Title: Flexible and Reproducible Label Designs
Description: An open-source R package to deploys flexible and reproducible labels using layers.
The 'huito' package is part of the 'inkaverse' project for developing different procedures and
tools used in plant science and experimental designs.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flavjack@gmail.com>
Diff between huito versions 0.1.3 dated 2022-04-01 and 0.1.4 dated 2022-05-26
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ NEWS.md | 5 +++++ R/label_print.R | 4 ++-- build/vignette.rds |binary inst/doc/huito.R | 8 ++------ inst/doc/huito.html | 18 +++++++++--------- inst/doc/labels.html | 14 ++++++++++---- inst/doc/stickers.R | 4 +++- inst/doc/stickers.Rmd | 4 +++- inst/doc/stickers.html | 10 ++++++---- vignettes/huito/_doc.Rmd | 18 ++++++++---------- vignettes/stickers.Rmd | 4 +++- 13 files changed, 68 insertions(+), 55 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre],
RStudio, PBC [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 0.15.4 dated 2022-03-02 and 0.15.5 dated 2022-05-26
renv-0.15.4/renv/inst/repos/src/contrib/renv_0.15.4.tar.gz |only renv-0.15.5/renv/DESCRIPTION | 12 renv-0.15.5/renv/MD5 | 188 ++++----- renv-0.15.5/renv/NEWS.md | 54 ++ renv-0.15.5/renv/R/available-packages.R | 107 +++-- renv-0.15.5/renv/R/bioconductor.R | 10 renv-0.15.5/renv/R/bootstrap.R | 11 renv-0.15.5/renv/R/clean.R | 5 renv-0.15.5/renv/R/cran.R | 2 renv-0.15.5/renv/R/dependencies.R | 17 renv-0.15.5/renv/R/download.R | 16 renv-0.15.5/renv/R/envir.R | 9 renv-0.15.5/renv/R/envvars.R | 25 - renv-0.15.5/renv/R/files.R | 32 + renv-0.15.5/renv/R/hydrate.R | 8 renv-0.15.5/renv/R/init.R | 7 renv-0.15.5/renv/R/install.R | 3 renv-0.15.5/renv/R/isolate.R | 4 renv-0.15.5/renv/R/json-read.R | 2 renv-0.15.5/renv/R/knitr.R | 9 renv-0.15.5/renv/R/load.R | 7 renv-0.15.5/renv/R/lockfiles.R | 2 renv-0.15.5/renv/R/migrate.R | 8 renv-0.15.5/renv/R/modify.R | 105 ++++- renv-0.15.5/renv/R/mran.R | 4 renv-0.15.5/renv/R/pak.R | 12 renv-0.15.5/renv/R/paths.R | 5 renv-0.15.5/renv/R/progress.R | 44 +- renv-0.15.5/renv/R/python.R | 2 renv-0.15.5/renv/R/records.R | 17 renv-0.15.5/renv/R/rehash.R | 4 renv-0.15.5/renv/R/remotes.R | 2 renv-0.15.5/renv/R/repos.R | 25 - renv-0.15.5/renv/R/restore.R | 26 + renv-0.15.5/renv/R/retrieve.R | 91 +++- renv-0.15.5/renv/R/rtools.R | 34 + renv-0.15.5/renv/R/scope.R | 29 - renv-0.15.5/renv/R/settings.R | 4 renv-0.15.5/renv/R/snapshot.R | 10 renv-0.15.5/renv/R/tests.R | 2 renv-0.15.5/renv/R/update.R | 4 renv-0.15.5/renv/R/use.R | 4 renv-0.15.5/renv/R/utils-format.R | 6 renv-0.15.5/renv/build/vignette.rds |binary renv-0.15.5/renv/inst/doc/bioconductor.html | 1 renv-0.15.5/renv/inst/doc/cellar.html | 1 renv-0.15.5/renv/inst/doc/ci.html | 1 renv-0.15.5/renv/inst/doc/collaborating.html | 1 renv-0.15.5/renv/inst/doc/docker.R | 4 renv-0.15.5/renv/inst/doc/docker.Rmd | 139 ++++--- renv-0.15.5/renv/inst/doc/docker.html | 254 ++++--------- renv-0.15.5/renv/inst/doc/faq.R | 3 renv-0.15.5/renv/inst/doc/faq.Rmd | 28 - renv-0.15.5/renv/inst/doc/faq.html | 33 - renv-0.15.5/renv/inst/doc/lockfile.html | 3 renv-0.15.5/renv/inst/doc/mran.html | 1 renv-0.15.5/renv/inst/doc/packages.html | 1 renv-0.15.5/renv/inst/doc/profiles.html | 1 renv-0.15.5/renv/inst/doc/python.html | 1 