Title: Interface to 'Zenodo' REST API
Description: Provides an Interface to 'Zenodo' (<https://zenodo.org>) REST API,
including management of depositions, attribution of DOIs by 'Zenodo' and
upload and download of files.
Author: Emmanuel Blondel [aut, cre] ,
Julien Barde [ctb] ,
Stephen Eglen [ctb] ,
Hans Van Calster [ctb] ,
Floris Vanderhaeghe [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between zen4R versions 0.7 dated 2022-08-19 and 0.7-1 dated 2023-01-09
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 10 +++++++++- R/ZenodoRequest.R | 23 +++++++++-------------- README.md | 4 ++-- inst/doc/zen4R.Rmd | 4 ++-- inst/doc/zen4R.html | 4 ++-- vignettes/zen4R.Rmd | 4 ++-- 8 files changed, 37 insertions(+), 34 deletions(-)
Title: Data Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Data menu includes interfaces for loading, saving,
viewing, visualizing, summarizing, transforming, and combining data. It also
contains functionality to generate reproducible reports of the analyses
conducted in the application.
Author: Vincent Nijs [aut, cre],
Niklas von Hertzen [aut]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.data versions 1.4.5 dated 2022-09-08 and 1.5.1 dated 2023-01-09
radiant.data-1.4.5/radiant.data/man/is_empty.Rd |only radiant.data-1.5.1/radiant.data/DESCRIPTION | 22 radiant.data-1.5.1/radiant.data/MD5 | 129 +-- radiant.data-1.5.1/radiant.data/NAMESPACE | 10 radiant.data-1.5.1/radiant.data/NEWS.md | 23 radiant.data-1.5.1/radiant.data/R/aaa.R | 2 radiant.data-1.5.1/radiant.data/R/combine.R | 31 radiant.data-1.5.1/radiant.data/R/deprecated.R | 6 radiant.data-1.5.1/radiant.data/R/explore.R | 105 +- radiant.data-1.5.1/radiant.data/R/manage.R | 57 - radiant.data-1.5.1/radiant.data/R/pivotr.R | 143 +-- radiant.data-1.5.1/radiant.data/R/radiant.R | 170 ++-- radiant.data-1.5.1/radiant.data/R/transform.R | 100 +- radiant.data-1.5.1/radiant.data/R/view.R | 139 ++- radiant.data-1.5.1/radiant.data/R/visualize.R | 275 ++++-- radiant.data-1.5.1/radiant.data/README.md | 4 radiant.data-1.5.1/radiant.data/inst/app/global.R | 40 radiant.data-1.5.1/radiant.data/inst/app/init.R | 57 - radiant.data-1.5.1/radiant.data/inst/app/radiant.R | 67 - radiant.data-1.5.1/radiant.data/inst/app/server.R | 10 radiant.data-1.5.1/radiant.data/inst/app/tools/app/about.md | 4 radiant.data-1.5.1/radiant.data/inst/app/tools/app/help.R | 12 radiant.data-1.5.1/radiant.data/inst/app/tools/app/report_funs.R | 26 radiant.data-1.5.1/radiant.data/inst/app/tools/app/report_r.R | 18 radiant.data-1.5.1/radiant.data/inst/app/tools/app/report_rmd.R | 18 radiant.data-1.5.1/radiant.data/inst/app/tools/app/state.R | 37 radiant.data-1.5.1/radiant.data/inst/app/tools/app/stop.R | 14 radiant.data-1.5.1/radiant.data/inst/app/tools/data/combine_ui.R | 14 radiant.data-1.5.1/radiant.data/inst/app/tools/data/data_ui.R | 58 - radiant.data-1.5.1/radiant.data/inst/app/tools/data/explore_ui.R | 45 - radiant.data-1.5.1/radiant.data/inst/app/tools/data/manage.R | 67 - radiant.data-1.5.1/radiant.data/inst/app/tools/data/manage_ui.R | 16 radiant.data-1.5.1/radiant.data/inst/app/tools/data/pivotr_ui.R | 79 + radiant.data-1.5.1/radiant.data/inst/app/tools/data/transform_ui.R | 135 +-- radiant.data-1.5.1/radiant.data/inst/app/tools/data/view_ui.R | 211 ++-- radiant.data-1.5.1/radiant.data/inst/app/tools/data/visualize_ui.R | 46 - radiant.data-1.5.1/radiant.data/inst/app/www/js/run_return.js | 42 radiant.data-1.5.1/radiant.data/inst/app/www/style.css | 4 radiant.data-1.5.1/radiant.data/inst/assets |only radiant.data-1.5.1/radiant.data/man/add_description.Rd |only radiant.data-1.5.1/radiant.data/man/arrange_data.Rd |only radiant.data-1.5.1/radiant.data/man/as_distance.Rd | 4 radiant.data-1.5.1/radiant.data/man/as_hms.Rd | 4 radiant.data-1.5.1/radiant.data/man/as_integer.Rd | 6 radiant.data-1.5.1/radiant.data/man/as_numeric.Rd | 6 radiant.data-1.5.1/radiant.data/man/as_ymd_hms.Rd | 6 radiant.data-1.5.1/radiant.data/man/combine_data.Rd | 6 radiant.data-1.5.1/radiant.data/man/copy_from.Rd | 1 radiant.data-1.5.1/radiant.data/man/cv.Rd | 2 radiant.data-1.5.1/radiant.data/man/dtab.data.frame.Rd | 5 radiant.data-1.5.1/radiant.data/man/dtab.explore.Rd | 12 radiant.data-1.5.1/radiant.data/man/dtab.pivotr.Rd | 7 radiant.data-1.5.1/radiant.data/man/explore.Rd | 11 radiant.data-1.5.1/radiant.data/man/get_data.Rd | 16 radiant.data-1.5.1/radiant.data/man/indexr.Rd | 6 radiant.data-1.5.1/radiant.data/man/is.empty.Rd |only radiant.data-1.5.1/radiant.data/man/level_list.Rd | 2 radiant.data-1.5.1/radiant.data/man/ln.Rd | 2 radiant.data-1.5.1/radiant.data/man/make_arrange_cmd.Rd |only radiant.data-1.5.1/radiant.data/man/pivotr.Rd | 11 radiant.data-1.5.1/radiant.data/man/radiant.data-deprecated.Rd | 1 radiant.data-1.5.1/radiant.data/man/refactor.Rd | 4 radiant.data-1.5.1/radiant.data/man/register.Rd | 4 radiant.data-1.5.1/radiant.data/man/show_duplicated.Rd | 6 radiant.data-1.5.1/radiant.data/man/slice_data.Rd |only radiant.data-1.5.1/radiant.data/man/table2data.Rd | 2 radiant.data-1.5.1/radiant.data/man/view_data.Rd | 3 radiant.data-1.5.1/radiant.data/man/visualize.Rd | 38 radiant.data-1.5.1/radiant.data/tests/testthat/test_funs.R | 423 +++++----- 69 files changed, 1720 insertions(+), 1104 deletions(-)
Title: Survival Analysis
Description: Contains the core survival analysis routines, including
definition of Surv objects,
Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,
and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre],
Thomas Lumley [ctb, trl] ,
Atkinson Elizabeth [ctb],
Crowson Cynthia [ctb]
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>
Diff between survival versions 3.4-0.1 dated 2023-01-03 and 3.5-0 dated 2023-01-09
survival-3.4-0.1/survival/noweb/cch.Rnw |only survival-3.4-0.1/survival/noweb/concordance2.Rnw |only survival-3.4-0.1/survival/noweb/coxsurv3.save |only survival-3.4-0.1/survival/noweb/coxsurv3.save2 |only survival-3.4-0.1/survival/noweb/msurv.rwt |only survival-3.4-0.1/survival/noweb/msurv.save |only survival-3.4-0.1/survival/noweb/msurvnew |only survival-3.4-0.1/survival/noweb/survfit.riskwt |only survival-3.4-0.1/survival/noweb/survfit.save |only survival-3.4-0.1/survival/noweb/survfitCI.riskwt |only survival-3.4-0.1/survival/noweb/survfitCI.save |only survival-3.4-0.1/survival/noweb/yates2new.Rnw |only survival-3.4-0.1/survival/src/agsurv3.c |only survival-3.5-0/survival/DESCRIPTION | 8 survival-3.5-0/survival/MD5 | 194 +- survival-3.5-0/survival/NAMESPACE | 4 survival-3.5-0/survival/R/basehaz.R | 30 survival-3.5-0/survival/R/concordance.R | 178 + survival-3.5-0/survival/R/cox.zph.R | 16 survival-3.5-0/survival/R/coxph.R | 20 survival-3.5-0/survival/R/coxph.getdata.R | 18 survival-3.5-0/survival/R/nsk.R | 15 survival-3.5-0/survival/R/predict.coxph.R | 7 survival-3.5-0/survival/R/residuals.survfit.R | 14 survival-3.5-0/survival/R/survcondense.R |only survival-3.5-0/survival/R/survfit.coxph.R | 25 survival-3.5-0/survival/R/survfit.coxphms.R | 71 survival-3.5-0/survival/R/survfitTurnbull.R | 2 survival-3.5-0/survival/R/tmerge.R | 28 survival-3.5-0/survival/build/vignette.rds |binary survival-3.5-0/survival/inst/NEWS.Rd | 44 survival-3.5-0/survival/inst/doc/adjcurve.pdf |binary survival-3.5-0/survival/inst/doc/approximate.pdf |binary survival-3.5-0/survival/inst/doc/compete.pdf |binary survival-3.5-0/survival/inst/doc/concordance.R | 269 +- survival-3.5-0/survival/inst/doc/concordance.Rnw | 1022 +++++++---- survival-3.5-0/survival/inst/doc/concordance.pdf |binary survival-3.5-0/survival/inst/doc/discrim.pdf |binary survival-3.5-0/survival/inst/doc/multi.pdf |binary survival-3.5-0/survival/inst/doc/other.pdf |binary survival-3.5-0/survival/inst/doc/population.pdf |binary survival-3.5-0/survival/inst/doc/splines.pdf |binary survival-3.5-0/survival/inst/doc/survival.Rnw | 4 survival-3.5-0/survival/inst/doc/survival.pdf |binary survival-3.5-0/survival/inst/doc/tiedtimes.pdf |binary survival-3.5-0/survival/inst/doc/timedep.R | 60 survival-3.5-0/survival/inst/doc/timedep.Rnw | 23 survival-3.5-0/survival/inst/doc/timedep.pdf |binary survival-3.5-0/survival/inst/doc/validate.R | 6 survival-3.5-0/survival/inst/doc/validate.Rnw | 22 survival-3.5-0/survival/inst/doc/validate.pdf |binary survival-3.5-0/survival/man/basehaz.Rd | 13 survival-3.5-0/survival/man/concordance.Rd | 86 survival-3.5-0/survival/man/concordancefit.Rd | 14 survival-3.5-0/survival/man/coxph.Rd | 28 survival-3.5-0/survival/man/dsurvreg.Rd | 51 survival-3.5-0/survival/man/rhDNase.Rd | 5 survival-3.5-0/survival/man/survcondense.Rd |only survival-3.5-0/survival/man/survfit.coxph.Rd | 43 survival-3.5-0/survival/man/survfit.object.Rd | 4 survival-3.5-0/survival/noweb/Makefile | 3 survival-3.5-0/survival/noweb/code.nw | 441 ++-- survival-3.5-0/survival/noweb/code.toc | 62 survival-3.5-0/survival/noweb/concordance.Rnw | 278 +- survival-3.5-0/survival/noweb/coxph.Rnw | 20 survival-3.5-0/survival/noweb/coxsurv.Rnw | 25 survival-3.5-0/survival/noweb/coxsurv3.Rnw | 46 survival-3.5-0/survival/noweb/predict.coxph.Rnw | 8 survival-3.5-0/survival/noweb/residuals.survfit.Rnw | 14 survival-3.5-0/survival/noweb/residuals.survfit2.Rnw |only survival-3.5-0/survival/noweb/survfitKM.Rnw | 4 survival-3.5-0/survival/noweb/tmerge.Rnw | 28 survival-3.5-0/survival/noweb/zph.Rnw | 18 survival-3.5-0/survival/src/concordance3.c | 75 survival-3.5-0/survival/src/concordance5.c | 55 survival-3.5-0/survival/src/cox_Rcallback.c | 6 survival-3.5-0/survival/src/coxscore2.c | 2 survival-3.5-0/survival/src/coxsurv1.c | 298 +-- survival-3.5-0/survival/src/coxsurv2.c | 30 survival-3.5-0/survival/src/coxsurv3.c |only survival-3.5-0/survival/src/coxsurv4.c |only survival-3.5-0/survival/src/fastkm.c |only survival-3.5-0/survival/src/init.c | 5 survival-3.5-0/survival/src/survfitkm.c | 4 survival-3.5-0/survival/src/survproto.h | 14 survival-3.5-0/survival/src/survreg6.c | 17 survival-3.5-0/survival/src/survreg7.c | 17 survival-3.5-0/survival/src/survregc2.c | 2 survival-3.5-0/survival/tests/Examples/survival-Ex.Rout.save | 52 survival-3.5-0/survival/tests/concordance.R | 4 survival-3.5-0/survival/tests/concordance.Rout.save | 10 survival-3.5-0/survival/tests/concordance3.R | 93 - survival-3.5-0/survival/tests/concordance3.Rout.save | 109 - survival-3.5-0/survival/tests/coxsurv.R | 8 survival-3.5-0/survival/tests/coxsurv.Rout.save | 16 survival-3.5-0/survival/tests/mstrata.R | 5 survival-3.5-0/survival/tests/mstrata.Rout.save | 11 survival-3.5-0/survival/tests/tmerge3.R | 31 survival-3.5-0/survival/tests/tmerge3.Rout.save | 39 survival-3.5-0/survival/tests/zph.R | 4 survival-3.5-0/survival/tests/zph.Rout.save | 10 survival-3.5-0/survival/vignettes/concordance.Rnw | 1022 +++++++---- survival-3.5-0/survival/vignettes/refer.bib | 25 survival-3.5-0/survival/vignettes/survival.Rnw | 4 survival-3.5-0/survival/vignettes/temp |only survival-3.5-0/survival/vignettes/timedep.Rnw | 23 survival-3.5-0/survival/vignettes/validate.Rnw | 22 107 files changed, 3357 insertions(+), 1927 deletions(-)
Title: Deployment Interface for R Markdown Documents and Shiny
Applications
Description: Programmatic deployment interface for 'RPubs', 'shinyapps.io', and
'Posit Connect'. Supported content types include R Markdown documents,
Shiny applications, Plumber APIs, plots, and static web content.
