Title: "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et
al.
Description: Methods for Cluster analysis. Much extended the original from
Peter Rousseeuw, Anja Struyf and Mia Hubert,
based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".
Author: Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>),
Peter Rousseeuw [aut] (Fortran original,
<https://orcid.org/0000-0002-3807-5353>),
Anja Struyf [aut] (S original),
Mia Hubert [aut] (S original, <https://orcid.org/0000-0001-6398-4850>),
Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000),
<https://orcid.org/0000-0003-4198-9911>),
Matthias Studer [ctb],
Pierre Roudier [ctb],
Juan Gonzalez [ctb],
Kamil Kozlowski [ctb],
Erich Schubert [ctb] (fastpam options for pam(),
<https://orcid.org/0000-0001-9143-4880>),
Keefe Murphy [ctb] (volume.ellipsoid({d >= 3}))
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between cluster versions 2.1.0 dated 2019-06-19 and 2.1.1 dated 2021-02-14
DESCRIPTION | 12 MD5 | 72 ++--- R/clara.q | 17 - R/pam.q | 77 ++++- R/silhouette.R | 33 +- README | 2 build/partial.rdb |binary inst/CITATION | 13 inst/NEWS.Rd | 20 + inst/po/de/LC_MESSAGES/R-cluster.mo |binary inst/po/de/LC_MESSAGES/cluster.mo |binary inst/po/en@quot/LC_MESSAGES/R-cluster.mo |binary inst/po/en@quot/LC_MESSAGES/cluster.mo |binary inst/po/fr/LC_MESSAGES/R-cluster.mo |binary inst/po/fr/LC_MESSAGES/cluster.mo |only inst/po/it |only inst/po/ko/LC_MESSAGES/R-cluster.mo |binary inst/po/ko/LC_MESSAGES/cluster.mo |binary inst/po/pl/LC_MESSAGES/R-cluster.mo |binary man/clara.Rd | 24 + man/pam.Rd | 56 +++ man/silhouette.Rd | 15 - po/R-cluster.pot | 15 - po/R-de.po | 21 + po/R-fr.po | 194 ++++--------- po/R-it.po |only po/R-ko.po | 14 po/R-pl.po | 14 po/cluster.pot | 6 po/de.po | 4 po/fr.po |only po/it.po |only po/ko.po | 4 po/update-me.sh | 2 src/pam.c | 396 ++++++++++++++++++--------- src/sildist.c | 4 tests/agnes-ex.Rout.save | 13 tests/pam.R | 36 +- tests/pam.Rout.save | 439 ++++++++++++++++++++++++------- 39 files changed, 1029 insertions(+), 474 deletions(-)
Title: Sparse Arrays and Multivariate Polynomials
Description: Sparse arrays interpreted as multivariate polynomials.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between spray versions 1.0-10 dated 2020-10-03 and 1.0-11 dated 2021-02-14
DESCRIPTION | 6 +-- MD5 | 23 +++++++------- R/spray.R | 72 +--------------------------------------------- build/spray.pdf |binary build/vignette.rds |binary inst/doc/spray.pdf |binary inst/missing_accessor.txt |only man/Extract.Rd | 5 +++ man/deriv.Rd | 2 - man/rspray.Rd | 4 +- src/spray_ops.cpp | 2 - tests/testthat/test_aaa.R | 2 - vignettes/spray.bib | 8 ++--- 13 files changed, 31 insertions(+), 93 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Daniel Adler <dadler@uni-goettingen.de>, Duncan Murdoch <murdoch.duncan@gmail.com>, and others (see README)
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between rgl versions 0.104.16 dated 2021-01-10 and 0.105.12 dated 2021-02-14
rgl-0.104.16/rgl/R/Sweave_knitr.R |only rgl-0.104.16/rgl/README |only rgl-0.104.16/rgl/po |only rgl-0.105.12/rgl/DESCRIPTION | 15 rgl-0.105.12/rgl/MD5 | 99 rgl-0.105.12/rgl/NAMESPACE | 10 rgl-0.105.12/rgl/R/Sweave.R |only rgl-0.105.12/rgl/R/animate.R | 454 rgl-0.105.12/rgl/R/as.mesh3d.default.R | 12 rgl-0.105.12/rgl/R/convertScene.R | 33 rgl-0.105.12/rgl/R/device.R | 2 rgl-0.105.12/rgl/R/filledContour3d.R | 5 rgl-0.105.12/rgl/R/knitr.R |only rgl-0.105.12/rgl/R/playwidget.R | 7 rgl-0.105.12/rgl/R/r3d.rgl.R | 71 rgl-0.105.12/rgl/R/rglMouse.R | 2 rgl-0.105.12/rgl/R/rglwidget.R | 120 rgl-0.105.12/rgl/R/thigmophobe3d.R | 5 rgl-0.105.12/rgl/R/zzz.R | 50 rgl-0.105.12/rgl/README.md |only rgl-0.105.12/rgl/build/vignette.rds |binary rgl-0.105.12/rgl/cleanup | 4 rgl-0.105.12/rgl/configure | 46 rgl-0.105.12/rgl/configure.ac | 42 rgl-0.105.12/rgl/configure.win | 115 rgl-0.105.12/rgl/inst/NEWS | 34 rgl-0.105.12/rgl/inst/WORDLIST |only rgl-0.105.12/rgl/inst/doc/WebGL.R | 8 rgl-0.105.12/rgl/inst/doc/WebGL.Rmd | 23 rgl-0.105.12/rgl/inst/doc/WebGL.html | 7194 ------------ rgl-0.105.12/rgl/inst/doc/rgl.R | 2 rgl-0.105.12/rgl/inst/doc/rgl.Rmd | 41 rgl-0.105.12/rgl/inst/doc/rgl.html | 7145 ----------- rgl-0.105.12/rgl/inst/doc/transparency.R |only rgl-0.105.12/rgl/inst/doc/transparency.Rmd |only rgl-0.105.12/rgl/inst/doc/transparency.html |only rgl-0.105.12/rgl/inst/htmlwidgets/lib/rglClass/utils.src.js | 14 rgl-0.105.12/rgl/inst/useNULL |only rgl-0.105.12/rgl/man/clipMesh3d.Rd | 36 rgl-0.105.12/rgl/man/contourLines3d.Rd | 3 rgl-0.105.12/rgl/man/figures |only rgl-0.105.12/rgl/man/par3d.Rd | 2 rgl-0.105.12/rgl/man/play3d.Rd | 2 rgl-0.105.12/rgl/man/postscript.Rd | 2 rgl-0.105.12/rgl/man/rgl.init.Rd | 7 rgl-0.105.12/rgl/man/rglwidget.Rd | 41 rgl-0.105.12/rgl/man/setGraphicsDelay.Rd | 2 rgl-0.105.12/rgl/man/shinyGetPar3d.Rd | 4 rgl-0.105.12/rgl/man/snapshot.Rd | 46 rgl-0.105.12/rgl/man/sprites.Rd | 2 rgl-0.105.12/rgl/src/Makevars.in | 29 rgl-0.105.12/rgl/src/Makevars.win |only rgl-0.105.12/rgl/src/gl2ps.c | 6 rgl-0.105.12/rgl/src/useNULL |only rgl-0.105.12/rgl/tools |only rgl-0.105.12/rgl/vignettes/WebGL.Rmd | 23 rgl-0.105.12/rgl/vignettes/rgl.Rmd | 41 rgl-0.105.12/rgl/vignettes/transparency.Rmd |only 58 files changed, 1165 insertions(+), 14634 deletions(-)
Title: Reproduce Statistical Analyses and Meta-Analyses
Description: Includes data analysis functions (e.g., to calculate effect sizes and 95% Confidence Intervals (CI) on Standardised Effect Sizes (d) for AB/BA cross-over repeated-measures experimental designs), data presentation functions (e.g., density curve overlaid on histogram), and the data sets analyzed in different research papers in software engineering (e.g., related to software defect prediction or multi-site experiment concerning the extent to which structured abstracts were clearer and more complete than conventional abstracts) to streamline reproducible research in software engineering.
