Title: Predictive Data Analysis System
Description: Perform a supervised data analysis on a database through a 'shiny' graphical interface. It includes methods such as K-Nearest Neighbors, Decision Trees, ADA Boosting, Extreme Gradient Boosting, Random Forest, Neural Networks, Deep Learning, Support Vector Machines and Bayesian Methods.
Author: Oldemar Rodriguez R. with contributions from Diego Jimenez A. and Andres Navarro D.
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between predictoR versions 1.0.9 dated 2019-05-10 and 1.1.0 dated 2019-06-24
predictoR-1.0.9/predictoR/inst/application/www/myscript.js |only predictoR-1.0.9/predictoR/inst/application/www/style_promidat.css |only predictoR-1.1.0/predictoR/DESCRIPTION | 6 +++--- predictoR-1.1.0/predictoR/MD5 | 8 ++++---- predictoR-1.1.0/predictoR/inst/application/ui.R | 6 +++--- predictoR-1.1.0/predictoR/inst/application/www/script_predictor.js |only predictoR-1.1.0/predictoR/inst/application/www/style_predictor.css |only 7 files changed, 10 insertions(+), 10 deletions(-)
Title: Protein Secondary Structure Prediction Using the Bamboo Method
Description: Implementation of the Bamboo methods described in Li, Dahl, Vannucci, Joo, and Tsai (2014) <DOI:10.1371/journal.pone.0109832>.
Author: David B. Dahl [aut, cre]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between bamboo versions 0.9.23 dated 2018-10-19 and 0.9.24 dated 2019-06-24
bamboo-0.9.23/bamboo/inst/java/scala-2.11/bamboo_2.11-0.9.23.jar |only bamboo-0.9.23/bamboo/inst/java/scala-2.12/bamboo_2.12-0.9.23.jar |only bamboo-0.9.23/bamboo/java/bamboo_2.12-0.9.23-sources.jar |only bamboo-0.9.24/bamboo/DESCRIPTION | 11 ++--- bamboo-0.9.24/bamboo/MD5 | 21 +++++----- bamboo-0.9.24/bamboo/NEWS | 4 + bamboo-0.9.24/bamboo/data/bamboo.MSA.astral30.RData |binary bamboo-0.9.24/bamboo/data/bamboo.MSA.casp9.RData |binary bamboo-0.9.24/bamboo/data/bamboo.training.RData |binary bamboo-0.9.24/bamboo/data/bamboo.validation.astral30.RData |binary bamboo-0.9.24/bamboo/data/bamboo.validation.casp9.RData |binary bamboo-0.9.24/bamboo/inst/java/scala-2.11/bamboo.jar |only bamboo-0.9.24/bamboo/inst/java/scala-2.12/bamboo.jar |only bamboo-0.9.24/bamboo/inst/java/scala-2.13 |only bamboo-0.9.24/bamboo/java/bamboo-source.jar |only 15 files changed, 21 insertions(+), 15 deletions(-)
Title: 'Htmlwidget' for 'Vega' and 'Vega-Lite'
Description: 'Vega' and 'Vega-Lite' parse text in 'JSON' notation to render
chart-specifications into 'HTML'. This package is used to facilitate the
rendering. It also provides a means to interact with signals, events,
and datasets in a 'Vega' chart using 'JavaScript' or 'Shiny'.
Author: Ian Lyttle [aut, cre] (<https://orcid.org/0000-0001-9962-4849>),
Vega/Vega-Lite Developers [aut],
Alicia Schep [ctb] (<https://orcid.org/0000-0002-3915-0618>),
Stuart Lee [ctb],
Kanit Wongsuphasawat [ctb] (Vega/Vega-Lite library),
Dominik Moritz [ctb] (Vega/Vega-Lite library),
Arvind Satyanarayan [ctb] (Vega/Vega-Lite library),
Jeffrey Heer [ctb] (Vega/Vega-Lite library),
Mike Bostock [ctb] (D3 library),
David Frank [ctb] (node-fetch library)
Maintainer: Ian Lyttle <ian.lyttle@schneider-electric.com>
Diff between vegawidget versions 0.1.0 dated 2019-01-30 and 0.2.1 dated 2019-06-24
vegawidget-0.1.0/vegawidget/R/usethis.R |only vegawidget-0.1.0/vegawidget/inst/htmlwidgets/lib/vega-embed/vega-embed-modified.js |only vegawidget-0.1.0/vegawidget/inst/htmlwidgets/lib/vega/promise.min.js |only vegawidget-0.1.0/vegawidget/inst/htmlwidgets/lib/vega/symbol.min.js |only vegawidget-0.1.0/vegawidget/inst/htmlwidgets/lib/vega/vega.js |only vegawidget-0.1.0/vegawidget/inst/schema/vega-lite/v2.6.0.json |only vegawidget-0.1.0/vegawidget/inst/schema/vega/v4.0.0.json |only vegawidget-0.1.0/vegawidget/inst/shiny-demo/data-set |only vegawidget-0.1.0/vegawidget/inst/shiny-demo/signal-set-get/readme.html |only vegawidget-0.1.0/vegawidget/tests/spec/spec_mtcars.vg.3.json |only vegawidget-0.1.0/vegawidget/tests/testthat/test-shiny.R |only vegawidget-0.2.1/vegawidget/DESCRIPTION | 29 - vegawidget-0.2.1/vegawidget/MD5 | 152 ++++---- vegawidget-0.2.1/vegawidget/NAMESPACE | 4 vegawidget-0.2.1/vegawidget/NEWS.md | 24 + vegawidget-0.2.1/vegawidget/R/autosize.R | 40 +- vegawidget-0.2.1/vegawidget/R/js-handler.R | 37 +- vegawidget-0.2.1/vegawidget/R/js-listener.R | 44 +- vegawidget-0.2.1/vegawidget/R/print.R | 121 +++++- vegawidget-0.2.1/vegawidget/R/shiny-demo.R | 2 vegawidget-0.2.1/vegawidget/R/shiny-getters.R | 72 +++- vegawidget-0.2.1/vegawidget/R/shiny-message.R | 17 vegawidget-0.2.1/vegawidget/R/shiny-setters.R | 8 vegawidget-0.2.1/vegawidget/R/sysdata.rda |binary vegawidget-0.2.1/vegawidget/R/to-image.R | 3 vegawidget-0.2.1/vegawidget/R/use-vegawidget.R | 129 ++++++- vegawidget-0.2.1/vegawidget/R/utils-vegaspec.R | 40 ++ vegawidget-0.2.1/vegawidget/R/vega-version.R | 2 vegawidget-0.2.1/vegawidget/R/vegaspec.R | 8 vegawidget-0.2.1/vegawidget/R/vegawidget.R | 49 +- vegawidget-0.2.1/vegawidget/README.md | 145 +++----- vegawidget-0.2.1/vegawidget/build |only vegawidget-0.2.1/vegawidget/data/data_category.rda |binary vegawidget-0.2.1/vegawidget/data/data_seattle_daily.rda |binary vegawidget-0.2.1/vegawidget/data/data_seattle_hourly.rda |binary vegawidget-0.2.1/vegawidget/data/spec_mtcars.rda |binary