Author: Aron Atkins [aut, cre],
Jonathan McPherson [aut],
JJ Allaire [aut],
Posit Software [cph, fnd]
Maintainer: Aron Atkins <aron@posit.co>
Diff between rsconnect versions 0.8.28 dated 2022-10-24 and 0.8.29 dated 2023-01-09
DESCRIPTION | 18 MD5 | 136 ++-- NEWS.md | 43 - R/accounts.R | 39 - R/appDependencies.R | 12 R/applications.R | 44 - R/auth.R | 76 +- R/bundle.R | 66 +- R/certificates.R | 2 R/client.R | 4 R/config.R | 14 R/configureApp.R | 18 R/connect.R | 30 - R/cookies.R | 115 +-- R/deployApp.R | 33 - R/deployDoc.R | 1 R/deploySite.R | 2 R/deployments.R | 20 R/http-curl.R | 20 R/http-internal.R | 21 R/http-libcurl.R | 8 R/http-rcurl.R | 12 R/http.R | 39 - R/ide.R | 4 R/json.R | 5 R/lint-framework.R | 4 R/lint-utils.R | 1 R/linters.R | 1 R/locale.R | 32 - R/lucid.R | 300 +++++----- R/packages.R | 44 + R/proxies.R | 2 R/purgeApp.R | 1 R/restartApp.R | 1 R/rmdindex.R | 47 - R/rpubs.R | 3 R/rsa.R | 4 R/rsconnect-package.R | 2 R/servers.R | 54 + R/tasks.R | 8 R/terminateApp.R | 1 R/title.R | 2 R/usage.R | 32 - R/utils.R | 52 - R/writeManifest.R | 4 README.md | 19 inst/examples/diamonds/server.R | 14 inst/examples/diamonds/ui.R | 20 inst/examples/sessioninfo/server.R | 2 inst/examples/sessioninfo/ui.R | 4 man/deployApp.Rd | 4 man/options.Rd | 2 man/rsconnect-package.Rd | 2 man/servers.Rd | 3 man/setAccountInfo.Rd | 4 man/showMetrics.Rd | 4 man/writeManifest.Rd | 2 tests/testthat/shinyapp-appR/app.R | 4 tests/testthat/shinyapp-singleR/single.R | 4 tests/testthat/shinyapp-with-absolute-paths/ShinyDocument.Rmd | 8 tests/testthat/shinyapp-with-absolute-paths/ShinyPresentation.Rmd | 4 tests/testthat/shinyapp-with-absolute-paths/server.R | 4 tests/testthat/shinyapp-with-absolute-paths/ui.R | 2 tests/testthat/test-accounts.R | 7 tests/testthat/test-bundle.R | 24 tests/testthat/test-connect.R | 4 tests/testthat/test-cookies.R | 44 - tests/testthat/test-http.R | 4 tests/testthat/test-lucid.R |only tests/testthat/test-server.R |only 70 files changed, 796 insertions(+), 770 deletions(-)
Title: Kriging Models using the 'libKriging' Library
Description: Interface to 'libKriging' 'C++' library <https://github.com/libKriging> that should
provide most standard Kriging / Gaussian process regression features
(like in 'DiceKriging', 'kergp' or 'RobustGaSP' packages).
'libKriging' relies on Armadillo linear algebra library (Apache 2 license) by Conrad Sanderson,
and 'lbfgsb_cpp' is a 'C++' wrapper by Colin Fang around 'lbfgsb' library (BSD-3 license) by
Ciyou Zhu, Richard Byrd, Jorge Nocedal and Jose Luis Morales used for hyperparameters optimization.
Author: Pascal Have [aut],
Yann Richet [aut, cre] ,
Yves Deville [aut],
Conrad Sanderson [ctb],
Colin Fang [ctb],
Ciyou Zhu [ctb],
Richard Byrd [ctb],
Jorge Nocedal [ctb],
Jose Luis Morales [ctb]
Maintainer: Yann Richet <yann.richet@irsn.fr>
Diff between rlibkriging versions 0.7-2 dated 2023-01-06 and 0.7-3 dated 2023-01-09
DESCRIPTION | 8 MD5 | 1092 +++++++++- configure | 1 configure.win | 1 src/libK/armadillo/cmake_aux/Modules/ARMA_FindLAPACK.cmake | 2 src/libK/armadillo/cmake_aux/Tools/build_external_project.cmake | 2 src/libK/bindings/Python/tests/loading_test.py | 2 src/libK/bindings/R/rlibkriging/DESCRIPTION | 4 src/libK/bindings/R/rlibkriging/tests/testthat/notest-LinearRegression.R | 2 src/libK/cmake/version.cmake | 2 src/libK/src/lib/CMakeLists.txt | 4 src/libK/travis-ci/linux-macos/loadenv.sh | 14 src/slapack |only tests/testthat/notest-LinearRegression.R | 2 tools/setup.sh | 6 15 files changed, 1112 insertions(+), 30 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,
Toph Allen
Maintainer: Aron Atkins <aron@posit.co>
Diff between packrat versions 0.8.1 dated 2022-06-29 and 0.9.0 dated 2023-01-09
DESCRIPTION | 13 MD5 | 93 +- R/aaa-globals.R | 20 R/augment-rprofile.R | 1 R/available-updates.R | 10 R/bitbucket.R | 93 +- R/bundle.R | 6 R/cranlike-repositories.R | 4 R/dependencies.R | 16 R/downloader.R | 151 +++- R/env.R | 36 R/external.R | 2 R/get-package-actions.R | 1 R/github.R | 114 ++- R/gitlab.R | 83 +- R/hooks.R | 4 R/install.R | 101 ++ R/lockfile-metadata.R | 2 R/lockfile.R | 2 R/packrat.R | 97 +- R/pkg.R | 8 R/platform.R | 6 R/pretty-print.R | 2 R/recursive-package-dependencies.R | 2 R/restore.R | 423 ++++------- R/rstudio-protocol.R | 2 R/search-path.R | 4 R/testthat-helpers.R | 9 R/utils.R | 26 inst/resources/init-rprofile.R | 2 inst/resources/init.R | 2 inst/resources/renv.R | 1017 +++++++++++++++++----------- man/bundle.Rd | 2 man/packrat.Rd | 5 man/restore.Rd | 78 +- tests/testthat/packages/packrat/DESCRIPTION | 10 tests/testthat/test-bitbucket.R | 97 ++ tests/testthat/test-cache.R | 6 tests/testthat/test-dependencies.R | 56 + tests/testthat/test-downloader.R | 35 tests/testthat/test-env.R |only tests/testthat/test-github.R | 111 ++- tests/testthat/test-gitlab.R | 107 ++ tests/testthat/test-hash.R | 7 tests/testthat/test-install.R |only tests/testthat/test-packrat.R | 5 tests/testthat/test-restore.R |only tests/testthat/test-shiny.R | 22 tools/tools-sync-renv.R | 27 49 files changed, 1891 insertions(+), 1029 deletions(-)
Title: 'FlexiBLAS' API Interface
Description: Provides functions to switch the 'BLAS'/'LAPACK' optimized backend
and change the number of threads without leaving the R session, which needs
to be linked against the 'FlexiBLAS' wrapper library
<https://www.mpi-magdeburg.mpg.de/projects/flexiblas>.
Author: Inaki Ucar [aut, cph, cre] ,
Martin Koehler [aut, cph]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between flexiblas versions 3.1.0 dated 2022-02-25 and 3.3.0 dated 2023-01-09
DESCRIPTION | 6 - MD5 | 12 +- NEWS.md | 5 + build/partial.rdb |binary src/flexiblas_api_standalone.c | 165 +++++++++++++++++++++++++---------------- src/init.c | 12 +- src/wrapper.c | 12 +- 7 files changed, 129 insertions(+), 83 deletions(-)
Title: Bridge to System Package Manager
Description: Enables binary package installations on Linux distributions.
Provides functions to manage packages via the distribution's package
manager. Also provides transparent integration with R's install.packages()
and a fallback mechanism. When installed as a system package, interacts
with the system's package manager without requiring administrative
privileges via an integrated D-Bus service; otherwise, uses sudo.
Currently, the following backends are supported: DNF, APT, ALPM.
Author: Inaki Ucar [aut, cph, cre]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between bspm versions 0.4.0 dated 2022-11-24 and 0.4.1 dated 2023-01-09
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 8 ++++++++ R/integration.R | 15 +++++++++++++-- 4 files changed, 27 insertions(+), 8 deletions(-)
Title: Applied Statistical Time Series Analysis
Description: Contains data sets and scripts for analyzing time series in both the frequency and time domains including state space modeling as well as supporting the texts Time Series Analysis and Its Applications: With R Examples (4th ed), by R.H. Shumway and D.S. Stoffer. Springer Texts in Statistics, 2017, <DOI:10.1007/978-3-319-52452-8>, and Time Series: A Data Analysis Approach Using R. Chapman-Hall, 2019, <DOI:10.1201/9780429273285>.
Author: David Stoffer [aut, cre], Nicky Poison [ctb, mus, spy]
Maintainer: David Stoffer <stoffer@pitt.edu>
Diff between astsa versions 1.16 dated 2022-08-28 and 2.0 dated 2023-01-09
astsa-1.16/astsa/R/EM0.R |only astsa-1.16/astsa/R/EM1.R |only astsa-1.16/astsa/R/Kfilter0.R |only astsa-1.16/astsa/R/Kfilter1.R |only astsa-1.16/astsa/R/Kfilter2.R |only astsa-1.16/astsa/R/Ksmooth0.R |only astsa-1.16/astsa/R/Ksmooth1.R |only astsa-1.16/astsa/R/Ksmooth2.R |only astsa-1.16/astsa/man/EM0.Rd |only astsa-1.16/astsa/man/EM1.Rd |only astsa-1.16/astsa/man/Kfilter0.Rd |only astsa-1.16/astsa/man/Kfilter1.Rd |only astsa-1.16/astsa/man/Kfilter2.Rd |only astsa-1.16/astsa/man/Ksmooth0.Rd |only astsa-1.16/astsa/man/Ksmooth1.Rd |only astsa-1.16/astsa/man/Ksmooth2.Rd |only astsa-2.0/astsa/DESCRIPTION | 14 - astsa-2.0/astsa/MD5 | 313 ++++++++++++++++++----------------- astsa-2.0/astsa/NAMESPACE | 6 astsa-2.0/astsa/R/ARMAtoAR.R | 5 astsa-2.0/astsa/R/EM.R |only astsa-2.0/astsa/R/Kfilter.R |only astsa-2.0/astsa/R/Ksmooth.R |only astsa-2.0/astsa/R/SV.mcmc.R | 40 ++-- astsa-2.0/astsa/R/SVfilter.R | 56 ++---- astsa-2.0/astsa/R/acf1.R | 18 +- astsa-2.0/astsa/R/acf2.R | 23 +- astsa-2.0/astsa/R/acfm.r | 6 astsa-2.0/astsa/R/ar.mcmc.r | 2 astsa-2.0/astsa/R/arma.spec.R | 7 astsa-2.0/astsa/R/autoParm.R |only astsa-2.0/astsa/R/autoSpec.R |only astsa-2.0/astsa/R/bart.R |only astsa-2.0/astsa/R/ccf2.R | 4 astsa-2.0/astsa/R/detrend.R | 2 astsa-2.0/astsa/R/ffbs.R | 63 ++----- astsa-2.0/astsa/R/lag1.plot.R | 50 ++--- astsa-2.0/astsa/R/lag2.plot.R | 57 +++--- astsa-2.0/astsa/R/matrixpwr.R | 2 astsa-2.0/astsa/R/mvspec.R | 10 - astsa-2.0/astsa/R/polyMul.R | 15 - astsa-2.0/astsa/R/sarima.R | 16 - astsa-2.0/astsa/R/sarima.for.R | 4 astsa-2.0/astsa/R/sarima.sim.R | 25 +- astsa-2.0/astsa/R/spec.ic.r | 16 - astsa-2.0/astsa/R/specenv.R | 2 astsa-2.0/astsa/R/ssm.R | 17 - astsa-2.0/astsa/R/test.linear.R | 94 +++++----- astsa-2.0/astsa/R/tsplot.R | 21 +- astsa-2.0/astsa/R/xEM0.R |only astsa-2.0/astsa/R/xEM1.R |only astsa-2.0/astsa/R/xKfilter0.R |only astsa-2.0/astsa/R/xKfilter1.R |only astsa-2.0/astsa/R/xKfilter2.R |only astsa-2.0/astsa/R/xKsmooth0.R |only astsa-2.0/astsa/R/xKsmooth1.R |only astsa-2.0/astsa/R/xKsmooth2.R |only astsa-2.0/astsa/README.md | 15 + astsa-2.0/astsa/build |only astsa-2.0/astsa/data/ENSO.rda |only astsa-2.0/astsa/data/gtemp_land.rda |binary astsa-2.0/astsa/data/gtemp_ocean.rda |binary astsa-2.0/astsa/data/xA_readme.rda |only astsa-2.0/astsa/man/ARMAtoAR.Rd | 5 astsa-2.0/astsa/man/BCJ.Rd | 5 astsa-2.0/astsa/man/EBV.Rd | 5 astsa-2.0/astsa/man/EM.Rd |only astsa-2.0/astsa/man/ENSO.Rd |only astsa-2.0/astsa/man/EQ5.Rd | 5 astsa-2.0/astsa/man/EQcount.Rd | 5 astsa-2.0/astsa/man/ESS.Rd | 5 astsa-2.0/astsa/man/EXP6.Rd | 5 astsa-2.0/astsa/man/FDR.Rd | 5 astsa-2.0/astsa/man/Grid.Rd | 5 astsa-2.0/astsa/man/HCT.Rd | 5 astsa-2.0/astsa/man/Hare.Rd | 5 astsa-2.0/astsa/man/Kfilter.Rd |only astsa-2.0/astsa/man/Ksmooth.Rd |only astsa-2.0/astsa/man/LagReg.Rd | 5 astsa-2.0/astsa/man/Lynx.Rd | 5 astsa-2.0/astsa/man/Months.Rd | 5 astsa-2.0/astsa/man/PLT.Rd | 5 astsa-2.0/astsa/man/SV.mcmc.Rd | 5 astsa-2.0/astsa/man/SVfilter.Rd | 7 astsa-2.0/astsa/man/SigExtract.Rd | 5 astsa-2.0/astsa/man/UnempRate.Rd | 4 astsa-2.0/astsa/man/WBC.Rd | 4 astsa-2.0/astsa/man/acf1.Rd | 9 - astsa-2.0/astsa/man/acf2.Rd | 9 - astsa-2.0/astsa/man/acfm.Rd | 7 astsa-2.0/astsa/man/ar.mcmc.Rd | 7 astsa-2.0/astsa/man/ar1miss.Rd | 5 astsa-2.0/astsa/man/arf.Rd | 5 astsa-2.0/astsa/man/arma.spec.Rd | 5 astsa-2.0/astsa/man/astsa-package.Rd | 11 - astsa-2.0/astsa/man/astsa.col.Rd | 5 astsa-2.0/astsa/man/autoParm.Rd |only astsa-2.0/astsa/man/autoSpec.Rd |only astsa-2.0/astsa/man/bart.Rd |only astsa-2.0/astsa/man/beamd.Rd | 5 astsa-2.0/astsa/man/birth.Rd | 5 astsa-2.0/astsa/man/blood.Rd | 5 astsa-2.0/astsa/man/bnrf1ebv.Rd | 5 astsa-2.0/astsa/man/bnrf1hvs.Rd | 5 astsa-2.0/astsa/man/cardox.Rd | 5 astsa-2.0/astsa/man/ccf2.Rd | 7 astsa-2.0/astsa/man/chicken.Rd | 6 astsa-2.0/astsa/man/climhyd.Rd | 5 astsa-2.0/astsa/man/cmort.Rd | 5 astsa-2.0/astsa/man/cpg.Rd | 5 astsa-2.0/astsa/man/detrend.Rd | 7 astsa-2.0/astsa/man/djia.Rd | 5 astsa-2.0/astsa/man/dna2vector.Rd | 15 - astsa-2.0/astsa/man/econ5.Rd | 6 astsa-2.0/astsa/man/eqexp.Rd | 5 astsa-2.0/astsa/man/ffbs.Rd | 34 ++- astsa-2.0/astsa/man/flu.Rd | 5 astsa-2.0/astsa/man/fmri.Rd | 5 astsa-2.0/astsa/man/fmri1.Rd | 5 astsa-2.0/astsa/man/gas.Rd | 5 astsa-2.0/astsa/man/gdp.Rd | 5 astsa-2.0/astsa/man/globtemp.Rd | 5 astsa-2.0/astsa/man/globtempl.Rd | 5 astsa-2.0/astsa/man/gnp.Rd | 5 astsa-2.0/astsa/man/gtemp.Rd | 5 astsa-2.0/astsa/man/gtemp2.Rd | 5 astsa-2.0/astsa/man/gtemp_land.Rd | 11 - astsa-2.0/astsa/man/gtemp_ocean.Rd | 11 - astsa-2.0/astsa/man/hor.Rd | 5 astsa-2.0/astsa/man/jj.Rd | 7 astsa-2.0/astsa/man/lag1.plot.Rd | 15 + astsa-2.0/astsa/man/lag2.plot.Rd | 17 + astsa-2.0/astsa/man/lap.Rd | 5 astsa-2.0/astsa/man/lead.Rd | 5 astsa-2.0/astsa/man/matrixpwr.Rd | 10 - astsa-2.0/astsa/man/mvspec.Rd | 5 astsa-2.0/astsa/man/nyse.Rd | 8 astsa-2.0/astsa/man/oil.Rd | 5 astsa-2.0/astsa/man/part.Rd | 5 astsa-2.0/astsa/man/polio.Rd | 5 astsa-2.0/astsa/man/polyMul.Rd | 9 - astsa-2.0/astsa/man/prodn.Rd | 5 astsa-2.0/astsa/man/qinfl.Rd | 5 astsa-2.0/astsa/man/qintr.Rd | 5 astsa-2.0/astsa/man/rec.Rd | 5 astsa-2.0/astsa/man/sales.Rd | 5 astsa-2.0/astsa/man/salmon.Rd | 5 astsa-2.0/astsa/man/salt.Rd | 5 astsa-2.0/astsa/man/saltemp.Rd | 5 astsa-2.0/astsa/man/sarima.Rd | 7 astsa-2.0/astsa/man/sarima.for.Rd | 5 astsa-2.0/astsa/man/sarima.sim.Rd | 9 - astsa-2.0/astsa/man/scatter.hist.Rd | 5 astsa-2.0/astsa/man/sleep1.Rd | 5 astsa-2.0/astsa/man/sleep2.Rd | 5 astsa-2.0/astsa/man/so2.Rd | 5 astsa-2.0/astsa/man/soi.Rd | 8 astsa-2.0/astsa/man/soiltemp.Rd | 5 astsa-2.0/astsa/man/sp500.gr.Rd | 5 astsa-2.0/astsa/man/sp500w.Rd | 5 astsa-2.0/astsa/man/spec.ic.Rd | 16 - astsa-2.0/astsa/man/specenv.Rd | 5 astsa-2.0/astsa/man/speech.Rd | 5 astsa-2.0/astsa/man/ssm.Rd | 16 + astsa-2.0/astsa/man/star.Rd | 5 astsa-2.0/astsa/man/stoch.reg.Rd | 5 astsa-2.0/astsa/man/sunspotz.Rd | 5 astsa-2.0/astsa/man/tempr.Rd | 5 astsa-2.0/astsa/man/test.linear.Rd | 5 astsa-2.0/astsa/man/trend.Rd | 5 astsa-2.0/astsa/man/tsplot.Rd | 8 astsa-2.0/astsa/man/unemp.Rd | 4 astsa-2.0/astsa/man/varve.Rd | 4 astsa-2.0/astsa/man/xA_readme.Rd |only astsa-2.0/astsa/man/xEM0.Rd |only astsa-2.0/astsa/man/xEM1.Rd |only astsa-2.0/astsa/man/xKfilter0.Rd |only astsa-2.0/astsa/man/xKfilter1.Rd |only astsa-2.0/astsa/man/xKfilter2.Rd |only astsa-2.0/astsa/man/xKsmooth0.Rd |only astsa-2.0/astsa/man/xKsmooth1.Rd |only astsa-2.0/astsa/man/xKsmooth2.Rd |only 182 files changed, 839 insertions(+), 722 deletions(-)
Title: Simulate and Model Family Pedigrees with Structured Founders
Description: The focus is on simulating and modeling families with founders drawn from a structured population (for example, with different ancestries or other potentially non-family relatedness), in contrast to traditional pedigree analysis that treats all founders as equally unrelated. Main function simulates a random pedigree for many generations, avoiding close relatives, pairing closest individuals according to a 1D geography and their randomly-drawn sex, and with variable children sizes to result in a target population size per generation. Auxiliary functions calculate kinship matrices, admixture matrices, and draw random genotypes across arbitrary pedigree structures starting from the corresponding founder values. The code is built around the plink FAM table format for pedigrees. Described in Yao and Ochoa (2022) <doi:10.1101/2022.03.25.485885>.
Author: Alejandro Ochoa [aut, cre]
Maintainer: Alejandro Ochoa <alejandro.ochoa@duke.edu>
Diff between simfam versions 1.0.3 dated 2021-10-05 and 1.1.6 dated 2023-01-09
DESCRIPTION | 12 MD5 | 54 +- NAMESPACE | 10 NEWS.md | 47 + R/data.R |only R/fam_ancestors.R |only R/recomb_admix_inds.R |only R/recomb_breaks.R |only R/recomb_chr.R |only R/recomb_fam.R |only R/recomb_geno_inds.R |only R/recomb_hap.R |only R/recomb_haplo_chr.R |only R/recomb_haplo_hap.R |only R/recomb_haplo_ind.R |only R/recomb_haplo_inds.R |only R/recomb_init_founders.R |only R/recomb_last_gen.R |only R/recomb_map_chr.R |only R/recomb_map_fix_ends_chr.R |only R/recomb_map_hap.R |only R/recomb_map_ind.R |only R/recomb_map_inds.R |only R/recomb_map_lengs.R |only R/recomb_map_posg.R |only R/recomb_map_simplify_chr.R |only build/vignette.rds |binary data |only inst/doc/simfam.R | 76 +++ inst/doc/simfam.Rmd | 90 +++ inst/doc/simfam.html | 1031 ++++++++++++++++++----------------------- man/fam_ancestors.Rd |only man/recomb_admix_inds.Rd |only man/recomb_fam.Rd |only man/recomb_geno_inds.Rd |only man/recomb_haplo_inds.Rd |only man/recomb_init_founders.Rd |only man/recomb_last_gen.Rd |only man/recomb_map_fix_ends_chr.Rd |only man/recomb_map_hg.Rd |only man/recomb_map_inds.Rd |only man/recomb_map_simplify_chr.Rd |only tests/testthat/test-recomb.R |only tests/testthat/test-simfam.R | 56 ++ vignettes/simfam.Rmd | 90 +++ 45 files changed, 877 insertions(+), 589 deletions(-)
Title: Translate 'SQL' Queries into 'R' Expressions
Description: Translate 'SQL' 'SELECT' statements into lists of 'R' expressions.
Author: Ian Cook [aut, cre],
Cloudera [cph]
Maintainer: Ian Cook <ianmcook@gmail.com>
Diff between queryparser versions 0.3.1 dated 2021-01-17 and 0.3.2 dated 2023-01-09
DESCRIPTION | 6 +-- MD5 | 54 ++++++++++++++++----------------- NEWS.md | 5 +++ R/agg_scalar.R | 2 - R/check_expressions.R | 2 - R/column_references.R | 5 ++- R/common.R | 2 - R/compat.R | 27 +++++++++++++++- R/extract_alias.R | 2 - R/parse_clauses.R | 2 - R/parse_expression.R | 2 - R/parse_join.R | 2 - R/parse_query.R | 4 +- R/parse_table_reference.R | 2 - R/process_translations.R | 2 - R/replace.R | 2 - R/secure.R | 2 - R/split_query.R | 2 - R/squish_sql.R | 2 - R/translate.R | 2 - R/translations.R | 4 +- R/unpipe.R | 2 - R/unqualify.R | 4 +- R/wrap_bangs.R | 2 - README.md | 34 ++++++++++---------- tests/testthat/test-parse_expression.R | 2 - tests/testthat/test-parse_query.R | 4 +- tests/testthat/test-unicode.R | 6 +++ 28 files changed, 114 insertions(+), 73 deletions(-)
Title: Linear Regressions with a Latent Outcome Variable
Description: Fit latent variable linear models, estimating score distributions for groups of people, following Cohen and Jiang (1999) <doi:10.2307/2669917>. In this model, a latent distribution is conditional on students item response, item characteristics, and conditioning variables the user includes. This latent trait is then integrated out. This software is intended to fit the same models as the existing software 'AM' <https://am.air.org/>. As of version 2, also allows the user to draw plausible values.
Author: Emmanuel Sikali [pdr],
Paul Bailey [aut, cre],
Eric Buehler [aut],
Sun-joo Lee [aut],
Harold Doran [aut],
Claire Kelley [ctb]
Maintainer: Paul Bailey <pbailey@air.org>
Diff between Dire versions 2.1.0 dated 2022-06-29 and 2.1.1 dated 2023-01-09
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/PV.R | 1 - R/helpers.R | 2 +- R/rr1.R | 3 +++ build/vignette.rds |binary inst/NEWS.Rd | 11 ++++++++++- inst/doc/MML.pdf |binary tests/testthat/test-2-composite.R | 17 ++++++++++++----- tests/testthat/test-6-primerReg.R | 1 + 10 files changed, 40 insertions(+), 21 deletions(-)
Title: Load US Census Boundary and Attribute Data as 'tidyverse' and
'sf'-Ready Data Frames
Description: An integrated R interface to several United States Census Bureau
APIs (<https://www.census.gov/data/developers/data-sets.html>) and the US Census Bureau's
geographic boundary files. Allows R users to return Census and ACS data as
tidyverse-ready data frames, and optionally returns a list-column with feature geometry for mapping
and spatial analysis.
Author: Kyle Walker [aut, cre],
Matt Herman [aut],
Kris Eberwein [ctb]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between tidycensus versions 1.3 dated 2022-12-09 and 1.3.1 dated 2023-01-09
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/acs.R | 8 +++++++- R/helpers.R | 5 +++++ R/load_data.R | 21 +++++++++++++-------- data/acs5_geography.rda |binary man/acs5_geography.Rd | 2 +- 7 files changed, 36 insertions(+), 20 deletions(-)
Title: Semantically Rich I/O for the 'NeXML' Format
Description: Provides access to phyloinformatic data in 'NeXML' format. The
package should add new functionality to R such as the possibility to
manipulate 'NeXML' objects in more various and refined way and compatibility
with 'ape' objects.
Author: Carl Boettiger [cre, aut] ,
Scott Chamberlain [aut] ,
Hilmar Lapp [aut] ,
Kseniia Shumelchyk [aut],
Rutger Vos [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between RNeXML versions 2.4.9 dated 2022-12-16 and 2.4.10 dated 2023-01-09
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 5 +++++ R/nexml_validate.R | 12 +++++++++--- man/nexml_validate.Rd | 6 ++++-- man/simmap_to_nexml.Rd | 4 ++-- tests/testthat/geiger_test.R | 8 ++++++++ tests/testthat/test_global_ids.R | 3 ++- 8 files changed, 41 insertions(+), 19 deletions(-)
Title: Parallel Programming Tools for 'Rcpp'
Description: High level functions for parallel programming with 'Rcpp'.
For example, the 'parallelFor()' function can be used to convert the work of
a standard serial "for" loop into a parallel one and the 'parallelReduce()'
function can be used for accumulating aggregate or other values.
Author: JJ Allaire [aut],
Romain Francois [aut, cph],
Kevin Ushey [aut, cre],
Gregory Vandenbrouck [aut],
Marcus Geelnard [aut, cph] ,
Hamada S. Badr [ctb] ,
Posit, PBC [cph],
Intel [aut, cph] ,
Microsoft [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between RcppParallel versions 5.1.5 dated 2022-01-05 and 5.1.6 dated 2023-01-09
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS.md | 7 +++++++ R/utils.R | 2 +- inst/include/tthread/tinythread.h | 33 ++++++++++++++++++++++++--------- src/tbb/include/tbb/task.h | 2 +- tools/config/configure.R | 10 ++++++++-- 7 files changed, 52 insertions(+), 24 deletions(-)
Title: Genetic Analysis Package
Description: As first reported [Zhao, J. H. 2007. "gap: Genetic Analysis Package". J Stat Soft 23(8):1-18.
