github.com/TakahiroShimada/SDLfilter
BugReports: https://github.com/TakahiroShimada/SDLfilter/issues
LazyData: true
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-23 21:31:05 UTC; taka
Repository: CRAN
Date/Publication: 2022-05-24 10:10:11 UTC

More information about SDLfilter at CRAN
Permanent link

New package rr with initial version 1.4.1
Package: rr
Version: 1.4.1
Title: Statistical Methods for the Randomized Response Technique
Depends: R (>= 3.0.0), utils
Imports: MASS, arm, coda, magic
Description: Enables researchers to conduct multivariate statistical analyses of survey data with randomized response technique items from several designs, including mirrored question, forced question, and unrelated question. This includes regression with the randomized response as the outcome and logistic regression with the randomized response item as a predictor. In addition, tools for conducting power analysis for designing randomized response items are included. The package implements methods described in Blair, Imai, and Zhou (2015) ''Design and Analysis of the Randomized Response Technique,'' Journal of the American Statistical Association <https://graemeblair.com/papers/randresp.pdf>.
LazyLoad: yes
LazyData: yes
License: GPL (>= 3)
Suggests: testthat
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2022-05-24 02:06:48 UTC; gdblair
Author: Graeme Blair [aut, cre], Yang-Yang Zhou [aut], Kosuke Imai [aut], Winston Chou [ctb]
Maintainer: Graeme Blair <graeme.blair@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-24 10:10:02 UTC

More information about rr at CRAN
Permanent link

Package npphen updated to version 1.5.0 with previous version 1.1.1 dated 2021-11-19

Title: Vegetation Phenological Cycle and Anomaly Detection using Remote Sensing Data
Description: Calculates phenological cycle and anomalies using a non-parametric approach applied to time series of vegetation indices derived from remote sensing data or field measurements. The package implements basic and high-level functions for manipulating vector data (numerical series) and raster data (satellite derived products). Processing of very large raster files is supported. For more information, please check the following paper: Estay, S., Chávez, R.O. (2018) <doi:10.1101/301143>.
Author: Roberto O. Chavez [cre, aut], Sergio A. Estay [cre, aut], Jose A. Lastra [cre,ctb] & Carlos G. Riquelme [ctb]
Maintainer: Jose A. Lastra <jose.lastra@pucv.cl>

Diff between npphen versions 1.1.1 dated 2021-11-19 and 1.5.0 dated 2022-05-24

 npphen-1.1.1/npphen/R/PhenAnoMap.R           |only
 npphen-1.1.1/npphen/R/PhenAnoma.R            |only
 npphen-1.1.1/npphen/inst/extdata             |only
 npphen-1.1.1/npphen/man/PhenAnoMap.Rd        |only
 npphen-1.1.1/npphen/man/PhenAnoma.Rd         |only
 npphen-1.5.0/npphen/DESCRIPTION              |   21 
 npphen-1.5.0/npphen/MD5                      |  761 ---------------------------
 npphen-1.5.0/npphen/NAMESPACE                |   35 -
 npphen-1.5.0/npphen/R/ExtremeAnoMap.R        |only
 npphen-1.5.0/npphen/R/ExtremeAnom.R          |only
 npphen-1.5.0/npphen/R/Phen.R                 |  155 +++--
 npphen-1.5.0/npphen/R/PhenKplot.R            |   99 ++-
 npphen-1.5.0/npphen/R/PhenMap.R              |  146 +++--
 npphen-1.5.0/npphen/R/data.R                 |only
 npphen-1.5.0/npphen/R/npphen-package.R       |    9 
 npphen-1.5.0/npphen/data                     |only
 npphen-1.5.0/npphen/inst/CITATION            |   33 -
 npphen-1.5.0/npphen/man/Bdesert_stack.Rd     |only
 npphen-1.5.0/npphen/man/ExtremeAnoMap.Rd     |only
 npphen-1.5.0/npphen/man/ExtremeAnom.Rd       |only
 npphen-1.5.0/npphen/man/MegaDrought_stack.Rd |only
 npphen-1.5.0/npphen/man/Phen.Rd              |  160 ++---
 npphen-1.5.0/npphen/man/PhenKplot.Rd         |  157 ++---
 npphen-1.5.0/npphen/man/PhenMap.Rd           |  169 +++--
 npphen-1.5.0/npphen/man/modis_dates.Rd       |only
 npphen-1.5.0/npphen/man/npphen.Rd            |   48 -
 npphen-1.5.0/npphen/man/phents.Rd            |only
 27 files changed, 600 insertions(+), 1193 deletions(-)