vegawidget-0.2.1/vegawidget/inst/bin/compile_spec.js | 2 vegawidget-0.2.1/vegawidget/inst/bin/vega_to_svg.js | 2 vegawidget-0.2.1/vegawidget/inst/doc |only vegawidget-0.2.1/vegawidget/inst/htmlwidgets/lib/vega-embed/vega-embed.js |only vegawidget-0.2.1/vegawidget/inst/htmlwidgets/lib/vega-lite/vega-lite.min.js | 2 vegawidget-0.2.1/vegawidget/inst/htmlwidgets/lib/vega/vega.min.js | 2 vegawidget-0.2.1/vegawidget/inst/htmlwidgets/vegawidget.js | 33 + vegawidget-0.2.1/vegawidget/inst/htmlwidgets/vegawidget.yaml | 12 vegawidget-0.2.1/vegawidget/inst/schema/vega-lite/v3.3.0.json |only vegawidget-0.2.1/vegawidget/inst/schema/vega/v5.4.0.json |only vegawidget-0.2.1/vegawidget/inst/shiny-demo/data-set-get |only vegawidget-0.2.1/vegawidget/inst/shiny-demo/event-get/server.R | 2 vegawidget-0.2.1/vegawidget/inst/shiny-demo/signal-set-get/DESCRIPTION | 2 vegawidget-0.2.1/vegawidget/inst/templates/utils-vegawidget-class.R |only vegawidget-0.2.1/vegawidget/inst/templates/utils-vegawidget-interactive.R |only vegawidget-0.2.1/vegawidget/inst/templates/utils-vegawidget.R | 179 +--------- vegawidget-0.2.1/vegawidget/inst/tutorials/overview/tutorial-overview.Rmd | 10 vegawidget-0.2.1/vegawidget/man/add-listeners.Rd | 23 - vegawidget-0.2.1/vegawidget/man/as_vegaspec.Rd | 6 vegawidget-0.2.1/vegawidget/man/figures/README-vegawidget-1.png |binary vegawidget-0.2.1/vegawidget/man/figures/README-vegawidget-1.svg |only vegawidget-0.2.1/vegawidget/man/figures/autosize-off.png |binary vegawidget-0.2.1/vegawidget/man/image.Rd | 5 vegawidget-0.2.1/vegawidget/man/knit_print.vegaspec.Rd | 51 ++ vegawidget-0.2.1/vegawidget/man/shiny-getters.Rd | 31 + vegawidget-0.2.1/vegawidget/man/shiny-setters.Rd | 2 vegawidget-0.2.1/vegawidget/man/use_vegawidget.Rd | 55 ++- vegawidget-0.2.1/vegawidget/man/vegawidget.Rd | 8 vegawidget-0.2.1/vegawidget/man/vw_as_json.Rd | 2 vegawidget-0.2.1/vegawidget/man/vw_autosize.Rd | 4 vegawidget-0.2.1/vegawidget/man/vw_examine.Rd | 2 vegawidget-0.2.1/vegawidget/man/vw_handler_signal.Rd | 14 vegawidget-0.2.1/vegawidget/man/vw_rename_datasets.Rd | 2 vegawidget-0.2.1/vegawidget/man/vw_shiny_demo.Rd | 2 vegawidget-0.2.1/vegawidget/man/vw_spec_version.Rd | 2 vegawidget-0.2.1/vegawidget/man/vw_to_vega.Rd | 2 vegawidget-0.2.1/vegawidget/tests/reference/mtcars.svg | 2 vegawidget-0.2.1/vegawidget/tests/spec/spec_mtcars.vg.5.json |only vegawidget-0.2.1/vegawidget/tests/testthat/test-autosize.R | 13 vegawidget-0.2.1/vegawidget/tests/testthat/test-spec-version.R | 10 vegawidget-0.2.1/vegawidget/tests/testthat/test-to-image.R | 2 vegawidget-0.2.1/vegawidget/tests/testthat/test-to-vega.R | 4 vegawidget-0.2.1/vegawidget/tests/testthat/test-vega-version.R | 14 vegawidget-0.2.1/vegawidget/vignettes |only 80 files changed, 882 insertions(+), 546 deletions(-)
Title: R Package Installation from Remote Repositories, Including
'GitHub'
Description: Download and install R packages stored in 'GitHub',
'BitBucket', or plain 'subversion' or 'git' repositories. This package
provides the 'install_*' functions in 'devtools'.
Indeed most of the code was copied over from 'devtools'.
Author: Jim Hester [aut, cre],
Gábor Csárdi [aut],
Hadley Wickham [aut],
Winston Chang [aut],
RStudio [cph],
Martin Morgan [aut],
Dan Tenenbaum [aut],
Mango Solutions [cph]
Maintainer: Jim Hester <james.hester@rstudio.com>
Diff between remotes versions 2.0.4 dated 2019-04-10 and 2.1.0 dated 2019-06-24
DESCRIPTION | 12 MD5 | 121 NAMESPACE | 2 NEWS.md | 68 R/bioc-standalone.R |only R/bioc.R | 149 R/decompress.R | 2 R/deps.R | 66 R/download.R | 189 R/github.R | 12 R/install-bioc.R | 13 R/install-bitbucket.R | 11 R/install-cran.R | 3 R/install-dev.R | 14 R/install-git.R | 36 R/install-github.R | 25 R/install-gitlab.R | 34 R/install-local.R | 10 R/install-remote.R | 40 R/install-svn.R | 5 R/install-url.R | 3 R/install-version.R | 9 R/install.R | 78 R/json.R | 279 - R/package-deps.R | 4 R/parse-git.R | 1 R/submodule.R | 4 R/utils.R | 38 README.md | 9 build/vignette.rds |binary inst/doc/dependencies.html | 4 inst/install-github.R | 9432 ++++++++++++++++++---------------- inst/install-github.Rin | 17 man/bioc_install_repos.Rd | 45 man/download.Rd |only man/git_credentials.Rd |only man/install_bioc.Rd | 15 man/install_bitbucket.Rd | 9 man/install_cran.Rd | 9 man/install_deps.Rd | 9 man/install_git.Rd | 20 man/install_github.Rd | 11 man/install_gitlab.Rd | 9 man/install_local.Rd | 9 man/install_svn.Rd | 11 man/install_url.Rd | 9 man/install_version.Rd | 14 man/package_deps.Rd | 9 man/parse-git-repo.Rd | 1 man/update_packages.Rd | 9 tests/testthat/helper.R | 2 tests/testthat/test-bioc.R | 90 tests/testthat/test-deps.R | 16 tests/testthat/test-download.R | 189 tests/testthat/test-install-git.R | 70 tests/testthat/test-install-github.R | 26 tests/testthat/test-install-local.R | 30 tests/testthat/test-install-version.R | 17 tests/testthat/test-install.R | 89 tests/testthat/test-json.R | 53 tests/testthat/test-package-deps.R | 11 tests/testthat/test-submodule.R | 23 tests/testthat/test-utils.R | 12 63 files changed, 6531 insertions(+), 4976 deletions(-)
Title: Text to Speech
Description: Unifies different text to speech engines, such as
Google, Microsoft, and Amazon. Text synthesis can be done
in any engine with a simple switch of an argument denoting
the service requested.