<doi:10.18637/jss.v023.i08>], it is designed as an integrated package for genetic data
analysis of both population and family data. Currently, it contains functions for
sample size calculations of both population-based and family-based designs, probability
of familial disease aggregation, kinship calculation, statistics in linkage analysis,
and association analysis involving genetic markers including haplotype analysis with or
without environmental covariates. Over years, the package has been developed in-between
many projects hence also in line with the name (gap).
Author: Jing Hua Zhao [aut, cre] ,
Kurt Hornik [ctb],
Brian Ripley [ctb],
Uwe Liggs [ctb],
Achim Zeileis [ctb]
Maintainer: Jing Hua Zhao <jinghuazhao@hotmail.com>
Diff between gap versions 1.3-1 dated 2022-10-21 and 1.4-2 dated 2023-01-09
gap-1.3-1/gap/R/gsmr.R |only gap-1.3-1/gap/data/mr.rda |only gap-1.3-1/gap/inst/scripts/ACE.R |only gap-1.3-1/gap/inst/scripts/PD.R |only gap-1.3-1/gap/inst/scripts/SH2B1.R |only gap-1.3-1/gap/inst/scripts/SH2B1.txt.gz |only gap-1.3-1/gap/inst/scripts/gap.Rnw |only gap-1.3-1/gap/inst/scripts/hg.R |only gap-1.3-1/gap/inst/scripts/renum.R |only gap-1.3-1/gap/inst/shinygap/README.Rmd |only gap-1.3-1/gap/inst/shinygap/README.md |only gap-1.3-1/gap/inst/shinygap/shinygap.bib |only gap-1.3-1/gap/man/gsmr.Rd |only gap-1.3-1/gap/vignettes/IL12B.png |only gap-1.4-2/gap/ChangeLog | 26 gap-1.4-2/gap/DESCRIPTION | 21 gap-1.4-2/gap/INDEX | 2 gap-1.4-2/gap/MD5 | 110 gap-1.4-2/gap/NAMESPACE | 5 gap-1.4-2/gap/R/2ld.R | 2 gap-1.4-2/gap/R/KCC.R | 18 gap-1.4-2/gap/R/METAL_forestplot.R | 10 gap-1.4-2/gap/R/chow.test.R | 3 gap-1.4-2/gap/R/comp.score.R | 2 gap-1.4-2/gap/R/gap-package.R | 2 gap-1.4-2/gap/R/hap.R | 38 gap-1.4-2/gap/R/hap.control.R |only gap-1.4-2/gap/R/makeped.R | 23 gap-1.4-2/gap/R/miamiplot2.R | 156 gap-1.4-2/gap/R/mr.R |only gap-1.4-2/gap/R/mr_forestplot.R | 4 gap-1.4-2/gap/R/pedtodot_verbatim.R | 5 gap-1.4-2/gap/build/partial.rdb |binary gap-1.4-2/gap/build/vignette.rds |binary gap-1.4-2/gap/data/datalist | 1 gap-1.4-2/gap/data/hg18.rda |binary gap-1.4-2/gap/data/hg19.rda |binary gap-1.4-2/gap/data/hg38.rda |binary gap-1.4-2/gap/inst/README.md |only gap-1.4-2/gap/inst/doc/gap.R | 116 gap-1.4-2/gap/inst/doc/gap.Rmd | 317 - gap-1.4-2/gap/inst/doc/gap.html | 5490 ++++++++++++++++++++++++------- gap-1.4-2/gap/inst/doc/jss.pdf |binary gap-1.4-2/gap/inst/doc/shinygap.html | 316 + gap-1.4-2/gap/inst/scripts/GRCh.R |only gap-1.4-2/gap/man/KCC.Rd |only gap-1.4-2/gap/man/METAL_forestplot.Rd | 4 gap-1.4-2/gap/man/chow.test.Rd | 4 gap-1.4-2/gap/man/comp.score.Rd | 2 gap-1.4-2/gap/man/gap-internal.Rd | 6 gap-1.4-2/gap/man/gap-package.Rd | 2 gap-1.4-2/gap/man/hap.Rd | 25 gap-1.4-2/gap/man/hap.control.Rd |only gap-1.4-2/gap/man/klem.Rd | 2 gap-1.4-2/gap/man/makeped.Rd | 30 gap-1.4-2/gap/man/mr.Rd |only gap-1.4-2/gap/man/mr_forestplot.Rd | 2 gap-1.4-2/gap/man/pedtodot_verbatim.Rd | 5 gap-1.4-2/gap/src/gcontrol_c.c | 3 gap-1.4-2/gap/src/hap_c.c | 8 gap-1.4-2/gap/src/makeped_c.c | 14 gap-1.4-2/gap/src/mia.c | 26 gap-1.4-2/gap/src/pgc.h | 2 gap-1.4-2/gap/vignettes/IL-12B.png |only gap-1.4-2/gap/vignettes/gap.Rmd | 317 - gap-1.4-2/gap/vignettes/gap.bib | 60 gap-1.4-2/gap/vignettes/shinygap.bib | 3 67 files changed, 5415 insertions(+), 1767 deletions(-)
Title: Compute Cluster Robust Standard Errors with Degrees of Freedom
Adjustments
Description: Estimate different types of cluster robust standard errors (CR0, CR1, CR2) with degrees of freedom adjustments. Standard errors are computed based on 'Liang and Zeger' (1986) <doi:10.1093/biomet/73.1.13> and Bell and 'McCaffrey' <https://www150.statcan.gc.ca/n1/en/pub/12-001-x/2002002/article/9058-eng.pdf?st=NxMjN1YZ>. Functions used in Huang and Li <doi:10.3758/s13428-021-01627-0>, Huang, 'Wiedermann', and 'Zhang' <doi:10.1080/00273171.2022.2077290>, and Huang, 'Zhang', and Li (forthcoming: Journal of Research on Educational Effectiveness).
Author: Francis Huang [aut, cre] ,
Bixi Zhang [aut]
Maintainer: Francis Huang <flhuang2000@yahoo.com>
Diff between CR2 versions 0.1.1 dated 2022-06-16 and 0.2.1 dated 2023-01-09
DESCRIPTION | 13 +++++++------ MD5 | 18 ++++++++++++------ NAMESPACE | 13 +++++++++++++ NEWS.md |only R/globals.R | 3 ++- R/robust_mixed.R | 2 ++ R/tidy_cr2.R |only R/utils-pipe.R |only build/partial.rdb |binary inst/CITATION | 9 ++++----- man/glance.CR2.Rd |only man/pipe.Rd |only man/tidy.CR2.Rd |only 13 files changed, 40 insertions(+), 18 deletions(-)
Title: Correspondence Analysis Variants
Description: Provides six variants of two-way correspondence analysis (ca):
simple ca, singly ordered ca, doubly ordered ca, non symmetrical ca,
singly ordered non symmetrical ca, and doubly ordered non symmetrical
ca.
Author: Rosaria Lombardo and Eric J Beh
Maintainer: Rosaria Lombardo <rosaria.lombardo@unicampania.it>
Diff between CAvariants versions 5.7 dated 2022-11-23 and 5.8 dated 2023-01-09
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/caRbiplot.R | 3 +-- R/plot.CAvariants.R | 22 ++++++++++++---------- man/CAvariants.Rd | 18 +++++++++--------- man/print.CAvariants.Rd | 2 +- 6 files changed, 32 insertions(+), 31 deletions(-)
Title: Simulated Stop Signal Task Data
Description: Stop signal task data of go and stop trials is generated per participant. The simulation process is based on the generally non-independent horse race model and fixed stop signal delay or tracking method. Each of go and stop process is assumed having exponentially modified Gaussian(ExG) or Shifted Wald (SW) distributions. The output data can be converted to 'BEESTS' software input data enabling researchers to test and evaluate various brain stopping processes manifested by ExG or SW distributional parameters of interest. Methods are described in: Soltanifar M (2020) <https://hdl.handle.net/1807/101208>, Matzke D, Love J, Wiecki TV, Brown SD, Logan GD and Wagenmakers E-J (2013) <doi:10.3389/fpsyg.2013.00918>, Logan GD, Van Zandt T, Verbruggen F, Wagenmakers EJ. (2014) <doi:10.1037/a0035230>.
Author: Mohsen Soltanifar [aut] ,
Chel Hee Lee [cre, aut]
Maintainer: Chel Hee Lee <chelhee.lee@ucalgary.ca>
Diff between SimSST versions 0.0.4.7 dated 2022-12-09 and 0.0.5.2 dated 2023-01-09
DESCRIPTION | 10 MD5 | 24 +- NAMESPACE | 1 R/simssfixed.R | 2 R/simssgen.R |only R/simsstrack.R | 4 README.md | 65 +++-- inst/doc/SimSST_Examples.R | 64 +++-- inst/doc/SimSST_Examples.Rmd | 71 ++++-- inst/doc/SimSST_Examples.html | 471 +++++++++++++++++++++++++++++++++++------- man/simssfixed.Rd | 9 man/simssgen.Rd |only man/simsstrack.Rd | 105 ++++----- vignettes/SimSST_Examples.Rmd | 71 ++++-- 14 files changed, 657 insertions(+), 240 deletions(-)
Title: Mendelian Randomization Package
Description: Encodes several methods for performing Mendelian randomization
analyses with summarized data. Summarized data on genetic associations with the
exposure and with the outcome can be obtained from large consortia. These data
can be used for obtaining causal estimates using instrumental variable methods.
Author: Olena Yavorska <olena.yavorska@ludwig.ox.ac.uk>
James Staley <james.staley@bristol.ac.uk>
Maintainer: Stephen Burgess <sb452@medschl.cam.ac.uk>
Diff between MendelianRandomization versions 0.6.0 dated 2022-02-22 and 0.7.0 dated 2023-01-09
DESCRIPTION | 8 MD5 | 32 NAMESPACE | 3 NEWS | 4 R/AllClasses.R | 1383 ++++++++++++++++++------------------ R/AllGenerics.R | 97 ++ R/getter-methods.R | 5 R/mr_cML-methods.R |only R/mr_divw-methods.R | 2 R/mr_egger-methods.R | 6 R/show-methods.R | 1152 +++++++++++++++--------------- build/vignette.rds |binary inst/doc/Vignette_MR.R | 462 ++++++------ man/MRcML-class.Rd |only man/cML_SdTheta.Rd |only man/cML_estimate.Rd |only man/cML_estimate_random.Rd |only man/getter.Rd | 3 man/mr_cML.Rd |only vignettes/Vignette_MR.html | 1708 +++++++++++++++++++-------------------------- 20 files changed, 2426 insertions(+), 2439 deletions(-)
More information about MendelianRandomization at CRAN
Permanent link
Title: Comprehensive and Easy to Use Quality Control of GWAS Results
Description: When evaluating the results of a genome-wide association study (GWAS), it is important to perform a quality control to ensure that the results are valid, complete, correctly formatted, and, in case of meta-analysis, consistent with other studies that have applied the same analysis. This package was developed to facilitate and streamline this process and provide the user with a comprehensive report.
Author: Alireza Ani [aut, cre],
Peter J. van der Most [aut],
Ahmad Vaez [aut],
Ilja M. Nolte [aut]
Maintainer: Alireza Ani <a.ani@umcg.nl>
Diff between GWASinspector versions 1.6.0 dated 2022-11-22 and 1.6.1 dated 2023-01-09
DESCRIPTION | 10 ++++----- MD5 | 12 +++++------ R/aaa.R | 2 - R/excelReportFunctions.R | 45 ++++++++++++++++++++---------------------- build/vignette.rds |binary inst/doc/GWASinspector.html | 18 ++++++++++++---- inst/rmd/mainReport_extra.rmd | 26 +++++++++++++----------- 7 files changed, 61 insertions(+), 52 deletions(-)
Title: Detecting Politeness Features in Text
Description: Detecting markers of politeness in English natural language. This package allows researchers to easily visualize and quantify politeness between groups of documents. This package combines prior research on the linguistic markers of politeness. We thank the Spencer Foundation, the Hewlett Foundation, and Harvard's Institute for Quantitative Social Science for support.
Author: Mike Yeomans, Alejandro Kantor, Dustin Tingley
Maintainer: Mike Yeomans <mk.yeomans@gmail.com>
Diff between politeness versions 0.8.7 dated 2022-06-28 and 0.8.8 dated 2023-01-09
politeness-0.8.7/politeness/man/hedge_list.Rd |only politeness-0.8.7/politeness/man/negative_list.Rd |only politeness-0.8.7/politeness/man/polite_dicts.Rd |only politeness-0.8.7/politeness/man/positive_list.Rd |only politeness-0.8.8/politeness/DESCRIPTION | 8 - politeness-0.8.8/politeness/MD5 | 23 +-- politeness-0.8.8/politeness/R/data.R | 60 ++++---- politeness-0.8.8/politeness/R/politeness.R | 59 +++++--- politeness-0.8.8/politeness/R/politenessPlot.R | 45 +++++- politeness-0.8.8/politeness/R/textTools.R | 12 + politeness-0.8.8/politeness/inst/doc/politeness.html | 140 +++++++++---------- politeness-0.8.8/politeness/man/noLeadDash.Rd |only politeness-0.8.8/politeness/man/phone_offers.Rd | 33 ++++ politeness-0.8.8/politeness/man/politeness.Rd | 2 politeness-0.8.8/politeness/man/politenessPlot.Rd | 14 + 15 files changed, 256 insertions(+), 140 deletions(-)
Title: Native Access Medical Record Retriever for High Yield Analytics
Description: A toolkit for medical records data analysis. The 'naryn'
package implements an efficient data structure for storing medical
records, and provides a set of functions for data extraction,
manipulation and analysis.