More information about npphen at CRAN
Permanent link

New package nodeSub with initial version 1.2.4
Package: nodeSub
Title: Simulate DNA Alignments Using Node Substitutions
Version: 1.2.4
Author: Thijs Janzen
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Description: Simulate DNA sequences for the node substitution model. In the node substitution model, substitutions accumulate additionally during a speciation event, providing a potential mechanistic explanation for substitution rate variation. This package provides tools to simulate such a process, simulate a reference process with only substitutions along the branches, and provides tools to infer phylogenies from alignments. More information can be found in Janzen (2021) <doi:10.1093/sysbio/syab085>.
URL: https://github.com/thijsjanzen/nodeSub
BugReports: https://github.com/thijsjanzen/nodeSub
License: GPL-3
Encoding: UTF-8
VignetteBuilder: knitr
LinkingTo: Rcpp
Depends: Rcpp, ape
Imports: apTreeshape, phangorn, tibble, DDD, Rmpfr, assertthat, pbapply, phylobase, geiger, babette, beautier, beastier, mauricer, tracerer, rappdirs, testit, stringr
Suggests: testthat, TreeSim, dplyr, knitr, rmarkdown, ggplot2, magrittr, tidyr
NeedsCompilation: yes
Packaged: 2022-05-23 11:14:43 UTC; p251362
Repository: CRAN
Date/Publication: 2022-05-24 10:10:04 UTC

More information about nodeSub at CRAN
Permanent link

New package nLTT with initial version 1.4.8
Package: nLTT
Title: Calculate the NLTT Statistic
Version: 1.4.8
Description: Provides functions to calculate the normalised Lineage-Through- Time (nLTT) statistic, given two phylogenetic trees. The nLTT statistic measures the difference between two Lineage-Through-Time curves, where each curve is normalised both in time and in number of lineages.
License: GPL-2
Imports: ape, coda, testit
Suggests: TreeSim, DDD, ggplot2, Hmisc, knitr, lintr, microbenchmark, plyr, reshape2, rmarkdown, TESS, testthat, DAISIE
NeedsCompilation: no
Encoding: UTF-8
VignetteBuilder: knitr
URL: https://github.com/thijsjanzen/nLTT
BugReports: https://github.com/thijsjanzen/nLTT/issues
Packaged: 2022-05-23 09:57:28 UTC; thijsjanzen
Author: Thijs Janzen [aut, cre], Richel J.C. Bilderbeek [aut] , Pedro Neves [ctb]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-24 11:00:12 UTC

More information about nLTT at CRAN
Permanent link

New package micompr with initial version 1.1.2
Package: micompr
Title: Multivariate Independent Comparison of Observations
Version: 1.1.2
Date: 2022-05-23
Maintainer: Nuno Fachada <faken@fakenmc.com>
Description: A procedure for comparing multivariate samples associated with different groups. It uses principal component analysis to convert multivariate observations into a set of linearly uncorrelated statistical measures, which are then compared using a number of statistical methods. The procedure is independent of the distributional properties of samples and automatically selects features that best explain their differences, avoiding manual selection of specific points or summary statistics. It is appropriate for comparing samples of time series, images, spectrometric measures or similar multivariate observations.
Depends: R (>= 3.6.0)
Imports: utils, graphics, methods, stats
Suggests: biotools, MVN (>= 5.0), testthat (>= 0.8), knitr, roxygen2, devtools
License: MIT + file LICENSE
URL: https://github.com/nunofachada/micompr
BugReports: https://github.com/nunofachada/micompr/issues
LazyData: true
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-23 18:22:17 UTC; nuno
Author: Nuno Fachada [aut, cre]
Repository: CRAN
Date/Publication: 2022-05-24 10:10:07 UTC

More information about micompr at CRAN
Permanent link

New package MBSP with initial version 2.0
Package: MBSP
Title: Multivariate Bayesian Model with Shrinkage Priors
Version: 2.0
Date: 2022-05-23
Author: Ray Bai, Malay Ghosh
Maintainer: Ray Bai <raybaistat@gmail.com>
Description: Gibbs sampler for fitting multivariate Bayesian linear regression with shrinkage priors (MBSP), using the three parameter beta normal family. The method is described in Bai and Ghosh (2018) <doi:10.1016/j.jmva.2018.04.010>.
License: GPL-3
Depends: R (>= 3.6.0)
Imports: stats, MCMCpack, GIGrvg, utils, MASS
NeedsCompilation: yes
Packaged: 2022-05-24 03:34:44 UTC; rayba
Repository: CRAN
Date/Publication: 2022-05-24 10:10:16 UTC