Author: John Muschelli [aut, cre] (<https://orcid.org/0000-0001-6469-1750>)
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between text2speech versions 0.2.4 dated 2019-06-14 and 0.2.5 dated 2019-06-24
DESCRIPTION | 6 MD5 | 12 - NEWS.md | 4 R/tts_voices.R | 21 ++ README.md | 20 +- build/vignette.rds |binary inst/doc/listing_voices.html | 374 +++++++++++++++++++++---------------------- 7 files changed, 231 insertions(+), 206 deletions(-)
Title: Permutation Tests for Nonparametric Statistics
Description: Performs a permutation test on the difference between two location parameters, a permutation correlation test, a permutation F-test, the Siegel-Tukey test, a ratio mean deviance test. Also performs some graphing techniques, such as for confidence intervals, vector addition, and Fourier analysis; and includes functions related to the Laplace (double exponential) and triangular distributions. Performs power calculations for the binomial test.
Author: Steven T. Garren [aut, cre]
Maintainer: Steven T. Garren <GARRENST@JMU.EDU>
Diff between jmuOutlier versions 1.4 dated 2018-01-26 and 1.5 dated 2019-06-24
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++++---- NAMESPACE | 2 +- R/coin.toss.R |only R/latin.R |only build/partial.rdb |binary man/coin.toss.Rd |only man/jmuOutlier-package.Rd | 2 ++ man/latin.Rd |only 9 files changed, 16 insertions(+), 9 deletions(-)
Title: Fast Drawing and Shading of Graphs of Statistical Distributions
Description: Provides functionality to produce graphs of probability density functions and cumulative distribution functions with few keystrokes, allows shading under the curve of the probability density function to illustrate concepts such as p-values and critical values, and fits a simple linear regression line on a scatter plot with the equation as the main title.
Author: Steven T. Garren [aut, cre]
Maintainer: Steven T. Garren <garrenst@jmu.edu>
Diff between fastGraph versions 1.1 dated 2016-07-07 and 1.3 dated 2019-06-24
DESCRIPTION | 8 ++--- MD5 | 12 +++---- R/fastGraph.R | 73 ++++++++++++++++++++++++++++++----------------- man/fastGraph-package.Rd | 4 +- man/plotDist.Rd | 14 +++++---- man/shadeDist.Rd | 41 ++++++++++++++------------ man/shadePhat.Rd | 10 +++--- 7 files changed, 97 insertions(+), 65 deletions(-)
Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre],
Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>
Diff between SSDforR versions 1.5.5 dated 2019-06-17 and 1.5.6 dated 2019-06-24
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/ABma.R | 4 ++-- R/Append.R | 4 ++-- R/Effectsize.R | 10 ++++++---- R/diffchart.R | 4 ++-- 6 files changed, 21 insertions(+), 19 deletions(-)
Title: Unit Root Tests for Seasonal Time Series
Description: Seasonal unit roots and seasonal stability tests.
P-values based on response surface regressions are available for both tests.
P-values based on bootstrap are available for seasonal unit root tests.
A parallel implementation of the bootstrap method requires a CUDA capable GPU
with compute capability >= 3.0, otherwise a debugging version fully coded in R is used.
Author: Javier López-de-Lacalle [aut],
Georgi N. Boshnakov [cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between uroot versions 2.0-9.1 dated 2019-03-24 and 2.0-10 dated 2019-06-24
uroot-2.0-10/uroot/DESCRIPTION | 24 ++++---- uroot-2.0-10/uroot/MD5 | 28 +++++----- uroot-2.0-10/uroot/NAMESPACE | 2 uroot-2.0-10/uroot/NEWS | 19 +++++++ uroot-2.0-10/uroot/README | 5 + uroot-2.0-10/uroot/build/vignette.rds |binary uroot-2.0-10/uroot/cleanup | 1 uroot-2.0-10/uroot/cleanup.win | 1 uroot-2.0-10/uroot/configure | 75 ++++++++++++++++++---------- uroot-2.0-10/uroot/configure.ac | 39 ++++++++------ uroot-2.0-10/uroot/configure.win | 2 uroot-2.0-10/uroot/inst/doc/index.html | 6 +- uroot-2.0-10/uroot/inst/doc/uroot-intro.pdf |binary uroot-2.0-10/uroot/man/uroot-package.Rd | 6 +- uroot-2.0-10/uroot/src/dummy.cpp.in |only uroot-2.0-9.1/uroot/src/dummy.cpp |only 16 files changed, 136 insertions(+), 72 deletions(-)
Title: EMF Graphics Output Device
Description: Output graphics to EMF+/EMF.
Author: Philip Johnson
Maintainer: Philip Johnson <plfj@umd.edu>
Diff between devEMF versions 3.6-2 dated 2019-01-03 and 3.6-3 dated 2019-06-24
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 10 ++++++++++ R/emf.R | 3 +++ src/devEMF.cpp | 10 +++++----- src/emf+.h | 8 ++++---- src/emf.h | 6 +++++- src/fontmetrics.h | 14 +++++++------- 8 files changed, 45 insertions(+), 28 deletions(-)
Title: Polygonal Symbolic Data Analysis
Description: A toolbox in symbolic data framework as a statistical learning and data mining solution for symbolic polygonal data analysis. This study is a new approach in data analysis and it was proposed by
Silva et al. (2019) <doi:10.1016/j.knosys.2018.08.009>. The package presents the estimation of main descriptive statistical measures, e.g, mean, covariance, variance, correlation and coefficient of variation.
In addition, a method to obtain polygonal data from classical data is presented. Empirical probability distribution function based on symbolic polygonal histogram and a regression model with its main measures are presented.
Author: Wagner Silva [aut, cre, ths],
Renata Souza [aut],
Francisco Cysneiros [aut]
Maintainer: Wagner Silva <wjfs@cin.ufpe.br>
Diff between psda versions 1.3.1 dated 2019-03-22 and 1.3.2 dated 2019-06-24
DESCRIPTION | 14 +++++++------- MD5 | 16 ++++++++-------- R/plr.R | 4 +--- R/print.summary.plr.R | 20 +------------------- R/psymbolic.R | 8 ++++++-- R/summary.plr.R | 45 ++++++++++++++------------------------------- man/plr.Rd | 2 -- man/psymbolic.Rd | 2 +- man/summary.plr.Rd | 15 ++++----------- 9 files changed, 42 insertions(+), 84 deletions(-)
Title: Visual Regression Testing and Graphical Diffing
Description: An extension to the 'testthat' package that makes it easy
to add graphical unit tests. It provides a Shiny application to
manage the test cases.