Author: Misha Hoichman [aut],
Aviezer Lifshitz [aut, cre],
Ben Gilat [aut],
Netta Mendelson-Cohen [ctb],
Rami Jaschek [ctb],
Weizmann Institute of Science [cph]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between naryn versions 2.6.13 dated 2022-12-14 and 2.6.14 dated 2023-01-09
DESCRIPTION | 6 - MD5 | 34 +++++----- NEWS.md | 4 + inst/doc/advanced.html | 13 ++- src/BufferedFile.h | 1 src/EMR.h | 1 src/EMRIteratorFilterItem.h | 1 src/EMRLogicalTrack.h | 1 src/EMRTimeStamp.h | 1 src/EMRTrack.h | 1 src/NRPoint.h | 1 src/NRTrackExpressionScanner.h | 1 src/NRTrackExpressionVars.h | 1 src/naryn.h | 1 tests/testthat/helper-regression.R | 16 ++++ tests/testthat/test-cor.R | 9 +- tests/testthat/test-extract.R | 14 ++-- tests/testthat/test-vtrack.R | 124 ++++++++++++++++++------------------- 18 files changed, 131 insertions(+), 99 deletions(-)
Title: Matrix Exponential, Log, 'etc'
Description: Computation of the matrix exponential, logarithm, sqrt,
and related quantities, using traditional and modern methods.
Author: Martin Maechler [aut, cre] ,
Christophe Dutang [aut] ,
Vincent Goulet [aut] ,
Douglas Bates [ctb] ,
David Firth [ctb] ),
Marina Shapira [ctb] ),
Michael Stadelmann [ctb]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between expm versions 0.999-6 dated 2021-01-13 and 0.999-7 dated 2023-01-09
ChangeLog | 14 +++++++++++ DESCRIPTION | 31 +++++++++++++++++++------- MD5 | 40 ++++++++++++++++++---------------- R/expm.R | 4 +-- R/expm2.R | 6 +++-- R/expmCond-all.R | 14 +++++------ R/logm.Higham08.R | 16 ++++++------- R/logm.R | 3 +- R/sqrtm.R | 8 ++++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/expm.pdf |binary inst/po/de |only inst/po/en@quot/LC_MESSAGES/R-expm.mo |binary inst/po/en@quot/LC_MESSAGES/expm.mo |binary inst/po/expm-de |only inst/po/fr/LC_MESSAGES/expm.mo |binary po/R-de.po |only po/R-expm.pot | 35 +++++------------------------ po/expm-de.po |only po/expm.pot | 34 ++++++++++++++++------------ po/fr.po | 32 +++++++++++++++------------ tests/ex.R | 2 - 23 files changed, 132 insertions(+), 107 deletions(-)
Title: Helpers for Developing Command Line Interfaces
Description: A suite of tools to build attractive command line interfaces
('CLIs'), from semantic elements: headings, lists, alerts, paragraphs,
etc. Supports custom themes via a 'CSS'-like language. It also
contains a number of lower level 'CLI' elements: rules, boxes, trees,
and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI
colors and text styles as well.
Author: Gabor Csardi [aut, cre],
Hadley Wickham [ctb],
Kirill Mueller [ctb],
RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between cli versions 3.5.0 dated 2022-12-20 and 3.6.0 dated 2023-01-09
DESCRIPTION | 6 +-- MD5 | 55 +++++++++++++++-------------- NAMESPACE | 4 ++ NEWS.md | 16 ++++++++ R/cli.R | 17 ++++++++- R/cliapp.R | 12 +++++- R/glue.R | 19 +++++----- R/hash.R | 70 ++++++++++++++++++++++++++++++++++++++ R/inline.R | 8 ++-- R/internals.R | 16 +++++--- R/progress-client.R | 12 ++++-- R/progress-server.R | 13 ++----- inst/include/cli/progress.h | 12 +++--- man/ansi_collapse.Rd | 14 +++---- man/cli-config.Rd | 2 + man/cli_progress_bar.Rd | 8 ++-- man/format_inline.Rd | 10 ++++- man/hash_animal.Rd | 1 man/hash_emoji.Rd | 1 man/hash_md5.Rd | 1 man/hash_sha1.Rd |only man/hash_sha256.Rd | 3 + src/Makevars | 2 - src/cli.h | 3 + src/init.c | 3 + src/inst.c |only src/progress.c | 50 +++++++++++++++++++++++---- src/sha1.c |only tests/testthat/_snaps/inline-2.md | 38 ++++++++++++++++++++ tests/testthat/test-inline-2.R | 16 ++++++++ 30 files changed, 323 insertions(+), 89 deletions(-)
Title: Dimension Reduction Methods for Multivariate Time Series
Description: Estimates VAR and VARX models with Structured Penalties using the methods developed by Nicholson et al (2017)<doi:10.1016/j.ijforecast.2017.01.003> and Nicholson et al (2020) <doi:10.48550/arXiv.1412.5250>.
Author: Will Nicholson [cre, aut],
David Matteson [aut],
Jacob Bien [aut],
Ines Wilms [aut]
Maintainer: Will Nicholson <wbn8@cornell.edu>
Diff between BigVAR versions 1.1.1 dated 2022-10-02 and 1.1.2 dated 2023-01-09
DESCRIPTION | 19 - MD5 | 14 - NEWS | 5 R/BigVARSupportFunctions.R | 7 build/vignette.rds |binary inst/doc/BigVAR.html | 391 ++++++++++++++++++++++++++--------- src/DataCons.cpp | 70 ++---- src/ExperimentalBigVARFunctionsX.cpp | 5 8 files changed, 347 insertions(+), 164 deletions(-)
Title: Add Standardized Regression Coefficients to Linear-Model-Objects
Description: Adds standardized regression coefficients to objects created by 'lm'. Also extends the S3 methods 'print', 'summary' and 'coef' with additional boolean argument 'standardized' an provides 'xtable'-support.
Author: Stefan Behrendt [aut, cre]
Maintainer: Stefan Behrendt <r@behrendt-stefan.de>
Diff between lm.beta versions 1.6-2 dated 2022-05-10 and 1.7-1 dated 2023-01-09
DESCRIPTION | 13 ++++---- MD5 | 30 +++++++++--------- NAMESPACE | 5 ++- NEWS | 16 +++++++-- R/lm.beta.R | 50 +++++++++++++++++++++++++++++-- R/xtable.lm.beta.R |only build/vignette.rds |binary inst/doc/comparison.pdf |binary inst/doc/implementation.Rnw | 32 +++++++++++++++++-- inst/doc/implementation.pdf |binary man/coef.lm.beta.Rd | 14 ++------ man/lm.beta.Rd | 15 +++------ man/print.lm.beta.Rd | 14 ++------ man/summary.lm.beta.Rd | 14 ++------ man/xtable.lm.beta.Rd |only vignettes/implementation-concordance.tex | 2 - vignettes/implementation.Rnw | 32 +++++++++++++++++-- 17 files changed, 163 insertions(+), 74 deletions(-)
More information about surveybootstrap at CRAN
Permanent link
Title: Empirical Dynamic Modeling ('EDM')
Description: An implementation of 'EDM' algorithms based on research software developed for internal use at the Sugihara Lab ('UCSD/SIO'). The package is implemented with 'Rcpp' wrappers around the 'cppEDM' library. It implements the 'simplex' projection method from Sugihara & May (1990) <doi:10.1038/344734a0>, the 'S-map' algorithm from Sugihara (1994) <doi:10.1098/rsta.1994.0106>, convergent cross mapping described in Sugihara et al. (2012) <doi:10.1126/science.1227079>, and, 'multiview embedding' described in Ye & Sugihara (2016) <doi:10.1126/science.aag0863>.
Author: Joseph Park [aut, cre] ,
Cameron Smith [aut] ,
George Sugihara [aut, ccp] ,
Ethan Deyle [aut] ,
Erik Saberski [ctb] ,
Hao Ye [ctb] ,
The Regents of the University of California [cph]
Maintainer: Joseph Park <JosephPark@IEEE.org>
Diff between rEDM versions 1.13.1 dated 2022-08-06 and 1.14.0 dated 2023-01-09
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NEWS.md | 5 ++++- build/vignette.rds |binary src/RcppEDMCommon.cpp | 2 ++ src/SMap.cpp | 10 +++++++--- src/Simplex.cpp | 5 +++++ src/cppEDM/src/API.cc | 24 +++++++++++++++++++----- src/cppEDM/src/API.h | 6 ++++++ src/cppEDM/src/Parameter.cc | 8 +++++++- src/cppEDM/src/Parameter.h | 12 +++++++----- src/cppEDM/src/SMap.cc | 14 +++++++++++++- src/cppEDM/src/Simplex.cc | 15 ++++++++++++++- vignettes/rEDM-tutorial.html | 18 +++++++++--------- 14 files changed, 110 insertions(+), 43 deletions(-)
Title: Performing Continuous-Time Microsimulation
Description: This toolkit allows performing continuous-time microsimulation for a wide range of life science (demography, social sciences, epidemiology) applications. Individual life-courses are specified by a continuous-time multi-state model as described in Zinn (2014) <doi:10.34196/IJM.00105>.
Author: Sabine Zinn [aut, cre],
Claudio Bosco [ctb],
Maurizio Teobaldell [ctb]
Maintainer: Sabine Zinn <szinn@diw.de>
Diff between MicSim versions 1.1.0 dated 2022-01-31 and 2.0.0 dated 2023-01-09
MicSim-1.1.0/MicSim/man/setSimHorizon.Rd |only MicSim-2.0.0/MicSim/DESCRIPTION | 26 - MicSim-2.0.0/MicSim/MD5 | 37 + MicSim-2.0.0/MicSim/NAMESPACE | 9 MicSim-2.0.0/MicSim/R/auxFctMicSim.r | 75 +++ MicSim-2.0.0/MicSim/R/convertToLong.r | 32 - MicSim-2.0.0/MicSim/R/micSim.r | 544 ++++++++++++++++++---------- MicSim-2.0.0/MicSim/build |only MicSim-2.0.0/MicSim/data |only MicSim-2.0.0/MicSim/inst/NEWS.Rd | 11 MicSim-2.0.0/MicSim/inst/doc |only MicSim-2.0.0/MicSim/man/MicSim-package.Rd | 11 MicSim-2.0.0/MicSim/man/getAgeInDays.Rd |only MicSim-2.0.0/MicSim/man/getDay.Rd |only MicSim-2.0.0/MicSim/man/getInDateFormat.Rd |only MicSim-2.0.0/MicSim/man/getInDays.Rd |only MicSim-2.0.0/MicSim/man/getInDays_my.Rd |only MicSim-2.0.0/MicSim/man/getMonth.Rd |only MicSim-2.0.0/MicSim/man/getYear.Rd |only MicSim-2.0.0/MicSim/man/immigrPopMigrExp.Rd |only MicSim-2.0.0/MicSim/man/initPopMigrExp.Rd |only MicSim-2.0.0/MicSim/man/micSim.Rd | 230 ++++++++--- MicSim-2.0.0/MicSim/man/micSimParallel.Rd | 94 ++-- MicSim-2.0.0/MicSim/man/migrExpRates.Rd |only MicSim-2.0.0/MicSim/vignettes |only 25 files changed, 723 insertions(+), 346 deletions(-)
Title: Compute Energy Landscapes
Description: Compute energy landscapes using a digital elevation model raster and body mass of animals.
Author: Emilio Berti
Maintainer: Emilio Berti <emilio.berti@idiv.de>
Diff between enerscape versions 0.1.3 dated 2021-10-01 and 1.0.0 dated 2023-01-09
enerscape-0.1.3/enerscape/R/en_extrapolation.R |only enerscape-0.1.3/enerscape/R/en_path.R |only enerscape-0.1.3/enerscape/R/enerscape_internals.R |only enerscape-0.1.3/enerscape/R/least-cost_path.R |only enerscape-0.1.3/enerscape/R/random_passage.R |only enerscape-0.1.3/enerscape/man/dot-calc_arc.Rd |only enerscape-0.1.3/enerscape/man/dot-calc_arc_cond.Rd |only enerscape-0.1.3/enerscape/man/dot-calc_cycling.Rd |only enerscape-0.1.3/enerscape/man/dot-calc_cycling_cond.Rd |only enerscape-0.1.3/enerscape/man/en_extrapolation.Rd |only enerscape-0.1.3/enerscape/man/en_lcp.Rd |only enerscape-0.1.3/enerscape/man/en_passage.Rd |only enerscape-0.1.3/enerscape/man/en_path.Rd |only enerscape-1.0.0/enerscape/DESCRIPTION | 19 +- enerscape-1.0.0/enerscape/MD5 | 51 ++++--- enerscape-1.0.0/enerscape/NAMESPACE | 7 enerscape-1.0.0/enerscape/R/RcppExports.R |only enerscape-1.0.0/enerscape/R/circuitscape.R | 28 ++- enerscape-1.0.0/enerscape/R/data.R | 5 enerscape-1.0.0/enerscape/R/enerscape.R | 121 ++++------------- enerscape-1.0.0/enerscape/R/omniscape.R | 12 - enerscape-1.0.0/enerscape/README.md |only enerscape-1.0.0/enerscape/build/partial.rdb |binary enerscape-1.0.0/enerscape/build/vignette.rds |only enerscape-1.0.0/enerscape/data/sirente.rda |only enerscape-1.0.0/enerscape/inst |only enerscape-1.0.0/enerscape/man/distances.Rd |only enerscape-1.0.0/enerscape/man/energy.Rd |only enerscape-1.0.0/enerscape/man/energyscape.Rd |only enerscape-1.0.0/enerscape/man/enerscape.Rd | 26 --- enerscape-1.0.0/enerscape/man/figures |only enerscape-1.0.0/enerscape/man/neighbours.Rd |only enerscape-1.0.0/enerscape/man/sirente.Rd |only enerscape-1.0.0/enerscape/man/slope.Rd |only enerscape-1.0.0/enerscape/src |only enerscape-1.0.0/enerscape/tests |only enerscape-1.0.0/enerscape/vignettes |only 37 files changed, 112 insertions(+), 157 deletions(-)
Title: Amos Tanay's Group High Performance Statistical Utilities
Description: A collection of high performance utilities to compute
distance, correlation, auto correlation, clustering and other tasks.
Contains graph clustering algorithm described in "MetaCell: analysis
of single-cell RNA-seq data using K-nn graph partitions" (Yael Baran,
Akhiad Bercovich, Arnau Sebe-Pedros, Yaniv Lubling, Amir Giladi, Elad
Chomsky, Zohar Meir, Michael Hoichman, Aviezer Lifshitz & Amos Tanay,
2019 <doi:10.1186/s13059-019-1812-2>).