More information about MBSP at CRAN
Permanent link

Package mand updated to version 1.1 with previous version 1.0 dated 2021-06-29

Title: Multivariate Analysis for Neuroimaging Data
Description: Several functions can be used to analyze neuroimaging data using multivariate methods based on the 'msma' package. The functions used in the book entitled "Multivariate Analysis for Neuroimaging Data" (2021, ISBN-13: 978-0367255329) are contained.
Author: Atsushi Kawaguchi [aut, cre]
Maintainer: Atsushi Kawaguchi <kawa_a24@yahoo.co.jp>

Diff between mand versions 1.0 dated 2021-06-29 and 1.1 dated 2022-05-24

 DESCRIPTION                                                |   12 
 MD5                                                        |   52 +-
 R/src.r                                                    |   15 
 build/vignette.rds                                         |binary
 data/atlas.rda                                             |binary
 data/atlasdatasets.rda                                     |binary
 data/baseimg.rda                                           |binary
 data/diffimg.rda                                           |binary
 data/exbrain.rda                                           |binary
 data/mask.rda                                              |binary
 data/sdevimg.rda                                           |binary
 data/template.rda                                          |binary
 inst/doc/a_overview.html                                   |  174 +++++---
 inst/doc/b_Introduction.html                               |   95 +++-
 inst/doc/c_Brain_Imaging_Data.html                         |   84 ++-
 inst/doc/d_Common_Statistical_Approach.html                |  205 +++++++--
 inst/doc/e_Multivariate_Approach_Matrix_Decomposition.R    |   35 -
 inst/doc/e_Multivariate_Approach_Matrix_Decomposition.Rmd  |   37 -
 inst/doc/e_Multivariate_Approach_Matrix_Decomposition.html |  258 +++++++----
 inst/doc/f_Multivariate_Approach_Prediction_Model.html     |  280 +++++++++----
 inst/doc/g_Multi-block_Approach.html                       |   78 ++-
 man/basisprod.Rd                                           |    3 
 man/mand-package.Rd                                        |    2 
 man/ptest.Rd                                               |   12 
 man/rec.Rd                                                 |    3 
 man/sizechange.Rd                                          |    3 
 vignettes/e_Multivariate_Approach_Matrix_Decomposition.Rmd |   37 -
 27 files changed, 921 insertions(+), 464 deletions(-)

More information about mand at CRAN
Permanent link

Package IPEC updated to version 1.0.3 with previous version 1.0.1 dated 2022-05-17

Title: Root Mean Square Curvature Calculation
Description: Calculates the RMS intrinsic and parameter-effects curvatures of a nonlinear regression model. The curvatures are global measures of assessing whether a model/data set combination is close-to-linear or not. See Bates and Watts (1980) <doi:10.1002/9780470316757> and Ratkowsky and Reddy (2017) <doi:10.1093/aesa/saw098> for details.
Author: Peijian Shi [aut, cre], Peter M. Ridland [aut], David A. Ratkowsky [aut], Yang Li [aut]
Maintainer: Peijian Shi <pjshi@njfu.edu.cn>

Diff between IPEC versions 1.0.1 dated 2022-05-17 and 1.0.3 dated 2022-05-24

 DESCRIPTION       |    8 +++----
 MD5               |   24 ++++++++++++-----------
 R/bootIPEC.R      |   22 ++++++++++++++-------
 R/fitIPEC.R       |   34 +++++++++++++++++++++++---------
 build/partial.rdb |binary
 data/crops.rda    |only
 man/IPEC.Rd       |   36 ++++++++++++++++++++--------------
 man/biasIPEC.Rd   |   19 +++++++++++-------
 man/bootIPEC.Rd   |   56 +++++++++++++++++++++++++++++++-----------------------
 man/crops.Rd      |only
 man/curvIPEC.Rd   |   17 ++++++++++------
 man/derivIPEC.Rd  |   13 ++++++++----
 man/fitIPEC.Rd    |   45 +++++++++++++++++++++++++------------------
 man/skewIPEC.Rd   |   17 ++++++++++------
 14 files changed, 179 insertions(+), 112 deletions(-)

More information about IPEC at CRAN
Permanent link


Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.