Author: Lionel Henry [cre, aut],
RStudio [cph],
Carl Sutherland [aut] (jg-imagediff library),
Humble Software [cph] (jg-imagediff library),
David Hong [aut] (TwoFace library),
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/htmlwidgets/lib/jquery-authors.txt),
T Jake Luciani [aut] (svglite),
Matthieu Decorde [aut] (svglite),
Vaudor Lise [aut] (svglite),
Tony Plate [ctb] (svglite: Early line dashing code),
David Gohel [ctb] (svglite: Line dashing code and raster code),
Yixuan Qiu [ctb] (svglite: Improved styles; polypath implementation),
Håkon Malmedal [ctb] (svglite: Opacity code)
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between vdiffr versions 0.3.0 dated 2019-01-02 and 0.3.1 dated 2019-06-24
DESCRIPTION | 8 - MD5 | 34 ++-- NEWS.md | 15 ++ R/cases-ui.R | 4 R/cases.R | 6 R/shiny-server.R | 46 +++++- R/shiny-ui.R | 1 R/testthat-reporter.R | 9 + R/testthat-ui.R | 3 R/utils.R | 2 README.md | 10 - inst/www/toggle.js | 7 tests/mock.Rout.fail | 74 +++++----- tests/testthat/mock-pkg/tests/figs/deps.txt | 2 tests/testthat/mock-pkg/tests/figs/ggplot/some-title.svg | 8 - tests/testthat/mock-pkg/tests/figs/myplot.svg | 110 +++++++-------- tests/testthat/mock-pkg/tests/testthat/test-failed.R | 2 tests/testthat/test-cases.R | 6 18 files changed, 208 insertions(+), 139 deletions(-)
Title: Pivotal Methods for Bayesian Relabelling and k-Means Clustering
Description: Collection of pivotal algorithms
for: relabelling the MCMC chains in order to undo the label
switching problem in Bayesian mixture models,
as proposed in Egidi, Pappadà, Pauli and Torelli (2018a)<doi:10.1007/s11222-017-9774-2>;
initializing the centers of the classical k-means algorithm
in order to obtain a better clustering solution. For further details see
Egidi, Pappadà, Pauli and Torelli (2018b)<ISBN:9788891910233>.
Author: Leonardo Egidi[aut, cre],
Roberta Pappadà[aut],
Francesco Pauli[aut],
Nicola Torelli[aut]
Maintainer: Leonardo Egidi <legidi@units.it>
Diff between pivmet versions 0.1.1 dated 2019-02-26 and 0.2.0 dated 2019-06-24
DESCRIPTION | 12 MD5 | 58 NAMESPACE | 49 NEWS.md | 9 R/bayes_mcmc.R | 920 +++++++--- R/mus.R | 643 ++++-- R/musk.R | 442 +++- R/pivotal.R | 38 R/plot.R | 592 +++--- R/relab.R | 123 - R/sim.R | 102 - README.md | 22 inst/doc/K-means_clustering_using_the_MUS_algorithm.R | 26 inst/doc/K-means_clustering_using_the_MUS_algorithm.Rmd | 53 inst/doc/K-means_clustering_using_the_MUS_algorithm.html | 86 inst/doc/Relabelling_in_Bayesian_mixtures_by_pivotal_units.R | 55 inst/doc/Relabelling_in_Bayesian_mixtures_by_pivotal_units.Rmd | 213 +- inst/doc/Relabelling_in_Bayesian_mixtures_by_pivotal_units.html | 292 ++- man/MUS.Rd | 36 man/figures/README-plot-1.png |binary man/figures/README-plot-2.png |binary man/piv_KMeans.Rd | 60 man/piv_MCMC.Rd | 187 +- man/piv_plot.Rd | 28 man/piv_rel.Rd | 43 man/piv_sel.Rd | 24 man/piv_sim.Rd | 42 vignettes/K-means_clustering_using_the_MUS_algorithm.Rmd | 53 vignettes/Relabelling_in_Bayesian_mixtures_by_pivotal_units.Rmd | 213 +- vignettes/ref.bib | 62 30 files changed, 3124 insertions(+), 1359 deletions(-)
Title: Horizontal 'ggplot2' Components
Description: A 'ggplot2' extension that provides flipped components:
horizontal versions of 'Stats' and 'Geoms', and vertical versions
of 'Positions'.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
Winston Chang [aut],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between ggstance versions 0.3.1 dated 2018-07-20 and 0.3.2 dated 2019-06-24
DESCRIPTION | 13 MD5 | 120 NEWS.md | 11 R/geom-barh.R | 1 R/geom-boxploth.R | 1 R/geom-colh.R | 1 R/geom-crossbarh.R | 1 R/geom-errorbarh.R | 16 R/geom-linerangeh.R | 1 R/geom-pointrangeh.R | 1 R/geom-violinh.R | 1 R/ggstance.R | 9 R/position-jitterdodgev.R | 2 R/position-stackv.R | 2 R/stat-binh.R | 2 R/stat-boxploth.R | 1 R/stat-counth.R | 1 R/stat-summaryh.R | 1 R/stat-xdensity.R | 1 README.md | 12 man/geom_barh.Rd | 46 man/geom_boxploth.Rd | 41 man/geom_histogramh.Rd | 20 man/geom_linerangeh.Rd | 81 man/geom_violinh.Rd | 27 man/position-vertical.Rd | 2 man/stat_binh.Rd | 64 man/stat_boxploth.Rd | 18 man/stat_counth.Rd | 23 man/stat_summaryh.Rd | 24 man/stat_xdensity.Rd | 18 tests/figs/deps.txt | 5 tests/figs/geom-errorbarh |only tests/figs/geoms/facet-grid-with-free-scales.svg | 122 tests/figs/geoms/geom-barh-facet-wrap.svg | 102 tests/figs/geoms/geom-barh-with-count-stat.svg | 72 tests/figs/geoms/geom-barh.svg | 70 tests/figs/geoms/geom-boxploth-and-continuous-y-scale.svg | 50 tests/figs/geoms/geom-boxploth-facet-wrap-with-fill.svg | 1502 +++++----- tests/figs/geoms/geom-boxploth-with-fill.svg | 284 - tests/figs/geoms/geom-boxploth.svg | 148 tests/figs/geoms/geom-colh.svg | 48 tests/figs/geoms/geom-crossbarh.svg | 78 tests/figs/geoms/geom-errorbarh.svg | 82 tests/figs/geoms/geom-histogramh-position-nudge-with-fill.svg | 244 - tests/figs/geoms/geom-histogramh-position-stack-with-fill.svg | 136 tests/figs/geoms/geom-histogramh.svg | 74 tests/figs/geoms/geom-linerangeh.svg | 66 tests/figs/geoms/geom-pointrangeh-facet-wrap.svg | 102 tests/figs/geoms/geom-pointrangeh-position-dodgev.svg | 78 tests/figs/geoms/geom-pointrangeh.svg | 78 tests/figs/geoms/geom-violinh-draw-quantiles.svg | 78 tests/figs/geoms/geom-violinh-facet-wrap.svg | 124 tests/figs/geoms/geom-violinh.svg | 76 tests/figs/geoms/scales.svg | 78 tests/figs/positions/position-dodge.svg | 114 tests/figs/positions/position-jitterdodge.svg | 296 - tests/figs/positions/position-stackv-with-hjust-argument.svg | 82 tests/figs/stats/stat-summaryh-with-fun-data.svg | 66 tests/figs/stats/stat-summaryh-with-fun-x.svg | 54 tests/figs/stats/stat-summaryh-with-median-hilow-h.svg | 58 tests/testthat/test-geom-errorbarh.R |only 62 files changed, 2600 insertions(+), 2329 deletions(-)
Title: Structural Data for Norway
Description: Provides structural data for Norway. Datasets relating to maps, population in municipalities, vaccination coverage for childhood vaccines, municipality/county matching, and how different municipalities have merged/redistricted over time from 2006 to 2019.