Author: Michael Hoichman [aut],
Aviezer Lifshitz [aut, cre]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between tgstat versions 2.3.19 dated 2022-11-24 and 2.3.21 dated 2023-01-09
DESCRIPTION | 9 +++--- MD5 | 16 ++++++------ NEWS.md | 4 +++ build/vignette.rds |binary inst/doc/manual.html | 66 ++++++++++++++++++-------------------------------- src/graph2cluster.cpp | 2 - src/tgstat.cpp | 1 src/tgstat.h | 1 src/utils.cpp | 1 9 files changed, 44 insertions(+), 56 deletions(-)
Title: Mixture Hidden Markov Models for Social Sequence Data and Other
Multivariate, Multichannel Categorical Time Series
Description: Designed for fitting hidden (latent) Markov models and mixture
hidden Markov models for social sequence data and other categorical time series.
Also some more restricted versions of these type of models are available: Markov
models, mixture Markov models, and latent class models. The package supports
models for one or multiple subjects with one or multiple parallel sequences
(channels). External covariates can be added to explain cluster membership in
mixture models. The package provides functions for evaluating and comparing
models, as well as functions for visualizing of multichannel sequence data and
hidden Markov models. Models are estimated using maximum likelihood via the EM
algorithm and/or direct numerical maximization with analytical gradients. All
main algorithms are written in C++ with support for parallel computation.
Documentation is available via several vignettes in this page, and the
paper by Helske and Helske (2019, <doi:10.18637/jss.v088.i03>).
Author: Jouni Helske [aut, cre] ,
Satu Helske [aut]
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between seqHMM versions 1.2.3 dated 2022-12-12 and 1.2.4 dated 2023-01-09
DESCRIPTION | 10 MD5 | 24 NEWS.md | 8 R/build_mm.R | 13 R/fit_model.R | 2692 +++++++++++++++++++------------------- inst/doc/seqHMM.pdf | 38 inst/doc/seqHMM_algorithms.pdf |binary inst/doc/seqHMM_estimation.pdf |binary inst/doc/seqHMM_visualization.pdf | 938 ++++++------- man/build_mm.Rd | 8 man/fit_model.Rd | 6 src/EM.cpp | 8 src/EMx.cpp | 8 13 files changed, 1899 insertions(+), 1854 deletions(-)
Title: Import, Plot and Analyze Bathymetric and Topographic Data
Description: Import xyz data from the NOAA (National Oceanic and Atmospheric Administration, <https://www.noaa.gov>), GEBCO (General Bathymetric Chart of the Oceans, <https://www.gebco.net>) and other sources, plot xyz data to prepare publication-ready figures, analyze xyz data to extract transects, get depth / altitude based on geographical coordinates, or calculate z-constrained least-cost paths.
Author: Eric Pante, Benoit Simon-Bouhet, and Jean-Olivier Irisson
Maintainer: Benoit Simon-Bouhet <besibo@gmail.com>
Diff between marmap versions 1.0.8 dated 2022-11-16 and 1.0.9 dated 2023-01-09
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 2 +- R/getNOAA.bathy.R | 9 +++++---- man/marmap.Rd | 4 ++-- man/subsetSQL.Rd | 2 +- 6 files changed, 18 insertions(+), 17 deletions(-)
Title: Gapped-Kmer Support Vector Machine
Description: Imports the 'gkmSVM' v2.0 functionalities into R <https://www.beerlab.org/gkmsvm/>
It also uses the 'kernlab' library (separate R package by different authors) for various SVM algorithms.
Users should note that the suggested packages 'rtracklayer', 'GenomicRanges', 'BSgenome', 'BiocGenerics',
'Biostrings', 'GenomeInfoDb', 'IRanges', and 'S4Vectors' are all BioConductor packages <https://bioconductor.org>.
Author: Mahmoud Ghandi
Maintainer: Mike Beer <mbeer@jhu.edu>
Diff between gkmSVM versions 0.81.0 dated 2020-09-01 and 0.82.0 dated 2023-01-09
DESCRIPTION | 10 ++++---- MD5 | 24 +++++++++---------- src/CiDLPasses.cpp | 8 +++--- src/Converter.cpp | 2 - src/MLEstimKLmers.cpp | 2 - src/Sequence.cpp | 22 ++++++++--------- src/gkmCommonLib.cpp | 2 - src/gkmsvm_classify.cpp | 60 ++++++++++++++++++++++++------------------------ src/gkmsvm_kernel.cpp | 56 +++++++++++++++++++++++--------------------- src/global.h | 1 src/mainGkmKernel.cpp | 56 ++++++++++++++++++++++---------------------- src/mainSVMclassify.cpp | 40 ++++++++++++++++---------------- src/mainSVMtrain.cpp | 22 ++++++++--------- 13 files changed, 155 insertions(+), 150 deletions(-)
Title: Automated Tuning and Evaluations of Ecological Niche Models
Description: Runs ecological niche models over all combinations of user-defined settings (i.e., tuning), performs cross validation to evaluate models, and returns data tables to aid in selection of optimal model settings that balance goodness-of-fit and model complexity. Also has functions to partition data spatially (or not) for cross validation, to plot multiple visualizations of results, to run null models to estimate significance and effect sizes of performance metrics, and to calculate niche overlap between model predictions, among others. The package was originally built for Maxent models (Phillips et al. 2006, Phillips et al. 2017), but the current version allows possible extensions for any modeling algorithm. The extensive vignette, which guides users through most package functionality but unfortunately has a file size too big for CRAN, can be found here on the package's Github Pages website: <https://jamiemkass.github.io/ENMeval/articles/ENMeval-2.0-vignette.html>.
Author: Jamie M. Kass [aut, cre],
Robert Muscarella [aut],
Peter J. Galante [aut],
Corentin Bohl [aut],
Gonzalo E. Buitrago-Pinilla [aut],
Robert A. Boria [aut],
Mariano Soley-Guardia [aut],
Robert P. Anderson [aut]
Maintainer: Jamie M. Kass <jamie.m.kass@gmail.com>
Diff between ENMeval versions 2.0.3 dated 2022-01-09 and 2.0.4 dated 2023-01-09
ENMeval-2.0.3/ENMeval/man/enm.varimp.Rd |only ENMeval-2.0.4/ENMeval/DESCRIPTION | 24 +- ENMeval-2.0.4/ENMeval/MD5 | 59 +++--- ENMeval-2.0.4/ENMeval/NAMESPACE | 5 ENMeval-2.0.4/ENMeval/NEWS | 15 + ENMeval-2.0.4/ENMeval/R/ENMevaluate.R | 154 ++++++++++++++---- ENMeval-2.0.4/ENMeval/R/ENMnulls.R | 37 ++++ ENMeval-2.0.4/ENMeval/R/classes.R | 95 +++++++++-- ENMeval-2.0.4/ENMeval/R/enm.bioclim.R | 10 - ENMeval-2.0.4/ENMeval/R/enm.maxent.jar.R | 9 - ENMeval-2.0.4/ENMeval/R/enm.maxnet.R | 14 - ENMeval-2.0.4/ENMeval/R/partitions.R | 4 ENMeval-2.0.4/ENMeval/R/rmm.R | 2 ENMeval-2.0.4/ENMeval/R/tune.enm.R | 45 +++-- ENMeval-2.0.4/ENMeval/R/utilities.R | 6 ENMeval-2.0.4/ENMeval/R/zzz.R | 2 ENMeval-2.0.4/ENMeval/README.md | 14 - ENMeval-2.0.4/ENMeval/build/partial.rdb |binary ENMeval-2.0.4/ENMeval/inst/CITATION | 8 ENMeval-2.0.4/ENMeval/man/ENMdetails.Rd | 4 ENMeval-2.0.4/ENMeval/man/ENMeval-package.Rd | 9 - ENMeval-2.0.4/ENMeval/man/ENMevaluate.Rd | 87 +++++++++- ENMeval-2.0.4/ENMeval/man/ENMevaluation.Rd | 50 +++++ ENMeval-2.0.4/ENMeval/man/ENMnull.Rd | 2 ENMeval-2.0.4/ENMeval/man/enm.variable.importance.Rd |only ENMeval-2.0.4/ENMeval/man/eval.models.Rd | 3 ENMeval-2.0.4/ENMeval/man/eval.variable.importance.Rd | 4 ENMeval-2.0.4/ENMeval/man/null.doClamp.Rd |only ENMeval-2.0.4/ENMeval/man/tune.enm.Rd | 20 ++ ENMeval-2.0.4/ENMeval/tests/testthat.R | 2 ENMeval-2.0.4/ENMeval/tests/testthat/helper_funcs.R | 14 + ENMeval-2.0.4/ENMeval/tests/testthat/test_mods.R | 4 32 files changed, 542 insertions(+), 160 deletions(-)
Title: Stochastic Blockmodels
Description: A collection of tools and functions to adjust a variety of stochastic blockmodels (SBM).
Supports at the moment Simple, Bipartite, 'Multipartite' and Multiplex SBM (undirected or directed with Bernoulli,
Poisson or Gaussian emission laws on the edges, and possibly covariate for Simple and Bipartite SBM).
See Léger (2016) <arxiv:1602.07587>, 'Barbillon et al.' (2020) <doi:10.1111/rssa.12193> and
'Bar-Hen et al.' (2020) <arxiv:1807.10138>.
Author: Julien Chiquet [aut, cre] ,
Sophie Donnet [aut] ,
großBM team [ctb],
Pierre Barbillon [aut]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between sbm versions 0.4.4 dated 2022-08-24 and 0.4.5 dated 2023-01-09
DESCRIPTION | 8 MD5 | 50 +- NEWS.md | 4 R/war.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 7 inst/doc/Multipartite_EcologicalNetwork.R | 29 - inst/doc/Multipartite_EcologicalNetwork.Rmd | 44 - inst/doc/Multipartite_EcologicalNetwork.html | 192 +++---- inst/doc/MultiplexNetwork_principle.R | 64 +- inst/doc/MultiplexNetwork_principle.Rmd | 84 +-- inst/doc/MultiplexNetwork_principle.html | 256 +++++----- inst/doc/Multiplex_allianceNwar_case_study.R | 48 + inst/doc/Multiplex_allianceNwar_case_study.Rmd | 66 +- inst/doc/Multiplex_allianceNwar_case_study.html | 598 ++++++++++++------------ inst/doc/SBM_fungus_tree_network.Rmd | 8 inst/doc/SBM_fungus_tree_network.html | 199 +++---- inst/visnetwork.Rmd |only man/war.Rd | 2 tests/testthat/Rplots.pdf |only tests/testthat/test-MultipartiteSBM.R | 7 vignettes/Multipartite_EcologicalNetwork.Rmd | 44 - vignettes/MultiplexNetwork_principle.Rmd | 84 +-- vignettes/Multiplex_allianceNwar_case_study.Rmd | 66 +- vignettes/SBM_fungus_tree_network.Rmd | 8 vignettes/references.bib | 25 - 27 files changed, 988 insertions(+), 909 deletions(-)
Title: Create Interactive Web Maps of Air Pollution Data
Description: Combine the air quality data analysis methods of 'openair'
with the JavaScript 'Leaflet' (<https://leafletjs.com/>) library.
Functionality includes plotting site maps, "directional analysis"
figures such as polar plots, and air mass trajectories.
Author: Jack Davison [cre, aut],
David Carslaw [aut]
Maintainer: Jack Davison <davison.jack.jd@gmail.com>
Diff between openairmaps versions 0.6.0 dated 2022-11-28 and 0.6.1 dated 2023-01-09
openairmaps-0.6.0/openairmaps/man/figures/README-addMarkers.png |only openairmaps-0.6.0/openairmaps/man/figures/README-addtrajpath.png |only openairmaps-0.6.0/openairmaps/man/figures/README-annuluslayers.png |only openairmaps-0.6.0/openairmaps/man/figures/README-networkmap.png |only openairmaps-0.6.0/openairmaps/man/figures/README-polarmap.png |only openairmaps-0.6.0/openairmaps/man/figures/README-trajcluster.png |only openairmaps-0.6.0/openairmaps/man/figures/README-trajlevel.png |only openairmaps-0.6.1/openairmaps/DESCRIPTION | 12 openairmaps-0.6.1/openairmaps/MD5 | 80 +-- openairmaps-0.6.1/openairmaps/NEWS.md | 10 openairmaps-0.6.1/openairmaps/R/addPolarMarkers.R | 39 + openairmaps-0.6.1/openairmaps/R/addTrajPaths.R | 36 - openairmaps-0.6.1/openairmaps/R/annulusMap.R | 19 openairmaps-0.6.1/openairmaps/R/buildPopup.R | 24 - openairmaps-0.6.1/openairmaps/R/freqMap.R | 28 - openairmaps-0.6.1/openairmaps/R/networkMap.R | 213 +++++----- openairmaps-0.6.1/openairmaps/R/openairmaps-package.R | 37 + openairmaps-0.6.1/openairmaps/R/percentileMap.R | 12 openairmaps-0.6.1/openairmaps/R/polarMap.R | 40 - openairmaps-0.6.1/openairmaps/R/polar_data.R | 14 openairmaps-0.6.1/openairmaps/R/pollroseMap.R | 26 - openairmaps-0.6.1/openairmaps/R/quickTextHTML.R | 4 openairmaps-0.6.1/openairmaps/R/trajLevelMap.R | 38 - openairmaps-0.6.1/openairmaps/R/trajMap.R | 38 - openairmaps-0.6.1/openairmaps/R/traj_data.R | 43 -- openairmaps-0.6.1/openairmaps/R/utils-map.R | 21 openairmaps-0.6.1/openairmaps/R/utils-pipe.R | 2 openairmaps-0.6.1/openairmaps/R/windroseMap.R | 18 openairmaps-0.6.1/openairmaps/README.md | 211 +-------- openairmaps-0.6.1/openairmaps/man/addPolarMarkers.Rd | 21 openairmaps-0.6.1/openairmaps/man/addTrajPaths.Rd | 34 - openairmaps-0.6.1/openairmaps/man/annulusMap.Rd | 179 ++++---- openairmaps-0.6.1/openairmaps/man/buildPopup.Rd | 14 openairmaps-0.6.1/openairmaps/man/figures/README-examplemap.png |only openairmaps-0.6.1/openairmaps/man/freqMap.Rd | 42 - openairmaps-0.6.1/openairmaps/man/networkMap.Rd | 66 +-- openairmaps-0.6.1/openairmaps/man/openairmaps-package.Rd | 40 + openairmaps-0.6.1/openairmaps/man/percentileMap.Rd | 73 +-- openairmaps-0.6.1/openairmaps/man/pipe.Rd | 2 openairmaps-0.6.1/openairmaps/man/polarMap.Rd | 185 ++++---- openairmaps-0.6.1/openairmaps/man/pollroseMap.Rd | 48 +- openairmaps-0.6.1/openairmaps/man/trajLevelMap.Rd | 23 - openairmaps-0.6.1/openairmaps/man/trajMap.Rd | 31 - openairmaps-0.6.1/openairmaps/man/traj_data.Rd | 41 - openairmaps-0.6.1/openairmaps/man/windroseMap.Rd | 165 +++---- 45 files changed, 916 insertions(+), 1013 deletions(-)
Title: Tools for Case 1 Best-Worst Scaling
Description: Provides basic functions that support an implementation of object case (Case 1) best-worst scaling: a function for converting a two-level orthogonal main-effect design/balanced incomplete block design into questions; two functions for creating a data set suitable for analysis; a function for calculating count-based scores; a function for calculating shares of preference; and a function for generating artificial responses to questions. See Louviere et al. (2015) <doi:10.1017/CBO9781107337855> for details on best-worst scaling, and Aizaki and Fogarty (2023) <doi:10.1016/j.jocm.2022.100394> for the package.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between support.BWS versions 0.4-4 dated 2021-10-13 and 0.4-5 dated 2023-01-09
DESCRIPTION | 10 +++++----- MD5 | 11 ++++++----- NEWS | 5 +++++ R/bws.response.R | 20 +++++++++++++++++--- R/onAttach.R |only inst/CITATION | 33 +++++++++++++++++---------------- man/support.BWS-package.Rd | 4 ++++ 7 files changed, 54 insertions(+), 29 deletions(-)
Title: Smooth and Tidy Spatial Features
Description: Tools for smoothing and tidying spatial features
(i.e. lines and polygons) to make them more aesthetically pleasing.