Author: Lech Madeyski [cre, aut, ctb] (The main contributor and maintainer),
Barbara Kitchenham [ctb] (Data and code contributor),
Tomasz Lewowski [ctb] (Data and code contributor),
Marian Jureczko [ctb] (Data contributor),
David Budgen [ctb] (Data contributor),
Pearl Brereton [ctb] (Data contributor),
Jacky Keung [ctb] (Data contributor),
Stuart Charters [ctb] (Data contributor),
Shirley Gibbs [ctb] (Data contributor),
Amnart Pohthong [ctb] (Data contributor),
Giuseppe Scanniello [ctb] (Data contributor),
Carmine Gravino [ctb] (Data contributor)
Maintainer: Lech Madeyski <lech.madeyski@gmail.com>
Diff between reproducer versions 0.4.0 dated 2020-11-04 and 0.4.1 dated 2021-02-14
DESCRIPTION | 8 ++-- MD5 | 32 ++++++++++++---- NAMESPACE | 17 ++++++++ NEWS.md | 28 ++++++++++++-- R/NPSimulation.R |only R/rPaperFunctions.R | 8 +++- man/Calc4GroupNPStats.Rd |only man/CalculateTheoreticalEffectSizes.Rd |only man/Cliffd.Rd |only man/ExtractMAStatistics.Rd | 48 ++++++++++++++++++++++-- man/Kendalltaupb.Rd |only man/LaplaceDist.Rd |only man/MetaAnalysisSimulations.Rd |only man/NP2GroupMetaAnalysisSimulation.Rd |only man/NP4GroupMetaAnalysisSimulation.Rd |only man/RandomExperimentSimulations.Rd |only man/RandomizedBlockDesignEffectSizes.Rd |only man/RandomizedBlocksAnalysis.Rd |only man/RandomizedBlocksExperimentSimulations.Rd |only man/RandomizedDesignEffectSizes.Rd |only man/calculateBasicStatistics.Rd | 15 +++++-- man/calculatePhat.Rd |only man/calculateSmallSampleSizeAdjustment.Rd | 32 +++++++++++++++- man/simulateRandomizedBlockDesignEffectSizes.Rd |only man/simulateRandomzedDesignEffectSizes.Rd |only man/varStandardizedEffectSize.Rd |only 26 files changed, 162 insertions(+), 26 deletions(-)
Title: Geocode with the OpenCage API
Description: Geocode with the OpenCage API, either from place name to longitude
and latitude (forward geocoding) or from longitude and latitude to the name
and address of a location (reverse geocoding), see
<https://opencagedata.com/>.
Author: Daniel Possenriede [aut, cre] (<https://orcid.org/0000-0002-6738-9845>),
Jesse Sadler [aut] (<https://orcid.org/0000-0001-6081-9681>),
Maëlle Salmon [aut] (<https://orcid.org/0000-0002-2815-0399>),
Noam Ross [ctb],
Jake Russ [ctb],
Julia Silge [rev] (Julia Silge reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/36.)
Maintainer: Daniel Possenriede <possenriede+r@gmail.com>
Diff between opencage versions 0.1.4 dated 2018-01-16 and 0.2.1 dated 2021-02-14
opencage-0.1.4/opencage/R/forward_geocoding.R |only opencage-0.1.4/opencage/R/globalVariables.R |only opencage-0.1.4/opencage/R/reverse_geocoding.R |only opencage-0.1.4/opencage/data/code_message.RData |only opencage-0.1.4/opencage/data/languagecodes.RData |only opencage-0.1.4/opencage/inst/doc/opencage.R |only opencage-0.1.4/opencage/inst/extdata/languagecodes.csv |only opencage-0.1.4/opencage/inst/extdata/messages.csv |only opencage-0.1.4/opencage/man/code_message.Rd |only opencage-0.1.4/opencage/man/languagecodes.Rd |only opencage-0.1.4/opencage/tests/testthat/test-lintr.R |only opencage-0.1.4/opencage/tests/testthat/test-opencage_check.R |only opencage-0.1.4/opencage/tests/testthat/test-opencage_get.R |only opencage-0.1.4/opencage/tests/testthat/test-opencage_parse.R |only opencage-0.1.4/opencage/tests/testthat/test-opencage_query_check.R |only opencage-0.1.4/opencage/tests/testthat/test-opencage_url.R |only opencage-0.2.1/opencage/DESCRIPTION | 54 opencage-0.2.1/opencage/MD5 | 103 opencage-0.2.1/opencage/NAMESPACE | 25 opencage-0.2.1/opencage/NEWS.md | 41 opencage-0.2.1/opencage/R/data_doc.R | 18 opencage-0.2.1/opencage/R/deprecated.R |only opencage-0.2.1/opencage/R/memoise.R |only opencage-0.2.1/opencage/R/oc_api_ok.R |only opencage-0.2.1/opencage/R/oc_bbox.R |only opencage-0.2.1/opencage/R/oc_check_query.R |only opencage-0.2.1/opencage/R/oc_config.R |only opencage-0.2.1/opencage/R/oc_forward.R |only opencage-0.2.1/opencage/R/oc_key.R |only opencage-0.2.1/opencage/R/oc_points.R |only opencage-0.2.1/opencage/R/oc_process.R |only opencage-0.2.1/opencage/R/oc_reverse.R |only opencage-0.2.1/opencage/R/opencage-package.R |only opencage-0.2.1/opencage/R/utils.R | 372 opencage-0.2.1/opencage/R/zzz.R |only opencage-0.2.1/opencage/build/vignette.rds |binary opencage-0.2.1/opencage/data/countrycodes.RData |binary opencage-0.2.1/opencage/inst/doc/customise_query.Rmd |only opencage-0.2.1/opencage/inst/doc/customise_query.html |only opencage-0.2.1/opencage/inst/doc/opencage.Rmd | 390 opencage-0.2.1/opencage/inst/doc/opencage.html | 4398 ---------- opencage-0.2.1/opencage/inst/doc/output_options.Rmd |only opencage-0.2.1/opencage/inst/doc/output_options.html |only opencage-0.2.1/opencage/inst/extdata/countrycodes.csv | 2 opencage-0.2.1/opencage/man/countrycodes.Rd | 4 opencage-0.2.1/opencage/man/figures |only opencage-0.2.1/opencage/man/oc_api_ok.Rd |only opencage-0.2.1/opencage/man/oc_bbox.Rd |only opencage-0.2.1/opencage/man/oc_clear_cache.Rd |only opencage-0.2.1/opencage/man/oc_config.Rd |only opencage-0.2.1/opencage/man/oc_forward.Rd |only opencage-0.2.1/opencage/man/oc_forward_df.Rd |only opencage-0.2.1/opencage/man/oc_key_present.Rd |only opencage-0.2.1/opencage/man/oc_points.Rd |only opencage-0.2.1/opencage/man/oc_reverse.Rd |only opencage-0.2.1/opencage/man/oc_reverse_df.Rd |only opencage-0.2.1/opencage/man/opencage-deprecated.Rd |only opencage-0.2.1/opencage/man/opencage.Rd |only opencage-0.2.1/opencage/man/opencage_forward.Rd | 122 opencage-0.2.1/opencage/man/opencage_key.Rd | 14 opencage-0.2.1/opencage/man/opencage_reverse.Rd | 117 opencage-0.2.1/opencage/tests/testthat.R | 5 opencage-0.2.1/opencage/tests/testthat/helper-opencage.R |only opencage-0.2.1/opencage/tests/testthat/test-deprecated.R |only opencage-0.2.1/opencage/tests/testthat/test-oc_api_ok.R |only opencage-0.2.1/opencage/tests/testthat/test-oc_bbox.R |only opencage-0.2.1/opencage/tests/testthat/test-oc_build_url.R |only opencage-0.2.1/opencage/tests/testthat/test-oc_check_query.R |only opencage-0.2.1/opencage/tests/testthat/test-oc_check_status.R |only opencage-0.2.1/opencage/tests/testthat/test-oc_clear_cache.R |only opencage-0.2.1/opencage/tests/testthat/test-oc_config.R |only opencage-0.2.1/opencage/tests/testthat/test-oc_forward.R |only opencage-0.2.1/opencage/tests/testthat/test-oc_get.R |only opencage-0.2.1/opencage/tests/testthat/test-oc_key.R |only opencage-0.2.1/opencage/tests/testthat/test-oc_points.R |only opencage-0.2.1/opencage/tests/testthat/test-oc_process.R |only opencage-0.2.1/opencage/tests/testthat/test-oc_reverse.R |only opencage-0.2.1/opencage/vignettes/customise_query.Rmd |only opencage-0.2.1/opencage/vignettes/opencage.Rmd | 390 opencage-0.2.1/opencage/vignettes/output_options.Rmd |only 80 files changed, 1218 insertions(+), 4837 deletions(-)
Title: Construct Complex Table with 'kable' and Pipe Syntax
Description: Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr'
and the piping syntax from 'magrittr'. Function 'kable()' is a light weight
table generator coming from 'knitr'. This package simplifies the way to
manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows
users to construct complex tables and customize styles using a readable
syntax.
Author: Hao Zhu [aut, cre] (<https://orcid.org/0000-0002-3386-6076>),
Thomas Travison [ctb],
Timothy Tsai [ctb],
Will Beasley [ctb],
Yihui Xie [ctb],
GuangChuang Yu [ctb],
Stéphane Laurent [ctb],
Rob Shepherd [ctb],
Yoni Sidi [ctb],
Brian Salzer [ctb],
George Gui [ctb],
Yeliang Fan [ctb],
Duncan Murdoch [ctb],
Bill Evans [ctb]
Maintainer: Hao Zhu <haozhu233@gmail.com>
Diff between kableExtra versions 1.3.0 dated 2020-10-22 and 1.3.2 dated 2021-02-14
DESCRIPTION | 8 MD5 | 40 - R/add_indent.R | 2 R/column_spec.R | 6 R/kable_styling.R | 2 R/magic_mirror.R | 20 R/mini_plots.R | 11 R/row_spec.R | 12 R/util.R | 4 R/zzz.R | 2 inst/doc/awesome_table_in_html.html | 402 ++++++++++++++---- inst/doc/awesome_table_in_pdf.Rmd | 5 inst/doc/awesome_table_in_pdf.pdf |binary inst/doc/best_practice_for_newline_in_latex_table.pdf |binary inst/doc/legacy_features.html | 16 inst/doc/use_kable_in_shiny.html | 12 man/spec_boxplot.Rd | 2 man/spec_hist.Rd | 2 man/spec_plot.Rd | 2 man/spec_pointrange.Rd | 2 vignettes/awesome_table_in_pdf.Rmd | 5 21 files changed, 423 insertions(+), 132 deletions(-)
Title: Toolbox for Model Building and Forecasting
Description: Implements functions and instruments for regression model building and its
application to forecasting. The main scope of the package is in variables selection
and models specification for cases of time series data. This includes promotional
modelling, selection between different dynamic regressions with non-standard
distributions of errors, selection based on cross validation, solutions to the fat
regression model problem and more. Models developed in the package are tailored
specifically for forecasting purposes. So as a results there are several methods
that allow producing forecasts from these models and visualising them.
Author: Ivan Svetunkov [aut, cre] (Lecturer at Centre for Marketing Analytics
and Forecasting, Lancaster University, UK),
Yves R. Sagaert [ctb] (Visiting Research at Centre for Marketing
Analytics and Forecasting, Lancaster University, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>
Diff between greybox versions 0.6.6 dated 2021-01-08 and 0.6.7 dated 2021-02-14
DESCRIPTION | 14 +-- MD5 | 52 ++++++------ NAMESPACE | 6 - NEWS | 19 ++++ R/alm.R | 151 +++++++++++++++++++++-------------- R/coefbootstrap.R | 55 ++++++++---- R/graphmaker.R | 12 +- R/lmCombine.R | 136 +++++++++++++++++++++++++++---- R/lmDynamic.R | 136 +++++++++++++++++++++++++++---- R/methods.R | 77 ++++++++++++++--- R/stepwise.R | 10 +- R/temporaldummy.R | 6 - build/partial.rdb |binary inst/doc/alm.R | 11 ++ inst/doc/alm.Rmd | 54 ++++++++++-- inst/doc/alm.html | 184 ++++++++++++++++++------------------------- inst/doc/greybox.html | 46 ---------- inst/doc/maUsingGreybox.html | 44 ---------- inst/doc/ro.html | 54 +----------- man/alm.Rd | 17 ++- man/coefbootstrap.Rd | 9 +- man/graphmaker.Rd | 12 +- man/lmCombine.Rd | 6 - man/lmDynamic.Rd | 6 - man/predict.greybox.Rd | 2 man/stepwise.Rd | 6 - vignettes/alm.Rmd | 54 ++++++++++-- 27 files changed, 718 insertions(+), 461 deletions(-)
Title: Simple Git Client for R
Description: Simple git client for R based on 'libgit2' with support for SSH and
HTTPS remotes. All functions in 'gert' use basic R data types (such as vectors
and data-frames) for their arguments and return values. User credentials are
shared with command line 'git' through the git-credential store and ssh keys
stored on disk or ssh-agent.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Jennifer Bryan [ctb] (<https://orcid.org/0000-0002-6983-2759>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between gert versions 1.1.0 dated 2021-01-25 and 1.2.0 dated 2021-02-14
DESCRIPTION | 12 - MD5 | 22 +- NAMESPACE | 2 NEWS | 3 R/commit.R | 11 + configure | 2 inst/WORDLIST | 7 inst/doc/gert.html | 410 +++++++++++++++++-------------------------- man/git_commit.Rd | 3 src/commit.c | 56 +++++ src/init.c | 2 tests/testthat/test-commit.R | 9 12 files changed, 268 insertions(+), 271 deletions(-)
Title: Larger-than-RAM Disk-Based Data Manipulation Framework
Description: A disk-based data manipulation tool for working with
large-than-RAM datasets. Aims to lower the barrier-to-entry for
manipulating large datasets by adhering closely to popular and
familiar data manipulation paradigms like 'dplyr' verbs and
'data.table' syntax.