Author: Richard White [aut, cre]
Maintainer: Richard White <w@rwhite.no>
Diff between fhidata versions 2019.5.19 dated 2019-05-21 and 2019.6.24 dated 2019-06-24
DESCRIPTION | 10 +++---- MD5 | 23 +++++++++-------- NEWS.md | 6 +++- R/aa_environments.r | 2 - R/data_gen_all.r | 3 ++ R/data_norway_childhood_vax.r |only R/onAttach.R | 2 - data/datalist | 1 data/norway_childhood_vax.rda |only inst/doc/datasets.R | 3 ++ inst/doc/datasets.Rmd | 10 +++++++ inst/doc/datasets.html | 55 ++++++++++++++++++++++++++++-------------- man/norway_childhood_vax.Rd |only vignettes/datasets.Rmd | 10 +++++++ 14 files changed, 89 insertions(+), 36 deletions(-)
Title: Bootstrap Methods for Various Network Estimation Routines
Description: Bootstrap methods to assess accuracy and stability of estimated network structures
and centrality indices. Allows for flexible specification of any undirected network
estimation procedure in R, and offers default sets for 'qgraph', 'IsingFit', 'IsingSampler',
'glasso', 'huge' and 'parcor' packages.
Author: Sacha Epskamp [aut, cre],
Eiko I. Fried [ctb]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between bootnet versions 1.2.2 dated 2019-05-09 and 1.2.3 dated 2019-06-24
bootnet-1.2.2/bootnet/R/checkDefault.R |only bootnet-1.2.3/bootnet/DESCRIPTION | 8 ++++---- bootnet-1.2.3/bootnet/MD5 | 21 ++++++++++----------- bootnet-1.2.3/bootnet/NEWS | 4 ++++ bootnet-1.2.3/bootnet/R/plotMethod.R | 4 ++++ bootnet-1.2.3/bootnet/man/bootInclude.Rd | 4 ++-- bootnet-1.2.3/bootnet/man/bootThreshold.Rd | 4 ++-- bootnet-1.2.3/bootnet/man/bootnet.Rd | 4 ++-- bootnet-1.2.3/bootnet/man/corStability.Rd | 4 ++-- bootnet-1.2.3/bootnet/man/differenceTest.Rd | 4 ++-- bootnet-1.2.3/bootnet/man/estimateNetwork.Rd | 4 ++-- bootnet-1.2.3/bootnet/man/netSimulator.Rd | 2 +- 12 files changed, 35 insertions(+), 28 deletions(-)
Title: Visible Vowels: Visualization of Vowel Variation
Description: Visualizes vowel variation in f0, F1, F2, F3 and duration.
Author: Wilbert Heeringa, Hans Van de Velde
Maintainer: Wilbert Heeringa <wjheeringa@gmail.com>
Diff between visvow versions 0.4.0 dated 2019-01-25 and 0.5.0 dated 2019-06-24
DESCRIPTION | 12 ++++---- MD5 | 8 ++--- R/visvow.R | 75 +++++++++++++++++++++++++++++++++++++++++++++++------ build/partial.rdb |binary build/vignette.rds |binary 5 files changed, 77 insertions(+), 18 deletions(-)
Title: Rendering Parameterized SQL and Translation to Dialects
Description: A rendering tool for parameterized SQL that also translates into
different SQL dialects. These dialects include 'Microsoft Sql Server', 'Oracle',
'PostgreSql', 'Amazon RedShift', 'Apache Impala', 'IBM Netezza', 'Google BigQuery', 'Microsoft PDW', and 'SQLite'.
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between SqlRender versions 1.6.0 dated 2019-02-15 and 1.6.2 dated 2019-06-24
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 24 ++++++++++++++++++++++++ README.md | 2 +- build/vignette.rds |binary inst/csv/replacementPatterns.csv | 5 ++++- inst/doc/UsingSqlRender.pdf |binary inst/java/SqlRender.jar |binary java/org/ohdsi/sql/BigQueryTranslate.java | 2 +- tests/testthat/test-translateSql.R | 28 ++++++++++++++++++++-------- 10 files changed, 63 insertions(+), 24 deletions(-)
Title: Multivariate Extreme Value Distributions
Description: Exact simulation from max-stable processes, R-Pareto processes for various parametric models. Threshold selection methods. Multivariate extreme diagnostics. Estimation and likelihoods for univariate extremes.