Smooth curves, fill holes, and remove small fragments from lines and
polygons.
Author: Matthew Strimas-Mackey [aut, cre]
Maintainer: Matthew Strimas-Mackey <mstrimas@gmail.com>
Diff between smoothr versions 0.2.2 dated 2021-06-22 and 1.0.0 dated 2023-01-09
smoothr-0.2.2/smoothr/R/data.R |only smoothr-0.2.2/smoothr/tests/testthat/test_smooth.R |only smoothr-1.0.0/smoothr/DESCRIPTION | 12 smoothr-1.0.0/smoothr/MD5 | 42 smoothr-1.0.0/smoothr/NAMESPACE | 4 smoothr-1.0.0/smoothr/NEWS.md | 4 smoothr-1.0.0/smoothr/R/data.r |only smoothr-1.0.0/smoothr/R/smoothr-package.R | 2 smoothr-1.0.0/smoothr/build/vignette.rds |binary smoothr-1.0.0/smoothr/data/jagged_lines.rda |binary smoothr-1.0.0/smoothr/data/jagged_lines_3d.rda |binary smoothr-1.0.0/smoothr/data/jagged_polygons.rda |binary smoothr-1.0.0/smoothr/data/jagged_raster.rda |binary smoothr-1.0.0/smoothr/inst/doc/smoothr.R | 33 smoothr-1.0.0/smoothr/inst/doc/smoothr.Rmd | 41 smoothr-1.0.0/smoothr/inst/doc/smoothr.html | 617 +++++++--- smoothr-1.0.0/smoothr/man/figures/README-smooth-lines-1.png |binary smoothr-1.0.0/smoothr/man/figures/README-smooth-polygons-1.png |binary smoothr-1.0.0/smoothr/man/jagged_lines.Rd | 8 smoothr-1.0.0/smoothr/man/jagged_lines_3d.Rd | 8 smoothr-1.0.0/smoothr/man/jagged_polygons.Rd | 12 smoothr-1.0.0/smoothr/man/jagged_raster.Rd | 11 smoothr-1.0.0/smoothr/tests/testthat/test_smooth.r |only smoothr-1.0.0/smoothr/vignettes/smoothr.Rmd | 41 24 files changed, 580 insertions(+), 255 deletions(-)
Title: Creates Simultaneous Testing Bands for QQ-Plots
Description: Provides functionality for creating Quantile-Quantile (QQ) and Probability-Probability (PP) plots with simultaneous
testing bands to asses significance of sample deviation from a reference distribution.
Author: Eric Weine [aut, cre],
Mary Sara McPeek [aut],
Abney Mark [aut]
Maintainer: Eric Weine <ericweine15@gmail.com>
Diff between qqconf versions 1.3.0 dated 2022-08-10 and 1.3.1 dated 2023-01-09
DESCRIPTION | 6 MD5 | 8 R/two_sided.R | 7 build/vignette.rds |binary inst/doc/qqconf_introduction.html | 424 ++++++++++++++++++++++++++------------ 5 files changed, 302 insertions(+), 143 deletions(-)
Title: Principal Variables
Description: Provides methods for reducing the number of features within a data set. See Bauer JO (2021) <doi:10.1145/3475827.3475832> and Bauer JO, Drabant B (2021) <doi:10.1016/j.jmva.2021.104754> for more information on principal loading analysis.
Author: Jan O. Bauer [aut],
Ron Holzapfel [aut, cre]
Maintainer: Ron Holzapfel <ronholzapfel@outlook.de>
Diff between prinvars versions 0.1.0 dated 2022-01-11 and 1.0.0 dated 2023-01-09
DESCRIPTION | 16 - MD5 | 57 ++--- NAMESPACE | 3 R/block.R | 57 ++--- R/cor.R | 2 R/explained-variance.R | 53 ++-- R/get-blocks.R | 31 +- R/pla.R | 342 +++++++++++++++++++++++++------ R/prinvars-package.R | 4 R/scale.R | 2 R/thresholding.R | 32 ++ R/utils.R | 222 ++++++++++++++++++-- README.md | 12 - build/partial.rdb |binary inst/REFERENCES.bib | 47 ++++ man/Block-class.Rd | 7 man/pla.Rd | 50 ++-- man/pla.drop_blocks.Rd | 11 man/pla.keep_blocks.Rd | 17 - man/print.pla.Rd | 2 man/prinvars-package.Rd | 8 man/show-Block-method.Rd | 8 man/spla.Rd |only man/str-Block-method.Rd | 8 tests/testthat/test-explained-variance.R | 13 + tests/testthat/test-get-blocks.R | 28 +- tests/testthat/test-pla.R | 34 ++- tests/testthat/test-spla.R |only tests/testthat/test-thresholding.R | 32 ++ tests/testthat/test-utils.R | 41 +++ tests/testthat/testthat-problems.rds |only 31 files changed, 879 insertions(+), 260 deletions(-)
Title: Visualization and Tools for Ichimoku Kinko Hyo Strategies
Description: An implementation of 'Ichimoku Kinko Hyo', also commonly known as
'cloud charts'. Static and interactive visualizations with tools for
creating, backtesting and development of quantitative 'ichimoku' strategies.
As described in Sasaki (1996, ISBN:4925152009), the technique is a refinement
on candlestick charting, originating from Japan and now in widespread use in
technical analysis worldwide. Translating as 'one-glance equilibrium chart',
it allows the price action and market structure of financial securities to
be determined 'at-a-glance'. Incorporates an interface with the OANDA
fxTrade API <https://developer.oanda.com/> for retrieving historical and
live streaming price data for major currencies, metals, commodities,
government bonds and stock indices.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between ichimoku versions 1.4.3 dated 2022-12-08 and 1.4.4 dated 2023-01-09
DESCRIPTION | 14 ++++----- MD5 | 22 +++++++-------- NEWS.md | 8 +++++ R/data.R | 10 +++--- R/ichimoku-package.R | 2 - R/ichimoku.R | 5 +-- R/oanda.R | 4 +- R/strat.R | 10 +++--- R/switch.R | 13 +++------ inst/CITATION | 2 - inst/doc/xoanda.html | 73 +++++++++++++++++++++++++-------------------------- src/shikokuchuo.c | 9 ++++-- 12 files changed, 89 insertions(+), 83 deletions(-)
Title: Schedule R Scripts and Processes with the 'cron' Job Scheduler
Description: Create, edit, and remove 'cron' jobs on your unix-alike system. The package provides a set of easy-to-use wrappers
to 'crontab'. It also provides an RStudio add-in to easily launch and schedule your scripts.
Author: Jan Wijffels [aut, cre, cph],
BNOSAC [cph],
Kevin Ushey [cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between cronR versions 0.6.2 dated 2022-02-17 and 0.6.5 dated 2023-01-09
DESCRIPTION | 7 ++- MD5 | 18 ++++----- R/cron_add.R | 20 ++++++++-- R/cron_rm.R | 12 +++++- R/cron_rscript.R | 78 ++++++++++++++++++++++++++++++++++++++---- R/deparse_crontab.R | 6 ++- README.md | 5 ++ inst/NEWS | 14 +++++++ inst/tinytest/test_cron_add.R | 9 ++++ man/cron_rscript.Rd | 18 ++++++++- 10 files changed, 157 insertions(+), 30 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-05 0.2.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-03-03 1.6.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-14 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-07 1.5-1
2020-04-15 1.4-1
2019-05-24 1.2-2
2019-05-24 1.3-1
2018-10-08 1.2
2018-06-05 1.1
2017-12-12 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-04-06 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-18 1.6.1
2017-04-21 1.5.1
2017-03-03 1.5.0
Title: Applying Partitioning Around Medoids to Single Cell Data with
High Number of Cells
Description: PAM (Partitioning Around Medoids) algorithm application to samples of single cell sequencing techniques
with a high number of cells (as many as the computer memory allows). The package uses a binary format to
store matrices (either full, sparse or symmetric) in files written in the disk that can contain any data type
(not just double) which allows its manipulation when memory is sufficient to load them as int or float, but not
as double. The PAM implementation is done in parallel, using several/all the cores of the machine, if it has them.
This package shares a great part of its code with packages 'jmatrix' and 'parallelpam' but their functionality is
included here so there is no need to install them.
Author: Juan Domingo [aut, cre] ,
Guillermo Ayala [ctb] ,
Spanish Ministry of Science and Innovation, MCIN/AEI
<doi:10.13039/501100011033> [fnd]
Maintainer: Juan Domingo <Juan.Domingo@uv.es>
Diff between scellpam versions 1.4 dated 2022-11-28 and 1.4.1 dated 2023-01-09
DESCRIPTION | 8 - MD5 | 8 - inst/doc/jmatrixsc.html | 187 +++++++++++++++++++-------------------- inst/doc/parallelpamsc.html | 147 +++++++++++++++--------------- inst/doc/scellpam.html | 210 ++++++++++++++++++++++---------------------- 5 files changed, 281 insertions(+), 279 deletions(-)
Title: Spatial Interpolation Based on Spatial Stratified Heterogeneity
Description: Spatial interpolation is a common practice in social and environmental science. This package enables the implementation of SSH-based spatial interpolation proposed by Wang et al. (2013) <doi:10.1068/a44710>. It provides functions to (1) evaluate stratification schemes, (2) interpolate sampling data over user-defined reporting units, (3) assess interpolation uncertainties, and (4) evaluate overall accuracy using the k-fold cross-validation estimate.
Author: Yue Lin [aut, cre],
Chengdong Xu [aut, ctb],
Jinfeng Wang [aut, ctb]
Maintainer: Yue Lin <lin.3326@osu.edu>
Diff between sandwichr versions 1.0.2 dated 2022-11-17 and 1.0.3 dated 2023-01-09
sandwichr-1.0.2/sandwichr/R/hs.data.r |only sandwichr-1.0.2/sandwichr/R/sandwich.ci.r |only sandwichr-1.0.2/sandwichr/data/hs.data.RData |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.reporting.shapefile.dbf |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.reporting.shapefile.prj |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.reporting.shapefile.sbn |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.reporting.shapefile.sbx |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.reporting.shapefile.shp |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.reporting.shapefile.shx |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.sampling.shapefile.cpg |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.sampling.shapefile.dbf |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.sampling.shapefile.gal |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.sampling.shapefile.prj |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.sampling.shapefile.sbn |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.sampling.shapefile.sbx |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.sampling.shapefile.shp |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.sampling.shapefile.shx |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.ssh.shapefile.cpg |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.ssh.shapefile.dbf |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.ssh.shapefile.prj |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.ssh.shapefile.sbn |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.ssh.shapefile.sbx |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.ssh.shapefile.shp |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.ssh.shapefile.shx |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.ssh2.shapefile.cpg |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.ssh2.shapefile.dbf |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.ssh2.shapefile.prj |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.ssh2.shapefile.sbn |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.ssh2.shapefile.sbx |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.ssh2.shapefile.shp |only sandwichr-1.0.2/sandwichr/inst/extdata/hs.ssh2.shapefile.shx |only sandwichr-1.0.2/sandwichr/man/hs.data.Rd |only sandwichr-1.0.2/sandwichr/man/sandwich.ci.Rd |only sandwichr-1.0.3/sandwichr/DESCRIPTION | 8 sandwichr-1.0.3/sandwichr/MD5 | 102 - 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Title: Collecting Twitter Data
Description: An implementation of calls designed to collect and organize
Twitter data via Twitter's REST and stream Application Program
Interfaces (API), which can be found at the following URL:
<https://developer.twitter.com/en/docs>.
Author: Michael W. Kearney [aut] ,
Lluis Revilla Sancho [aut, cre]
,
Hadley Wickham [aut] ,
Andrew Heiss [rev] ,
Francois Briatte [rev],
Jonathan Sidi [ctb]
Maintainer: Lluis Revilla Sancho <lluis.revilla@gmail.com>
Diff between rtweet versions 1.0.2 dated 2022-07-21 and 1.1.0 dated 2023-01-09
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rtweet-1.1.0/rtweet/tests/testthat/test-users.R | 21 rtweet-1.1.0/rtweet/tests/testthat/testing_plot.jpg |only rtweet-1.1.0/rtweet/tests/testthat/testing_plot.png |only rtweet-1.1.0/rtweet/vignettes/files/plot1-1.png |binary rtweet-1.1.0/rtweet/vignettes/rtweet.Rmd | 462 +++++--- rtweet-1.1.0/rtweet/vignettes/rtweet.Rmd.orig | 106 -- rtweet-1.1.0/rtweet/vignettes/stream.Rmd | 224 +--- rtweet-1.1.0/rtweet/vignettes/stream.Rmd.orig | 141 +- 337 files changed, 2871 insertions(+), 2391 deletions(-)
Title: Collecting and Analyzing Mastodon Data
Description: An implementation of calls designed to collect and organize Mastodon data via its Application Program Interfaces (API), which can be found at the following URL: <https://docs.joinmastodon.org/>.