Author: Dai ZJ [aut, cre],
Jacky Poon [ctb]
Maintainer: Dai ZJ <zhuojia.dai@gmail.com>
Diff between disk.frame versions 0.3.7 dated 2020-07-07 and 0.4.0 dated 2021-02-14
disk.frame-0.3.7/disk.frame/man/create_dplyr_mapper.Rd |only disk.frame-0.4.0/disk.frame/DESCRIPTION | 20 +- disk.frame-0.4.0/disk.frame/MD5 | 45 ++--- disk.frame-0.4.0/disk.frame/NAMESPACE | 7 disk.frame-0.4.0/disk.frame/NEWS.md | 4 disk.frame-0.4.0/disk.frame/R/anti_join.r | 1 disk.frame-0.4.0/disk.frame/R/cmap.r | 23 +- disk.frame-0.4.0/disk.frame/R/collect.r | 8 disk.frame-0.4.0/disk.frame/R/collect.summarized_disk.frame.r | 1 disk.frame-0.4.0/disk.frame/R/csv2disk.frame.r | 3 disk.frame-0.4.0/disk.frame/R/data.table.r | 12 + disk.frame-0.4.0/disk.frame/R/dplyr_verbs.r | 17 - disk.frame-0.4.0/disk.frame/R/foverlaps.disk.frame.r | 31 ++- disk.frame-0.4.0/disk.frame/R/full_join.r | 2 disk.frame-0.4.0/disk.frame/R/hard_group_by.r | 1 disk.frame-0.4.0/disk.frame/R/map2.r | 7 disk.frame-0.4.0/disk.frame/R/names.r | 20 +- disk.frame-0.4.0/disk.frame/R/rbindlist.disk.frame.r | 12 - disk.frame-0.4.0/disk.frame/R/rechunk.r | 2 disk.frame-0.4.0/disk.frame/R/zip_to_disk.frame.r | 2 disk.frame-0.4.0/disk.frame/README.md | 89 +++++----- disk.frame-0.4.0/disk.frame/man/colnames.Rd | 55 +++--- disk.frame-0.4.0/disk.frame/man/dplyr_verbs.Rd | 6 disk.frame-0.4.0/disk.frame/man/foverlaps.disk.frame.Rd | 5 24 files changed, 189 insertions(+), 184 deletions(-)
Title: A Dipping Sauce for Data Analysis and Visualizations
Description: Works as an "add-on" to packages like 'shiny', 'future', as well as
'rlang', and provides utility functions. Just like dipping sauce adding
flavors to potato chips or pita bread, 'dipsaus' for data analysis and
visualizations adds handy functions and enhancements to popular packages.
The goal is to provide simple solutions that are frequently asked for
online, such as how to synchronize 'shiny' inputs without freezing the app,
or how to get memory size on 'Linux' or 'MacOS' system. The enhancements
roughly fall into these four categories: 1. 'shiny' input widgets; 2.
high-performance computing using 'RcppParallel' and 'future' package; 3.
modify R calls and convert among numbers, strings, and other objects. 4.
utility functions to get system information such like CPU chip-set, memory
limit, etc.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <zhengjia.wang@rice.edu>
Diff between dipsaus versions 0.1.3 dated 2021-02-13 and 0.1.4 dated 2021-02-14
DESCRIPTION | 6 MD5 | 24 ++- NAMESPACE | 1 R/parallels-future.R | 2 R/parallels.R | 4 R/systems.R | 140 ++++++++++++++++++---- inst/doc/r_expr_addons.html | 6 inst/doc/utility_functions.html | 2 man/get_cpu.Rd | 5 man/get_os.Rd |only man/get_ram.Rd | 7 - tests/testthat/test-commandline.R |only tests/testthat/test.maps.R | 236 +++++++++++++++++++------------------- tests/testthat/test.queues.R | 198 +++++++++++++++---------------- 14 files changed, 367 insertions(+), 264 deletions(-)
Title: Composite-Based Structural Equation Modeling
Description: Estimate, assess, test, and study linear, nonlinear, hierarchical
and multigroup structural equation models using composite-based approaches
and procedures, including estimation techniques such as partial least squares
path modeling (PLS-PM) and its derivatives (PLSc, ordPLSc, robustPLSc),
generalized structured component analysis (GSCA), generalized structured
component analysis with uniqueness terms (GSCAm), generalized canonical
correlation analysis (GCCA), principal component analysis (PCA),
factor score regression (FSR) using sum score, regression or
bartlett scores (including bias correction using Croon’s approach),
as well as several tests and typical postestimation procedures
(e.g., verify admissibility of the estimates, assess the model fit,
test the model fit etc.).
Author: Manuel E. Rademaker [aut, cre]
(<https://orcid.org/0000-0002-8902-3561>),
Florian Schuberth [aut] (<https://orcid.org/0000-0002-2110-9086>),
Tamara Schamberger [ctb] (<https://orcid.org/0000-0002-7845-784X>),
Michael Klesel [ctb] (<https://orcid.org/0000-0002-2884-1819>),
Theo K. Dijkstra [ctb],
Jörg Henseler [ctb] (<https://orcid.org/0000-0002-9736-3048>)
Maintainer: Manuel E. Rademaker <manuel.rademaker@uni-wuerzburg.de>
Diff between cSEM versions 0.3.0 dated 2020-10-12 and 0.3.1 dated 2021-02-14
DESCRIPTION | 8 MD5 | 48 NAMESPACE | 3 R/00_csem.R | 11 R/helper_assess.R | 138 R/plot.cSEMIPMA.R | 12 R/postestimate_assess.R | 7 R/postestimate_summarize.R | 29 R/postestimate_test_MGD.R | 2 R/postestimate_test_OMF.R | 1 R/print.cSEMAssess.R | 5 R/zz_arguments.R | 4 R/zz_package.R | 8 README.md | 252 - build/cSEM.pdf |10769 +++++++++++++++++++++++---------------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Notation.html | 49 inst/doc/Terminology.html | 57 inst/doc/Using-assess.html | 169 inst/doc/cSEM.html | 485 -- man/cSEM-package.Rd | 6 man/calculateHTMT.Rd | 14 man/csem.Rd | 11 man/csem_arguments.Rd | 4 25 files changed, 6197 insertions(+), 5895 deletions(-)
Title: Tensor Composition Analysis
Description: Tensor Composition Analysis (TCA) allows the deconvolution of two-dimensional data (features by observations) coming from a mixture of heterogeneous sources into a three-dimensional matrix of signals (features by observations by sources). The TCA framework further allows to test the features in the data for different statistical relations with an outcome of interest while modeling source-specific effects; particularly, it allows to look for statistical relations between source-specific signals and an outcome. For example, TCA can deconvolve bulk tissue-level DNA methylation data (methylation sites by individuals) into a three-dimensional tensor of cell-type-specific methylation levels for each individual (i.e. methylation sites by individuals by cell types) and it allows to detect cell-type-specific statistical relations (associations) with phenotypes. For more details see Rahmani et al. (2019) <DOI:10.1038/s41467-019-11052-9>.