Author: Leo Belzile [aut, cre] (<https://orcid.org/0000-0002-9135-014X>),
Jennifer L. Wadsworth [aut],
Paul J. Northrop [aut],
Scott D. Grimshaw [aut],
Jin Zhang [ctb],
Michael A. Stephens [ctb],
Art B. Owen [ctb],
Raphael Huser [aut]
Maintainer: Leo Belzile <belzilel@gmail.com>
Diff between mev versions 1.11 dated 2018-02-22 and 1.12 dated 2019-06-24
mev-1.11/mev/R/bivpot_methods.R |only mev-1.11/mev/R/infomat_test.R |only mev-1.11/mev/R/rmev_wrapper.R |only mev-1.11/mev/man/confint.extprof.Rd |only mev-1.11/mev/man/confint.fr.Rd |only mev-1.11/mev/man/egp2-functions.Rd |only mev-1.11/mev/man/egp2.G.Rd |only mev-1.11/mev/man/egp2.Rd |only mev-1.11/mev/man/mev-package.Rd |only mev-1.11/mev/man/plot.extprof.Rd |only mev-1.11/mev/src/emp_lik.cpp |only mev-1.11/mev/src/ev_sampling.cpp |only mev-1.11/mev/src/gp_bayes.cpp |only mev-1.12/mev/DESCRIPTION | 28 mev-1.12/mev/MD5 | 265 + mev-1.12/mev/NAMESPACE | 107 mev-1.12/mev/NEWS | 42 mev-1.12/mev/R/NCdiag.R |only mev-1.12/mev/R/RcppExports.R | 188 - mev-1.12/mev/R/Wdiag.R | 962 ++----- mev-1.12/mev/R/bias.R | 948 ++++--- mev-1.12/mev/R/bivpot.R |only mev-1.12/mev/R/datasets.R |only mev-1.12/mev/R/egp.R | 1667 ++++++------ mev-1.12/mev/R/extcoef.R |only mev-1.12/mev/R/extremogram.R |only mev-1.12/mev/R/gp.R | 2755 ++++++++------------ mev-1.12/mev/R/infomattest.R |only mev-1.12/mev/R/maxstabtest.R |only mev-1.12/mev/R/mgplikelihoods.R |only mev-1.12/mev/R/mle.R |only mev-1.12/mev/R/multivar.R | 285 +- mev-1.12/mev/R/packageImports.R | 25 mev-1.12/mev/R/penultimate.R | 1004 ++++--- mev-1.12/mev/R/profile.R | 3778 ++++++++++++++-------------- mev-1.12/mev/R/rgparp.R |only mev-1.12/mev/R/rmev.R |only mev-1.12/mev/R/rparpcs.R |only mev-1.12/mev/R/spatial.R |only mev-1.12/mev/R/specdens.R | 443 +-- mev-1.12/mev/R/spunif.R |only mev-1.12/mev/R/taildep.R |only mev-1.12/mev/R/threshold.R |only mev-1.12/mev/R/univdist.R | 2404 +++++++++++++---- mev-1.12/mev/build/vignette.rds |binary mev-1.12/mev/data |only mev-1.12/mev/inst/doc/mev-vignette.Rnw | 4 mev-1.12/mev/inst/doc/mev-vignette.pdf |binary mev-1.12/mev/inst/include/mev_RcppExports.h | 177 + mev-1.12/mev/man/Lambda2cov.Rd |only mev-1.12/mev/man/NC.diag.Rd | 11 mev-1.12/mev/man/W.diag.Rd | 35 mev-1.12/mev/man/angextrapo.Rd | 4 mev-1.12/mev/man/angmeas.Rd | 21 mev-1.12/mev/man/angmeasdir.Rd | 15 mev-1.12/mev/man/chibar.Rd | 34 mev-1.12/mev/man/clikmgp.Rd |only mev-1.12/mev/man/confint.eprof.Rd |only mev-1.12/mev/man/distg.Rd |only mev-1.12/mev/man/dot-C1.Rd |only mev-1.12/mev/man/dot-Joint_MLE_Expl.Rd |only mev-1.12/mev/man/dot-Joint_MLE_NHPP.Rd |only mev-1.12/mev/man/dot-exp_info_algebraic.Rd |only mev-1.12/mev/man/dot-fit.gpd.grimshaw.Rd |only mev-1.12/mev/man/dot-fit.gpd.rob.Rd |only mev-1.12/mev/man/dot-gev.postpred.Rd |only mev-1.12/mev/man/dot-is.CNSD.Rd |only mev-1.12/mev/man/dot-mvasym.check.Rd |only mev-1.12/mev/man/dot-mvrnorm_arma.Rd |only mev-1.12/mev/man/dot-rPBrownResnick.Rd |only mev-1.12/mev/man/dot-rPHuslerReiss.Rd |only mev-1.12/mev/man/dot-rPSmith.Rd |only mev-1.12/mev/man/dot-rPbilog.Rd |only mev-1.12/mev/man/dot-rPdir.Rd |only mev-1.12/mev/man/dot-rPdirmix.Rd |only mev-1.12/mev/man/dot-rPexstud.Rd |only mev-1.12/mev/man/dot-rPlog.Rd |only mev-1.12/mev/man/dot-rPneglog.Rd |only mev-1.12/mev/man/dot-rPsite.Rd |only mev-1.12/mev/man/dot-rbilogspec.Rd |only mev-1.12/mev/man/dot-rbrspec.Rd |only mev-1.12/mev/man/dot-rdirmixspec.Rd |only mev-1.12/mev/man/dot-rdirspec.Rd |only mev-1.12/mev/man/dot-rexstudspec.Rd |only mev-1.12/mev/man/dot-rhrspec.Rd |only mev-1.12/mev/man/dot-rlogspec.Rd |only mev-1.12/mev/man/dot-rmevA1.Rd |only mev-1.12/mev/man/dot-rmevA2.Rd |only mev-1.12/mev/man/dot-rmevasy.Rd |only mev-1.12/mev/man/dot-rmevspec_cpp.Rd |only mev-1.12/mev/man/dot-rneglogspec.Rd |only mev-1.12/mev/man/dot-rsmithspec.Rd |only mev-1.12/mev/man/dot-score_algebraic.Rd |only mev-1.12/mev/man/dot-wecdf.Rd |only mev-1.12/mev/man/egp-function.Rd | 1 mev-1.12/mev/man/egp.Rd | 29 mev-1.12/mev/man/egp.fit.Rd | 43 mev-1.12/mev/man/egp.fitrange.Rd |only mev-1.12/mev/man/egp2.fit.Rd | 43 mev-1.12/mev/man/emplik.Rd | 2 mev-1.12/mev/man/eskrain.Rd |only mev-1.12/mev/man/expme.Rd |only mev-1.12/mev/man/ext.index.Rd | 14 mev-1.12/mev/man/extcoef.Rd |only mev-1.12/mev/man/extgp-functions.Rd |only mev-1.12/mev/man/extgp.G.Rd |only mev-1.12/mev/man/extgp.Rd |only mev-1.12/mev/man/extremo.Rd |only mev-1.12/mev/man/fit.egp.Rd |only mev-1.12/mev/man/fit.extgp.Rd |only mev-1.12/mev/man/fit.gev.Rd |only mev-1.12/mev/man/fit.gpd.Rd |only mev-1.12/mev/man/fit.pp.Rd |only mev-1.12/mev/man/fit.rlarg.Rd |only mev-1.12/mev/man/gev.Fscore.Rd | 2 mev-1.12/mev/man/gev.Rd | 6 mev-1.12/mev/man/gev.bcor.Rd | 31 mev-1.12/mev/man/gev.bias.Rd | 4 mev-1.12/mev/man/gev.infomat.Rd | 2 mev-1.12/mev/man/gev.mle.Rd | 16 mev-1.12/mev/man/gev.pll.Rd | 27 mev-1.12/mev/man/gev.tem.Rd | 23 mev-1.12/mev/man/gevN.Rd | 14 mev-1.12/mev/man/gevN.temstat.Rd | 2 mev-1.12/mev/man/gevr.Rd | 4 mev-1.12/mev/man/gevr.infomat.Rd | 2 mev-1.12/mev/man/gevr.ll.Rd | 2 mev-1.12/mev/man/gevr.temstat.Rd | 4 mev-1.12/mev/man/gp.fit.Rd | 81 mev-1.12/mev/man/gpd.Fscore.Rd | 2 mev-1.12/mev/man/gpd.Rd | 6 mev-1.12/mev/man/gpd.bcor.Rd | 33 mev-1.12/mev/man/gpd.infomat.Rd | 2 mev-1.12/mev/man/gpd.mle.Rd | 14 mev-1.12/mev/man/gpd.pll.Rd | 33 mev-1.12/mev/man/gpd.tem.Rd | 18 mev-1.12/mev/man/gpdN.Rd | 2 mev-1.12/mev/man/gpdN.temstat.Rd | 2 mev-1.12/mev/man/gpde.Rd | 4 mev-1.12/mev/man/gpde.infomat.Rd | 2 mev-1.12/mev/man/gpde.ll.Rd | 2 