Author: David Schoch [aut, cre] ,
Chung-hong Chan [aut] ,
Johannes Gruber [ctb]
Maintainer: David Schoch <david@schochastics.net>
Diff between rtoot versions 0.2.0 dated 2022-11-30 and 0.3.0 dated 2023-01-09
rtoot-0.2.0/rtoot/tests/fixtures/get_fedi_instances_pr29.yml |only rtoot-0.3.0/rtoot/DESCRIPTION | 8 rtoot-0.3.0/rtoot/MD5 | 36 - rtoot-0.3.0/rtoot/NAMESPACE | 1 rtoot-0.3.0/rtoot/NEWS.md | 7 rtoot-0.3.0/rtoot/R/auth.R | 19 rtoot-0.3.0/rtoot/R/instances.R | 31 - rtoot-0.3.0/rtoot/R/rtoot-package.R | 1 rtoot-0.3.0/rtoot/R/utils.R | 88 ++- rtoot-0.3.0/rtoot/inst/CITATION | 6 rtoot-0.3.0/rtoot/man/auth_setup.Rd | 5 rtoot-0.3.0/rtoot/man/create_token.Rd | 4 rtoot-0.3.0/rtoot/man/get_fedi_instances.Rd | 8 rtoot-0.3.0/rtoot/man/rtoot-package.Rd | 2 rtoot-0.3.0/rtoot/man/rtoot.Rd |only rtoot-0.3.0/rtoot/tests/fixtures/get_fedi_instances_default.yml | 271 +++------- rtoot-0.3.0/rtoot/tests/fixtures/rtoot_examples.yml |only rtoot-0.3.0/rtoot/tests/testthat/setup-rtoot.R | 3 rtoot-0.3.0/rtoot/tests/testthat/test-instances.R | 15 rtoot-0.3.0/rtoot/tests/testthat/test-rate_limit.R | 49 + rtoot-0.3.0/rtoot/tests/testthat/test-rtoot.R |only 21 files changed, 293 insertions(+), 261 deletions(-)
Title: Statistical Framework to Define Subgroups in Complex Datasets
Description: High-dimensional datasets that do not exhibit a clear intrinsic clustered structure pose a challenge to conventional clustering algorithms. For this reason, we developed an unsupervised framework that helps scientists to better subgroup their datasets based on visual cues, please see Gao S, Mutter S, Casey A, Makinen V-P (2019) Numero: a statistical framework to define multivariable subgroups in complex population-based datasets, Int J Epidemiology, 48:369-37, <doi:10.1093/ije/dyy113>. The framework includes the necessary functions to construct a self-organizing map of the data, to evaluate the statistical significance of the observed data patterns, and to visualize the results.
Author: Song Gao [aut],
Stefan Mutter [aut],
Aaron E. Casey [aut],
Ville-Petteri Makinen [aut, cre]
Maintainer: Ville-Petteri Makinen <vpmakine@gmail.com>
Diff between Numero versions 1.9.3 dated 2022-08-08 and 1.9.5 dated 2023-01-09
DESCRIPTION | 8 +-- MD5 | 40 ++++++++-------- build/vignette.rds |binary inst/doc/intro.html | 68 +++++++++++++--------------- src/medusa.long2string.cpp | 2 src/medusa.long2text.cpp | 12 ++--- src/medusa.real2string.cpp | 6 +- src/medusa.real2text.cpp | 25 ++++++---- src/medusa.string2real.cpp | 2 src/medusa.time2text.cpp | 10 ++-- src/medusa.version.cpp | 2 src/punos.topology.paint.cpp | 6 +- src/punos.version.cpp | 2 src/scriptum.artistbuffer.prolog.cpp | 83 ++++++++++++++++++----------------- src/scriptum.color.cpp | 4 - src/scriptum.frame.curve.cpp | 14 ++--- src/scriptum.frame.shape.cpp | 14 ++--- src/scriptum.frame.slice.cpp | 32 +++++++------ src/scriptum.frame.text.cpp | 4 - src/scriptum.style2code.cpp | 36 ++++++++------- src/scriptum.version.cpp | 2 21 files changed, 191 insertions(+), 181 deletions(-)
Title: Latent Variable Analysis
Description: Fit a variety of latent variable models, including confirmatory
factor analysis, structural equation modeling and latent growth curve models.
Author: Yves Rosseel [aut, cre] ,
Terrence D. Jorgensen [aut] ,
Nicholas Rockwood [aut] ,
Daniel Oberski [ctb],
Jarrett Byrnes [ctb],
Leonard Vanbrabant [ctb],
Victoria Savalei [ctb],
Ed Merkle [ctb],
Michael Hallquist [ctb],
Mijke Rhemtulla [ctb],
Myrsini K [...truncated...]
Maintainer: Yves Rosseel <Yves.Rosseel@UGent.be>
Diff between lavaan versions 0.6-12 dated 2022-07-04 and 0.6-13 dated 2023-01-09
DESCRIPTION | 6 MD5 | 150 +-- NAMESPACE | 19 R/00class.R | 2 R/00generic.R | 34 R/lav_bootstrap.R | 293 +++--- R/lav_bootstrap_lrt.R | 4 R/lav_cfa_1fac.R | 2 R/lav_cfa_fabin.R | 115 ++ R/lav_cor.R | 4 R/lav_data.R | 43 R/lav_efa_print.R |only R/lav_efa_summary.R |only R/lav_efa_utils.R |only R/lav_fit_aic.R |only R/lav_fit_cfi.R |only R/lav_fit_gfi.R |only R/lav_fit_measures.R | 1966 +++++++++++------------------------------- R/lav_fit_other.R |only R/lav_fit_rmsea.R |only R/lav_fit_srmr.R |only R/lav_fit_utils.R |only R/lav_h1_implied.R | 1 R/lav_matrix.R | 86 + R/lav_matrix_rotate.R | 54 + R/lav_matrix_rotate_utils.R | 25 R/lav_model.R | 17 R/lav_model_efa.R | 2 R/lav_model_estimate.R | 6 R/lav_model_gradient.R | 29 R/lav_model_h1_information.R | 12 R/lav_model_loglik.R | 11 R/lav_model_objective.R | 19 R/lav_model_utils.R | 62 + R/lav_model_vcov.R | 31 R/lav_model_wls.R | 23 R/lav_mvnorm.R | 11 R/lav_mvnorm_h1.R | 15 R/lav_object_generate.R | 109 ++ R/lav_object_inspect.R | 92 + R/lav_object_methods.R | 104 +- R/lav_object_summary.R | 38 R/lav_optim_gn.R | 2 R/lav_optim_noniter.R |only R/lav_options.R | 1118 +++++++++++++++-------- R/lav_partable.R | 128 -- R/lav_partable_bounds.R | 79 - R/lav_partable_constraints.R | 3 R/lav_partable_efa.R |only R/lav_partable_flat.R | 23 R/lav_partable_subset.R | 156 ++- R/lav_partable_unrestricted.R | 34 R/lav_partable_utils.R | 6 R/lav_predict.R | 30 R/lav_predict_y.R |only R/lav_print.R | 317 ++++++ R/lav_residuals.R | 128 ++ R/lav_samplestats.R | 133 ++ R/lav_samplestats_gamma.R | 61 + R/lav_samplestats_wls_obs.R | 21 R/lav_start.R | 33 R/lav_test.R | 287 +++++- R/lav_test_LRT.R | 105 +- R/lav_test_browne.R | 123 ++ R/lav_test_diff.R | 65 + R/lav_test_print.R | 99 +- R/lav_test_satorra_bentler.R | 554 ++++++++--- R/lav_test_yuan_bentler.R | 209 ++-- R/lav_utils.R | 192 +++- R/xxx_efa.R |only R/xxx_lavaan.R | 102 +- R/xxx_sam.R | 283 +++--- build/partial.rdb |binary man/bootstrap.Rd | 25 man/efa.Rd |only man/fitMeasures.Rd | 28 man/lavOptions.Rd | 45 man/lavPredict.Rd | 11 man/lavPredictY.Rd |only man/lavTablesFit.Rd | 1 man/lavTest.Rd |only man/lavaan-class.Rd | 28 man/model.syntax.Rd | 17 man/sam.Rd | 18 man/summary.efaList.Rd |only 85 files changed, 4845 insertions(+), 3004 deletions(-)
Title: Comprehensive Statistical Analysis of Plant Breeding Experiments
Description: Performs statistical data analysis of various Plant Breeding experiments. Contains functions for Line by Tester analysis as per Arunachalam, V.(1974) <http://repository.ias.ac.in/89299/> and Diallel analysis as per Griffing, B. (1956) <https://www.publish.csiro.au/bi/pdf/BI9560463>.
Author: Nandan Patil [cre, aut] ,
Lakshmi R. Gangavati [aut, ctb]
Maintainer: Nandan Patil <tryanother609@gmail.com>
Diff between gpbStat versions 0.3.5 dated 2021-10-30 and 0.4.0 dated 2023-01-09
gpbStat-0.3.5/gpbStat/R/check.R |only gpbStat-0.3.5/gpbStat/R/hcc.R |only gpbStat-0.3.5/gpbStat/R/hybrid.R |only gpbStat-0.3.5/gpbStat/R/utils-pipe.R |only gpbStat-0.3.5/gpbStat/data/check.rda |only gpbStat-0.3.5/gpbStat/data/hybrid.rda |only gpbStat-0.3.5/gpbStat/inst/doc/hcc.R |only gpbStat-0.3.5/gpbStat/inst/doc/hcc.Rmd |only gpbStat-0.3.5/gpbStat/inst/doc/hcc.html |only gpbStat-0.3.5/gpbStat/man/check.Rd |only gpbStat-0.3.5/gpbStat/man/hcc.Rd |only gpbStat-0.3.5/gpbStat/man/hybrid.Rd |only gpbStat-0.3.5/gpbStat/man/pipe.Rd |only gpbStat-0.3.5/gpbStat/vignettes/hcc.Rmd |only gpbStat-0.4.0/gpbStat/DESCRIPTION | 14 gpbStat-0.4.0/gpbStat/MD5 | 52 - gpbStat-0.4.0/gpbStat/NAMESPACE | 5 gpbStat-0.4.0/gpbStat/R/alphaltcs.R |only gpbStat-0.4.0/gpbStat/R/ltc.R | 4 gpbStat-0.4.0/gpbStat/R/ltcmt.R | 942 ++++++++++++++--------------- gpbStat-0.4.0/gpbStat/R/ltcs.R |only gpbStat-0.4.0/gpbStat/R/rcbdltcs.R |only gpbStat-0.4.0/gpbStat/R/sysdata.rda |binary gpbStat-0.4.0/gpbStat/README.md | 294 ++++----- gpbStat-0.4.0/gpbStat/build/vignette.rds |binary gpbStat-0.4.0/gpbStat/data/alphaltcmt.rda |binary gpbStat-0.4.0/gpbStat/data/alphaltcs.rda |only gpbStat-0.4.0/gpbStat/data/rcbdltcmt.rda |binary gpbStat-0.4.0/gpbStat/data/rcbdltcs.rda |only gpbStat-0.4.0/gpbStat/inst/doc/dm2.html | 327 ++++++++-- gpbStat-0.4.0/gpbStat/inst/doc/ltc.html | 334 ++++++++-- gpbStat-0.4.0/gpbStat/inst/doc/ltcchk.html | 334 ++++++++-- gpbStat-0.4.0/gpbStat/inst/doc/ltcmt.html | 883 +++++++++++++++++---------- gpbStat-0.4.0/gpbStat/inst/doc/ltcs.R |only gpbStat-0.4.0/gpbStat/inst/doc/ltcs.Rmd |only gpbStat-0.4.0/gpbStat/inst/doc/ltcs.html |only gpbStat-0.4.0/gpbStat/man/alphaltcs.Rd |only gpbStat-0.4.0/gpbStat/man/ltcs.Rd |only gpbStat-0.4.0/gpbStat/man/rcbdltcs.Rd |only gpbStat-0.4.0/gpbStat/vignettes/ltcs.Rmd |only 40 files changed, 2033 insertions(+), 1156 deletions(-)
Title: Analysis of Factorial Experiments
Description: Convenience functions for analyzing factorial experiments using ANOVA or
mixed models. aov_ez(), aov_car(), and aov_4() allow specification of
between, within (i.e., repeated-measures), or mixed (i.e., split-plot)
ANOVAs for data in long format (i.e., one observation per row),
automatically aggregating multiple observations per individual and cell
of the design. mixed() fits mixed models using lme4::lmer() and computes
p-values for all fixed effects using either Kenward-Roger or Satterthwaite
approximation for degrees of freedom (LMM only), parametric bootstrap
(LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs).
afex_plot() provides a high-level interface for interaction or one-way
plots using ggplot2, combining raw data and model estimates. afex uses
type 3 sums of squares as default (imitating commercial statistical software).
Author: Henrik Singmann [aut, cre] ,
Ben Bolker [aut],
Jake Westfall [aut],
Frederik Aust [aut] ,
Mattan S. Ben-Shachar [aut],
Soeren Hoejsgaard [ctb],
John Fox [ctb],
Michael A. Lawrence [ctb],
Ulf Mertens [ctb],
Jonathon Love [ctb],
Russell Lenth [ctb],
Rune [...truncated...]
Maintainer: Henrik Singmann <singmann@gmail.com>
Diff between afex versions 1.2-0 dated 2022-10-30 and 1.2-1 dated 2023-01-09
DESCRIPTION | 6 MD5 | 22 +-- NEWS | 1 build/partial.rdb |binary inst/doc/afex_analysing_accuracy_data.html | 115 ++++++++-------- inst/doc/afex_anova_example.html | 161 +++++++++++------------ inst/doc/afex_mixed_example.html | 115 ++++++++-------- inst/doc/afex_plot_introduction.html | 201 ++++++++++++++--------------- inst/doc/afex_plot_supported_models.html | 177 ++++++++++++------------- inst/doc/assumptions_of_ANOVAs.html | 115 ++++++++-------- inst/extdata/plots_brms.rda |binary inst/extdata/plots_rstanarm.rda |binary 12 files changed, 453 insertions(+), 460 deletions(-)