Author: Elior Rahmani [aut, cre],
Brandon Jew [ctb]
Maintainer: Elior Rahmani <elior.rahmani@gmail.com>
Diff between TCA versions 1.1.0 dated 2019-11-16 and 1.2.1 dated 2021-02-14
TCA-1.1.0/TCA/vignettes/figs |only TCA-1.2.1/TCA/DESCRIPTION | 28 TCA-1.2.1/TCA/MD5 | 53 - TCA-1.2.1/TCA/NAMESPACE | 2 TCA-1.2.1/TCA/NEWS.md | 20 TCA-1.2.1/TCA/R/TCA.R | 201 +++--- TCA-1.2.1/TCA/R/model_fit.R | 673 ++++++++++++++++----- TCA-1.2.1/TCA/R/refactor.R | 3 TCA-1.2.1/TCA/R/utils.R | 68 +- TCA-1.2.1/TCA/README.md | 4 TCA-1.2.1/TCA/build/vignette.rds |binary TCA-1.2.1/TCA/inst/doc/tca-vignette.R | 2 TCA-1.2.1/TCA/inst/doc/tca-vignette.Rmd | 642 +++++++++++++++----- TCA-1.2.1/TCA/inst/doc/tca-vignette.html | 890 +++++++++++++++++++++------- TCA-1.2.1/TCA/inst/extdata/config.yml | 7 TCA-1.2.1/TCA/man/refactor.Rd | 32 - TCA-1.2.1/TCA/man/tca.Rd | 74 +- TCA-1.2.1/TCA/man/tcareg.Rd | 84 +- TCA-1.2.1/TCA/man/tcasub.Rd | 13 TCA-1.2.1/TCA/man/tensor.Rd | 24 TCA-1.2.1/TCA/man/test_data.Rd | 6 TCA-1.2.1/TCA/vignettes/W.paquette.txt |only TCA-1.2.1/TCA/vignettes/exp1.fig1.PNG |only TCA-1.2.1/TCA/vignettes/exp1.fig2.PNG |only TCA-1.2.1/TCA/vignettes/exp1.fig3.PNG |only TCA-1.2.1/TCA/vignettes/exp1.fig4.PNG |only TCA-1.2.1/TCA/vignettes/exp2.fig1.PNG |only TCA-1.2.1/TCA/vignettes/exp2.fig2.PNG |only TCA-1.2.1/TCA/vignettes/exp2.fig3.PNG |only TCA-1.2.1/TCA/vignettes/exp2.fig4.PNG |only TCA-1.2.1/TCA/vignettes/gender.paquette.txt |only TCA-1.2.1/TCA/vignettes/tca-vignette.Rmd | 642 +++++++++++++++----- TCA-1.2.1/TCA/vignettes/vignette_analysis.R |only 33 files changed, 2563 insertions(+), 905 deletions(-)
Title: Declare and Diagnose Research Designs
Description: Researchers can characterize and learn about the properties of
research designs before implementation using `DeclareDesign`. Ex ante
declaration and diagnosis of designs can help researchers clarify the
strengths and limitations of their designs and to improve their
properties, and can help readers evaluate a research strategy prior
to implementation and without access to results. It can also make it
easier for designs to be shared, replicated, and critiqued.
Author: Graeme Blair [aut, cre] (<https://orcid.org/0000-0001-9164-2102>),
Jasper Cooper [aut] (<https://orcid.org/0000-0002-8639-3188>),
Alexander Coppock [aut] (<https://orcid.org/0000-0002-5733-2386>),
Macartan Humphreys [aut] (<https://orcid.org/0000-0001-7029-2326>),
Neal Fultz [aut]
Maintainer: Graeme Blair <graeme.blair@ucla.edu>
Diff between DeclareDesign versions 0.24.0 dated 2020-11-14 and 0.26.0 dated 2021-02-14
DeclareDesign-0.24.0/DeclareDesign/R/declare_estimand.R |only DeclareDesign-0.24.0/DeclareDesign/man/declare_estimand.Rd |only DeclareDesign-0.24.0/DeclareDesign/man/reveal_outcomes.Rd |only DeclareDesign-0.26.0/DeclareDesign/DESCRIPTION | 8 DeclareDesign-0.26.0/DeclareDesign/MD5 | 226 ++++---- DeclareDesign-0.26.0/DeclareDesign/NAMESPACE | 14 DeclareDesign-0.26.0/DeclareDesign/NEWS.md | 10 DeclareDesign-0.26.0/DeclareDesign/R/DeclareDesign.R | 29 - DeclareDesign-0.26.0/DeclareDesign/R/compare_designs.R | 35 - DeclareDesign-0.26.0/DeclareDesign/R/compare_diagnoses.R | 56 +- DeclareDesign-0.26.0/DeclareDesign/R/construct_design.R | 87 --- DeclareDesign-0.26.0/DeclareDesign/R/declare_assignment.R | 274 ++++++---- DeclareDesign-0.26.0/DeclareDesign/R/declare_diagnosands.R | 92 +-- DeclareDesign-0.26.0/DeclareDesign/R/declare_estimator.R | 264 +++------ DeclareDesign-0.26.0/DeclareDesign/R/declare_inquiry.R |only DeclareDesign-0.26.0/DeclareDesign/R/declare_measurement.R | 37 + DeclareDesign-0.26.0/DeclareDesign/R/declare_model.R |only DeclareDesign-0.26.0/DeclareDesign/R/declare_population.R | 36 - DeclareDesign-0.26.0/DeclareDesign/R/declare_potential_outcomes.R | 189 +----- DeclareDesign-0.26.0/DeclareDesign/R/declare_reveal.R | 121 +--- DeclareDesign-0.26.0/DeclareDesign/R/declare_sampling.R | 209 +++++-- DeclareDesign-0.26.0/DeclareDesign/R/declare_step.R | 2 DeclareDesign-0.26.0/DeclareDesign/R/declare_test.R | 30 - DeclareDesign-0.26.0/DeclareDesign/R/deprecated.R | 7 DeclareDesign-0.26.0/DeclareDesign/R/design_helper_functions.R | 64 +- DeclareDesign-0.26.0/DeclareDesign/R/design_print_summary.R | 34 - DeclareDesign-0.26.0/DeclareDesign/R/diagnose_design.R | 93 ++- DeclareDesign-0.26.0/DeclareDesign/R/diagnosis_helper_functions.R | 66 +- DeclareDesign-0.26.0/DeclareDesign/R/draw_functions.R | 50 + DeclareDesign-0.26.0/DeclareDesign/R/expand_design.R | 16 DeclareDesign-0.26.0/DeclareDesign/R/get_functions.R | 30 - DeclareDesign-0.26.0/DeclareDesign/R/modify_design.R | 34 - DeclareDesign-0.26.0/DeclareDesign/R/modify_edit.R | 4 DeclareDesign-0.26.0/DeclareDesign/R/redesign.R | 15 DeclareDesign-0.26.0/DeclareDesign/R/set_citation.R | 4 DeclareDesign-0.26.0/DeclareDesign/R/set_diagnosands.R | 10 DeclareDesign-0.26.0/DeclareDesign/R/simulate_design.R | 65 +- DeclareDesign-0.26.0/DeclareDesign/R/utilities.R | 4 DeclareDesign-0.26.0/DeclareDesign/inst/CITATION | 4 DeclareDesign-0.26.0/DeclareDesign/man/DeclareDesign.Rd | 19 DeclareDesign-0.26.0/DeclareDesign/man/compare_diagnoses.Rd | 22 DeclareDesign-0.26.0/DeclareDesign/man/compare_functions.Rd | 35 - DeclareDesign-0.26.0/DeclareDesign/man/declare_assignment.Rd | 81 +- DeclareDesign-0.26.0/DeclareDesign/man/declare_design.Rd | 68 -- DeclareDesign-0.26.0/DeclareDesign/man/declare_diagnosands.Rd | 35 - DeclareDesign-0.26.0/DeclareDesign/man/declare_estimator.Rd | 209 ++----- DeclareDesign-0.26.0/DeclareDesign/man/declare_inquiry.Rd |only DeclareDesign-0.26.0/DeclareDesign/man/declare_measurement.Rd | 31 - DeclareDesign-0.26.0/DeclareDesign/man/declare_model.Rd |only DeclareDesign-0.26.0/DeclareDesign/man/declare_population.Rd | 34 - DeclareDesign-0.26.0/DeclareDesign/man/declare_potential_outcomes.Rd | 70 +- DeclareDesign-0.26.0/DeclareDesign/man/declare_reveal.Rd |only DeclareDesign-0.26.0/DeclareDesign/man/declare_sampling.Rd | 44 - DeclareDesign-0.26.0/DeclareDesign/man/declare_step.Rd | 2 