mev-1.12/mev/man/gpde.temstat.Rd | 2 mev-1.12/mev/man/gpdr.Rd | 4 mev-1.12/mev/man/gpdr.infomat.Rd | 2 mev-1.12/mev/man/gpdr.ll.Rd | 6 mev-1.12/mev/man/gpdr.temstat.Rd | 4 mev-1.12/mev/man/gpdtopar.Rd |only mev-1.12/mev/man/ibvpot.Rd | 6 mev-1.12/mev/man/infomat.test.Rd | 4 mev-1.12/mev/man/intensBR.Rd |only mev-1.12/mev/man/intensXstud.Rd |only mev-1.12/mev/man/jac.Rd |only mev-1.12/mev/man/lambdadep.Rd | 13 mev-1.12/mev/man/likmgp.Rd |only mev-1.12/mev/man/maiquetia.Rd |only mev-1.12/mev/man/maxstabtest.Rd |only mev-1.12/mev/man/nidd.Rd |only mev-1.12/mev/man/plot.eprof.Rd |only mev-1.12/mev/man/power.vario.Rd |only mev-1.12/mev/man/powerexp.cor.Rd |only mev-1.12/mev/man/pp.Rd |only mev-1.12/mev/man/rgparp.Rd |only mev-1.12/mev/man/rlarg.Rd |only mev-1.12/mev/man/rlarg.ll.Rd |only mev-1.12/mev/man/rlarg.score.Rd |only mev-1.12/mev/man/rmev.Rd | 52 mev-1.12/mev/man/rmevspec.Rd | 28 mev-1.12/mev/man/rparp.Rd | 32 mev-1.12/mev/man/rparpcs.Rd |only mev-1.12/mev/man/rparpcshr.Rd |only mev-1.12/mev/man/rrlarg.Rd |only mev-1.12/mev/man/schlather.vario.Rd |only mev-1.12/mev/man/smith.penult.Rd | 67 mev-1.12/mev/man/smith.penult.fn.Rd | 60 mev-1.12/mev/man/spline.corr.Rd | 2 mev-1.12/mev/man/spunif.Rd |only mev-1.12/mev/man/taildep.Rd |only mev-1.12/mev/man/tstab.gpd.Rd |only mev-1.12/mev/man/venice.Rd |only mev-1.12/mev/man/w1500m.Rd |only mev-1.12/mev/src/Makevars | 1 mev-1.12/mev/src/Makevars.win |only mev-1.12/mev/src/RcppExports.cpp | 349 ++ mev-1.12/mev/src/auxiliary_fun.cpp |only mev-1.12/mev/src/emplik.cpp |only mev-1.12/mev/src/gpdbayes.cpp |only mev-1.12/mev/src/sampling.cpp |only mev-1.12/mev/vignettes/mev-vignette.Rnw | 4 188 files changed, 8971 insertions(+), 7339 deletions(-)
Title: Advanced Forest Plot Using 'grid' Graphics
Description: A forest plot that allows for
multiple confidence intervals per row,
custom fonts for each text element,
custom confidence intervals,
text mixed with expressions, and more.
The aim is to extend the use of forest plots beyond meta-analyses.
This is a more general version of the original 'rmeta' package's forestplot()
function and relies heavily on the 'grid' package.
Author: Max Gordon [aut, cre],
Thomas Lumley [aut, ctb]
Maintainer: Max Gordon <max@gforge.se>
Diff between forestplot versions 1.8 dated 2019-06-01 and 1.9 dated 2019-06-24
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 4 ++++ R/forestplot.R | 6 ++++-- R/private.R | 2 +- inst/doc/forestplot.html | 4 ++-- 6 files changed, 20 insertions(+), 14 deletions(-)
Title: Local Interpretable Model-Agnostic Explanations
Description: When building complex models, it is often difficult to explain why
the model should be trusted. While global measures such as accuracy are
useful, they cannot be used for explaining why a model made a specific
prediction. 'lime' (a port of the 'lime' 'Python' package) is a method for
explaining the outcome of black box models by fitting a local model around
the point in question an perturbations of this point. The approach is
described in more detail in the article by Ribeiro et al. (2016)
<arXiv:1602.04938>.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>),
Michaël Benesty [aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between lime versions 0.4.1 dated 2018-11-21 and 0.5.0 dated 2019-06-24
lime-0.4.1/lime/R/dataframe.R |only lime-0.5.0/lime/DESCRIPTION | 27 lime-0.5.0/lime/MD5 | 72 - lime-0.5.0/lime/NAMESPACE | 1 lime-0.5.0/lime/NEWS.md | 17 lime-0.5.0/lime/R/a_dataframe.R |only lime-0.5.0/lime/R/character.R | 15 lime-0.5.0/lime/R/data.R | 6 lime-0.5.0/lime/R/explain.R | 2 lime-0.5.0/lime/R/image.R | 4 lime-0.5.0/lime/R/lime.R | 9 lime-0.5.0/lime/R/permute_cases.R | 2 lime-0.5.0/lime/R/plot.R | 16 lime-0.5.0/lime/R/plot_image.R | 2 lime-0.5.0/lime/R/plot_text.R | 5 lime-0.5.0/lime/R/shiny.R | 3 lime-0.5.0/lime/R/tibble_shim.R | 2 lime-0.5.0/lime/README.md | 32 lime-0.5.0/lime/build/vignette.rds |binary lime-0.5.0/lime/inst/doc/Understanding_lime.R | 2 lime-0.5.0/lime/inst/doc/Understanding_lime.Rmd | 2 lime-0.5.0/lime/inst/doc/Understanding_lime.html | 382 ++++------ lime-0.5.0/lime/inst/htmlwidgets/lib/plot_text_explanations.css | 24 lime-0.5.0/lime/man/dot-load_text_example.Rd |only lime-0.5.0/lime/man/explain.Rd | 27 lime-0.5.0/lime/man/figures/README-unnamed-chunk-2-1.png |binary lime-0.5.0/lime/man/figures/README-unnamed-chunk-3-1.png |binary lime-0.5.0/lime/man/figures/logo.svg |only lime-0.5.0/lime/man/interactive_text_explanations.Rd | 3 lime-0.5.0/lime/man/lime-package.Rd | 4 lime-0.5.0/lime/man/lime.Rd | 54 - lime-0.5.0/lime/man/plot_explanations.Rd | 6 lime-0.5.0/lime/man/plot_image_explanation.Rd | 2 lime-0.5.0/lime/man/stop_words_sentences.Rd | 2 lime-0.5.0/lime/man/test_sentences.Rd | 2 lime-0.5.0/lime/man/text_explanations.Rd | 3 lime-0.5.0/lime/man/train_sentences.Rd | 2 lime-0.5.0/lime/tests/testthat/test-h2o.R | 49 - lime-0.5.0/lime/vignettes/Understanding_lime.Rmd | 2 39 files changed, 380 insertions(+), 401 deletions(-)
Title: Spatial Inference using Integrated Nested Laplace Approximation
Description: Facilitates spatial modeling using integrated nested Laplace approximation via the
INLA package (<http://www.r-inla.org>). Additionally, implements a log Gaussian Cox process likelihood for
modeling univariate and spatial point processes based on ecological survey data. See Yuan Yuan,
Fabian E. Bachl, Finn Lindgren, David L. Borchers, Janine B. Illian, Stephen T. Buckland, Havard Rue,
Tim Gerrodette (2017), <arXiv:1604.06013>.