renv-0.15.5/renv/inst/doc/renv.Rmd | 20 - renv-0.15.5/renv/inst/doc/renv.html | 12 renv-0.15.5/renv/inst/doc/rsconnect.html | 1 renv-0.15.5/renv/inst/doc/use.html | 1 renv-0.15.5/renv/inst/repos/src/contrib/PACKAGES | 8 renv-0.15.5/renv/inst/repos/src/contrib/PACKAGES.gz |binary renv-0.15.5/renv/inst/repos/src/contrib/PACKAGES.rds |binary renv-0.15.5/renv/inst/repos/src/contrib/renv_0.15.5.tar.gz |only renv-0.15.5/renv/inst/resources/activate.R | 15 renv-0.15.5/renv/inst/resources/scripts-git-askpass.cmd |only renv-0.15.5/renv/man/autoload.Rd | 12 renv-0.15.5/renv/man/config.Rd | 6 renv-0.15.5/renv/man/consent.Rd | 6 renv-0.15.5/renv/man/dependencies.Rd | 18 renv-0.15.5/renv/man/install.Rd | 24 - renv-0.15.5/renv/man/isolate.Rd | 12 renv-0.15.5/renv/man/lockfiles.Rd | 8 renv-0.15.5/renv/man/modify.Rd | 17 renv-0.15.5/renv/man/paths.Rd | 27 - renv-0.15.5/renv/man/restore.Rd | 6 renv-0.15.5/renv/man/snapshot.Rd | 10 renv-0.15.5/renv/man/use.Rd | 4 renv-0.15.5/renv/tests/testthat/resources/chunk-yaml.Rmd |only renv-0.15.5/renv/tests/testthat/test-archive.R | 39 + renv-0.15.5/renv/tests/testthat/test-bioconductor.R | 3 renv-0.15.5/renv/tests/testthat/test-cellar.R |only renv-0.15.5/renv/tests/testthat/test-dependencies.R | 5 renv-0.15.5/renv/tests/testthat/test-download.R | 21 + renv-0.15.5/renv/tests/testthat/test-init.R | 18 renv-0.15.5/renv/tests/testthat/test-load.R | 4 renv-0.15.5/renv/tests/testthat/test-modify.R |only renv-0.15.5/renv/tests/testthat/test-python.R | 27 + renv-0.15.5/renv/tests/testthat/test-remotes.R | 9 renv-0.15.5/renv/tests/testthat/test-repos.R | 14 renv-0.15.5/renv/tests/testthat/test-sandbox.R | 4 renv-0.15.5/renv/tests/testthat/test-snapshot.R | 30 + renv-0.15.5/renv/vignettes/docker.Rmd | 139 ++++--- renv-0.15.5/renv/vignettes/faq.Rmd | 28 - renv-0.15.5/renv/vignettes/renv.Rmd | 20 - 98 files changed, 1311 insertions(+), 697 deletions(-)
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(-)
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(-)
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(-)
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(-)
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 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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(-)
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(-)
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(-)
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(-)
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
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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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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
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(-)
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(-)
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
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(-)
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(-)
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(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-21 1.0.0
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(-)
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
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-16 0.9.0