DeclareDesign-0.26.0/DeclareDesign/man/declare_test.Rd | 28 - DeclareDesign-0.26.0/DeclareDesign/man/diagnose_design.Rd | 58 +- DeclareDesign-0.26.0/DeclareDesign/man/diagnosis_helpers.Rd | 34 - DeclareDesign-0.26.0/DeclareDesign/man/draw_functions.Rd | 35 - DeclareDesign-0.26.0/DeclareDesign/man/edit.Rd | 4 DeclareDesign-0.26.0/DeclareDesign/man/expand_design.Rd | 16 DeclareDesign-0.26.0/DeclareDesign/man/get_functions.Rd | 24 DeclareDesign-0.26.0/DeclareDesign/man/modify_design.Rd | 34 - DeclareDesign-0.26.0/DeclareDesign/man/post_design.Rd | 54 - DeclareDesign-0.26.0/DeclareDesign/man/redesign.Rd | 15 DeclareDesign-0.26.0/DeclareDesign/man/reshape_diagnosis.Rd | 8 DeclareDesign-0.26.0/DeclareDesign/man/run_design.Rd | 19 DeclareDesign-0.26.0/DeclareDesign/man/set_citation.Rd | 4 DeclareDesign-0.26.0/DeclareDesign/man/set_diagnosands.Rd | 10 DeclareDesign-0.26.0/DeclareDesign/man/simulate_design.Rd | 25 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-alternative-df-compatibility.R | 4 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-assignment.R | 106 ++- DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-attrition.R | 10 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-bootstrap-diagnosands.R | 24 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-citation.R | 4 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-compare-designs.R | 28 - DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-compare-diagnoses.R | 15 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-conduct-custom.R | 10 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-continuous-pos.R | 12 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-declare-design.R | 31 - DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-declare-step.R | 2 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-demo.R | 44 - DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-deprecated.R | 28 + DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-design-summary.R | 22 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-diagnosands.R | 53 - DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-diagnose-design.R | 164 ++--- DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-environment-issues.R | 12 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-estimands.R | 98 ++- DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-estimators.R | 84 +-- DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-expand-design.R | 84 +-- DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-factorial.R | 14 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-fanout.R | 52 - DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-get-estimates.R | 8 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-get-star.R | 17 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-labels.R | 10 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-model-summary.R | 30 - DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-model.R | 10 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-modify-design.R | 12 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-multiple-coefficients.R | 4 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-multiple-estimands-one-estimator.R | 29 - DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-multiple-estimators.R | 24 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-multiple-pos.R | 6 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-name-steps.R | 14 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-names-and-labels.R | 62 +- DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-noncompliance.R | 22 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-paper.R | 16 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-plus.R | 24 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-potential-outcomes.R | 62 -- DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-print-code.R | 22 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-quick-design.R | 36 - DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-reshape-diagnosis.R | 55 +- DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-reveal-outcomes.R | 46 - DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-sampling.R | 85 ++- DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-save-reload-redesign.R | 2 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-simulate-design.R | 45 - DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-subset.R | 16 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-sugar.R | 14 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-test.R | 1 DeclareDesign-0.26.0/DeclareDesign/tests/testthat/test-utilities.R | 6 118 files changed, 2444 insertions(+), 2372 deletions(-)
Title: Validation of Clustering Results
Description: Statistical and biological validation of clustering results. This package implements Dunn Index, Silhouette, Connectivity, Stability, BHI and BSI. Further information can be found in Brock, G et al. (2008) <doi: 10.18637/jss.v025.i04>.
Author: Guy Brock <guy.brock@louisville.edu>, Vasyl Pihur <vpihur@gmail.com>,
Susmita Datta <susmita.datta@louisville.edu>, and
Somnath Datta <somnath.datta@louisville.edu>
Maintainer: Vasyl Pihur <vpihur@gmail.com>
Diff between clValid versions 0.6-9 dated 2020-07-14 and 0.7 dated 2021-02-14
ChangeLog | 6 ++++++ DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/clValid-functions.R | 10 +++++----- build/vignette.rds |binary inst/CITATION | 4 ++-- inst/doc/clValid.pdf |binary man/clValid-class.Rd | 4 ++-- man/clValid.Rd | 4 ++-- man/getRanksWeights.Rd | 4 ++-- 10 files changed, 32 insertions(+), 26 deletions(-)
Title: Prediction Limits for Poisson Distribution
Description: Prediction limits for the Poisson distribution
are produced from both frequentist and Bayesian viewpoints. Limiting results
are provided in a Bayesian setting with uniform, Jeffreys and gamma as prior
distributions. More details on the methodology are discussed in Bejleri and
Nandram (2018) <doi:10.1080/03610926.2017.1373814>.
Author: Valbona Bejleri [aut] (<https://orcid.org/0000-0001-9828-968X>),
Luca Sartore [aut, cre] (<https://orcid.org/0000-0002-0446-1328>),
Balgobin Nandram [aut] (<https://orcid.org/0000-0002-3204-0301>)
Maintainer: Luca Sartore <drwolf85@gmail.com>
Diff between plpoisson versions 0.1.1 dated 2020-06-04 and 0.2.0 dated 2021-02-14
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS | 29 +++++++++++++++++++++-------- R/poisBayes.R | 4 ++-- R/poisJEFF.R | 4 ++-- R/poisUNIF.R | 4 ++-- README.md | 2 +- build/partial.rdb |binary inst/INSTALL.md | 4 ++-- man/plpoisson-package.Rd | 4 ++-- man/poisBayes.Rd | 4 ---- man/poisJEFF.Rd | 4 ---- man/poisUNIF.Rd | 4 ---- 13 files changed, 48 insertions(+), 47 deletions(-)
Title: Stepwise Elimination and Term Reordering for Mixed-Effects
Regression
Description: Finds the largest possible regression model that will still converge
for various types of regression analyses (including mixed models and generalized
additive models) and then optionally performs stepwise elimination similar to the
forward and backward effect-selection methods in SAS, based on the change in
log-likelihood or its significance, Akaike's Information Criterion, the Bayesian
Information Criterion, the explained deviance, or the F-test of the change in R².
Author: Cesko C. Voeten [aut, cre] (<https://orcid.org/0000-0003-4687-9973>)
Maintainer: Cesko C. Voeten <cvoeten@gmail.com>
Diff between buildmer versions 1.7.1 dated 2020-08-26 and 1.8 dated 2021-02-14
ChangeLog | 28 + DESCRIPTION | 6 MD5 | 16 - R/buildmer-S4.R | 12 R/buildmer-private.R | 22 - R/control.R | 16 - build/vignette.rds |binary inst/doc/buildmer.html | 690 ++++++++++++++++++------------------------------- man/buildmerControl.Rd | 19 - 9 files changed, 313 insertions(+), 496 deletions(-)
Title: Helper Functions for Simulation Studies
Description: Calculates performance criteria measures and associated Monte Carlo standard errors for simulation results. Includes functions to help run simulation studies. Our derivation and explanation of formulas and our general simulation workflow is closely aligned with the approach described by Morris, White, and Crowther (2019) <DOI: 10.1002/sim.8086>.
Author: Megha Joshi [aut, cre],
James Pustejovsky [aut] (<https://orcid.org/0000-0003-0591-9465>)
Maintainer: Megha Joshi <megha.j456@gmail.com>
Diff between simhelpers versions 0.1.0 dated 2020-03-31 and 0.1.1 dated 2021-02-14
simhelpers-0.1.0/simhelpers/README.md |only simhelpers-0.1.1/simhelpers/DESCRIPTION | 8 simhelpers-0.1.1/simhelpers/MD5 | 49 simhelpers-0.1.1/simhelpers/NEWS.md | 5 simhelpers-0.1.1/simhelpers/R/calc_absolute.R | 2 simhelpers-0.1.1/simhelpers/R/calc_relative.R | 5 simhelpers-0.1.1/simhelpers/R/calc_relative_var.R | 6 simhelpers-0.1.1/simhelpers/build/partial.rdb |binary simhelpers-0.1.1/simhelpers/build/vignette.rds |binary simhelpers-0.1.1/simhelpers/inst/REFERENCES.bib | 2 simhelpers-0.1.1/simhelpers/inst/doc/MCSE.R | 8 simhelpers-0.1.1/simhelpers/inst/doc/MCSE.Rmd | 24 simhelpers-0.1.1/simhelpers/inst/doc/MCSE.html | 613 ++---- simhelpers-0.1.1/simhelpers/inst/doc/simulation_workflow.R | 8 simhelpers-0.1.1/simhelpers/inst/doc/simulation_workflow.Rmd | 16 simhelpers-0.1.1/simhelpers/inst/doc/simulation_workflow.html | 927 ++++------ simhelpers-0.1.1/simhelpers/inst/doc/visualization.Rmd | 8 simhelpers-0.1.1/simhelpers/inst/doc/visualization.html | 381 +--- simhelpers-0.1.1/simhelpers/man/evaluate_by_row.Rd | 15 simhelpers-0.1.1/simhelpers/tests/testthat/test_ebr.R | 1 simhelpers-0.1.1/simhelpers/tests/testthat/test_perfm_conv.R | 16 simhelpers-0.1.1/simhelpers/tests/testthat/test_perfm_mcse.R | 26 simhelpers-0.1.1/simhelpers/vignettes/MCSE.Rmd | 24 simhelpers-0.1.1/simhelpers/vignettes/references.bib | 13 simhelpers-0.1.1/simhelpers/vignettes/simulation_workflow.Rmd | 16 simhelpers-0.1.1/simhelpers/vignettes/visualization.Rmd | 8 26 files changed, 933 insertions(+), 1248 deletions(-)
Title: Keyword Assisted Topic Model
Description: Fits keyword assisted topic models (keyATM) using collapsed Gibbs samplers. The keyATM combines the latent dirichlet allocation (LDA) models with a small number of keywords selected by researchers in order to improve the interpretability and topic classification of the LDA. The keyATM can also incorporate covariates and directly model time trends. The keyATM is proposed in Eshima, Imai, and Sasaki (2020) <arXiv:2004.05964>.
Author: Shusei Eshima [aut, cre] (<https://orcid.org/0000-0003-3613-4046>),
Tomoya Sasaki [aut],
William Lowe [ctb],
Kosuke Imai [aut],
Chung-hong Chan [ctb] (<https://orcid.org/0000-0002-6232-7530>),
Romain François [ctb] (<https://orcid.org/0000-0002-2444-4226>)
Maintainer: Shusei Eshima <shuseieshima@g.harvard.edu>
Diff between keyATM versions 0.3.1 dated 2020-07-29 and 0.4.0 dated 2021-02-14
keyATM-0.3.1/keyATM/tests/testthat/test-keyATMCov.R |only keyATM-0.4.0/keyATM/DESCRIPTION | 13 keyATM-0.4.0/keyATM/MD5 | 78 +- keyATM-0.4.0/keyATM/NAMESPACE | 1 keyATM-0.4.0/keyATM/NEWS.md | 13 keyATM-0.4.0/keyATM/R/RcppExports.R | 29 keyATM-0.4.0/keyATM/R/analysis_covariates.R |only keyATM-0.4.0/keyATM/R/keyATM.R | 5 keyATM-0.4.0/keyATM/R/keyATMvb.R | 28 keyATM-0.4.0/keyATM/R/model.R | 148 +++- keyATM-0.4.0/keyATM/R/multiPGreg.R |only keyATM-0.4.0/keyATM/R/plots.R | 16 keyATM-0.4.0/keyATM/R/posterior.R | 325 ++-------- keyATM-0.4.0/keyATM/R/predict.R | 147 ++-- keyATM-0.4.0/keyATM/R/utils.R | 53 + keyATM-0.4.0/keyATM/man/by_strata_DocTopic.Rd | 2 keyATM-0.4.0/keyATM/man/by_strata_TopicWord.Rd | 2 keyATM-0.4.0/keyATM/man/calc_PGtheta_R.Rd |only keyATM-0.4.0/keyATM/man/covariates_get.Rd | 2 keyATM-0.4.0/keyATM/man/covariates_info.Rd | 2 keyATM-0.4.0/keyATM/man/keyATM.Rd | 2 keyATM-0.4.0/keyATM/man/keyATM_fit_cov.Rd | 4 keyATM-0.4.0/keyATM/man/keyATM_fit_covPG.Rd |only keyATM-0.4.0/keyATM/man/keyATM_read.Rd | 17 keyATM-0.4.0/keyATM/man/multiPGreg.Rd |only keyATM-0.4.0/keyATM/man/predict.keyATM_output.Rd | 5 keyATM-0.4.0/keyATM/man/read_dfm_cpp.Rd | 8 keyATM-0.4.0/keyATM/src/RcppExports.cpp | 39 + keyATM-0.4.0/keyATM/src/helper.cpp |only keyATM-0.4.0/keyATM/src/keyATM_HMM.cpp | 2 keyATM-0.4.0/keyATM/src/keyATM_base.cpp | 2 keyATM-0.4.0/keyATM/src/keyATM_cov.cpp | 2 keyATM-0.4.0/keyATM/src/keyATM_covPG.cpp |only keyATM-0.4.0/keyATM/src/keyATM_covPG.h |only keyATM-0.4.0/keyATM/src/keyATM_label.cpp | 2 keyATM-0.4.0/keyATM/src/keyATM_meta.cpp | 3 keyATM-0.4.0/keyATM/src/keyATM_meta.h | 3 keyATM-0.4.0/keyATM/src/read.cpp | 42 + keyATM-0.4.0/keyATM/src/train.cpp | 19 keyATM-0.4.0/keyATM/src/utils.cpp |only keyATM-0.4.0/keyATM/src/utils.h |only keyATM-0.4.0/keyATM/tests/testthat/test-Initialization.R | 31 keyATM-0.4.0/keyATM/tests/testthat/test-keyATMCovDirMulti.R |only keyATM-0.4.0/keyATM/tests/testthat/test-keyATMCovPG.R |only keyATM-0.4.0/keyATM/tests/testthat/test-keyATMHeterogeneity.R | 6 keyATM-0.4.0/keyATM/tests/testthat/test-read_keywords.R | 2 keyATM-0.4.0/keyATM/tests/testthat/test-read_texts.R |only 47 files changed, 607 insertions(+), 446 deletions(-)
Title: Unit Testing for R
Description: Software testing is important, but, in part because
it is frustrating and boring, many of us avoid it. 'testthat' is a
testing framework for R that is easy to learn and use, and integrates
with your existing 'workflow'.
Author: Hadley Wickham [aut, cre],
RStudio [cph, fnd],
R Core team [ctb] (Implementation of utils::recover())
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between testthat versions 3.0.1 dated 2020-12-17 and 3.0.2 dated 2021-02-14
DESCRIPTION | 8 - MD5 | 136 ++++++++++++++-------------- NEWS.md | 17 +++ R/auto-test.R | 8 + R/compare.R | 2 R/expect-comparison.R | 3 R/expect-constant.R | 3 R/expect-equality.R | 3 R/expect-inheritance.R | 81 ++++++++++------ R/expect-known.R | 3 R/expect-that.R | 5 - R/expect-vector.R | 5 - R/expectation.R | 25 ++++- R/local.R | 33 +++--- R/reporter-check.R | 11 +- R/reporter-progress.R | 2 R/skip.R | 4 R/snapshot.R | 20 ++-- R/source.R | 2 R/test-that.R | 2 R/utils.R | 5 - inst/doc/custom-expectation.html | 11 +- inst/doc/parallel.html | 9 + inst/doc/skipping.html | 11 +- inst/doc/snapshotting.Rmd | 4 inst/doc/snapshotting.html | 13 ++ inst/doc/test-fixtures.Rmd | 2 inst/doc/test-fixtures.html | 11 +- inst/doc/third-edition.Rmd | 2 inst/doc/third-edition.html | 11 +- man/capture_condition.Rd | 2 man/compare.Rd | 2 man/context.Rd | 4 man/expect.Rd | 14 ++ man/expect_equivalent.Rd | 2 man/expect_is.Rd | 8 + man/expect_known_output.Rd | 2 man/expect_output_file.Rd | 2 man/expect_reference.Rd | 2 man/expect_snapshot.Rd | 6 - man/expect_that.Rd | 4 man/fail.Rd | 11 ++ man/inheritance-expectations.Rd | 6 + man/is_informative_error.Rd | 2 man/local_test_context.Rd | 35 +++---- man/oldskool.Rd | 2 man/teardown.Rd | 2 man/verify_output.Rd | 2 man/with_mock.Rd | 4 tests/testthat/_snaps/expect-inheritance.md |only tests/testthat/_snaps/reporter-check.md | 43 ++++++++ tests/testthat/_snaps/reporter-junit.md | 5 - tests/testthat/_snaps/reporter-progress.md | 31 +++++- tests/testthat/_snaps/reporter-stop.md | 3 tests/testthat/_snaps/reporter-summary.md | 9 + tests/testthat/_snaps/reporter-tap.md | 3 tests/testthat/_snaps/reporter-teamcity.md | 2 tests/testthat/_snaps/skip.md |only tests/testthat/_snaps/snapshot.md | 21 ++++ tests/testthat/reporters/backtraces.R | 10 ++ tests/testthat/test-compare.R | 8 - tests/testthat/test-expect-inheritance.R | 14 ++ tests/testthat/test-expect-known.R | 1 tests/testthat/test-local.R | 20 +++- tests/testthat/test-reporter-check.R | 13 ++ tests/testthat/test-skip.R | 2 tests/testthat/test-snapshot.R | 9 + vignettes/snapshotting.Rmd | 4 vignettes/test-fixtures.Rmd | 2 vignettes/third-edition.Rmd | 2 70 files changed, 545 insertions(+), 221 deletions(-)
Title: Coenocline Simulation
Description: Simulate species occurrence and abundances (counts) along
gradients.
Author: Gavin L. Simpson [aut, cre],
Jari Oksanen [ctb],
Francisco Rodriguez-Sanchez [ctb]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between coenocliner versions 0.2-2 dated 2016-05-19 and 0.2-3 dated 2021-02-14
DESCRIPTION | 10 +++--- MD5 | 47 ++++++++++++++++---------------- R/jamil-sim.R | 2 - README.md | 2 - build/partial.rdb |only build/vignette.rds |binary inst/ChangeLog | 6 ++++ inst/NEWS | 6 ++++ inst/doc/coenocliner.R | 42 ++++++++++++++-------------- inst/doc/coenocliner.Rnw | 4 +- inst/doc/coenocliner.pdf |binary man/coenocline.Rd | 15 ++++++---- man/coenocliner-internal.Rd | 1 man/coenocliner.Rd | 7 ++-- man/distributions.Rd | 19 ++++++------ man/expand.Rd | 7 ++-- man/locations.Rd | 1 man/persp.coenocline.Rd | 1 man/plot.coenocline.Rd | 3 -- man/showParams.Rd | 7 ++-- man/simJamil.Rd | 20 +++++++++---- man/species-response.Rd | 5 +-- man/stack.coenocline.Rd | 1 tests/Examples/coenocliner-Ex.Rout.save | 26 +++++++++-------- vignettes/coenocliner.Rnw | 4 +- 25 files changed, 127 insertions(+), 109 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-10-22 1.2
2014-06-25 1.1
2012-04-16 1.0