Author: Fabian E. Bachl [aut, cre] (Fabian Bachl wrote the main code),
Finn Lindgren [aut] (<https://orcid.org/0000-0002-5833-2011>, Finn
Lindgren wrote code for SPDE posterior plotting, and continued
development of the main code),
David L. Borchers [ctb] (David Borchers wrote code for Gorilla data
import and sampling, multiplot tool),
Daniel Simpson [ctb] (Daniel Simpson wrote the basic LGCP sampling
method),
Lindesay Scott-Howard [ctb] (Lindesay Scott-Howard provied MRSea data
import code)
Maintainer: Fabian E. Bachl <bachlfab@gmail.com>
Diff between inlabru versions 2.1.9 dated 2018-07-24 and 2.1.12 dated 2019-06-24
DESCRIPTION | 8 ++-- MD5 | 67 +++++++++++++++++++-------------------- NEWS.md | 12 ++++++ R/bru.integration.R | 2 - R/inla.R | 8 +++- R/integration.R | 4 +- inst/CITATION |only man/generate.Rd | 1 man/generate.bru.Rd | 4 +- man/generate.inla.Rd | 1 man/gg.RasterLayer.Rd | 5 +- man/gg.Rd | 4 ++ man/gg.SpatialGridDataFrame.Rd | 1 man/gg.SpatialLines.Rd | 1 man/gg.SpatialPixels.Rd | 1 man/gg.SpatialPixelsDataFrame.Rd | 1 man/gg.SpatialPoints.Rd | 1 man/gg.SpatialPolygons.Rd | 1 man/gg.data.frame.Rd | 1 man/gg.inla.mesh.1d.Rd | 1 man/gg.inla.mesh.Rd | 1 man/gg.matrix.Rd | 1 man/gg.prediction.Rd | 5 +- man/globe.Rd | 1 man/glplot.Rd | 1 man/glplot.SpatialLines.Rd | 1 man/glplot.SpatialPoints.Rd | 1 man/glplot.inla.mesh.Rd | 1 man/gm.Rd | 4 ++ man/ipoints.Rd | 3 + man/like.Rd | 4 +- man/materncov.bands.Rd | 4 +- man/plotsample.Rd | 3 + man/sample.lgcp.Rd | 4 +- man/vertices.Rd | 2 - 35 files changed, 103 insertions(+), 57 deletions(-)
Title: Portable Tools for 'UTF-8' Character Data
Description: Implements an S3 class for storing 'UTF-8' strings, based on regular character vectors.
Also contains routines to portably read and write 'UTF-8' encoded text files,
to convert all strings in an object to 'UTF-8',
and to create character vectors with various encodings.
Author: Kirill Müller [aut, cre]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between enc versions 0.2.0 dated 2018-03-03 and 0.2.1 dated 2019-06-24
DESCRIPTION | 10 ++-- MD5 | 20 ++++----- NEWS.md | 10 ++++ R/io.R | 3 - R/to-encoding.R | 2 README.md | 92 ++++++++++++++++++++++++++++++-------------- man/enc-package.Rd | 6 +- man/to_encoding.Rd | 2 man/utf8.Rd | 8 ++- src/encoding.c | 10 ++-- tests/testthat/test-ascii.R | 11 +++-- 11 files changed, 110 insertions(+), 64 deletions(-)
Title: Scheduling Interim Analyses in Clinical Trials
Description: Allows the simulation of the recruitment and both the event and treatment phase of a clinical trial. Based on these simulations, the timing of interim analyses can be assessed.
Author: Bastian Becker, Katharina Mueller, Hermann Kulmann
Maintainer: Bastian Becker <bastian.becker@bayer.com>
Diff between interim versions 0.7.0 dated 2017-07-12 and 0.8.0 dated 2019-06-24
DESCRIPTION | 16 ++-- MD5 | 13 ++- NAMESPACE | 3 NEWS | 7 + R/interim.r | 202 +++++++++++++++++++++++++++++++++++++++++++++++++++-- man/cross.Rd | 10 +- man/event.Rd |only man/eventCourse.Rd |only man/eventWeek.Rd |only 9 files changed, 230 insertions(+), 21 deletions(-)
Title: Easily Create and Style Tables for LaTeX, HTML and Other Formats
Description: Like 'xtable', creates styled tables. Export to HTML, LaTeX, 'Word',
'Excel', 'PowerPoint' and RTF. Simple, modern interface to manipulate
borders, size, position, captions, colours, text styles and number formatting.
Table cells can span multiple rows and/or columns.
Includes a 'huxreg' function for creation of regression tables, and 'quick_*'
one-liners to print data to a new document.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between huxtable versions 4.5.0 dated 2019-03-19 and 4.6.0 dated 2019-06-24
DESCRIPTION | 6 - MD5 | 53 ++++++------ NEWS.md | 9 ++ R/knitr.R | 8 + R/latex.R | 7 + R/manipulation.R | 56 ++++++++----- R/misc.R | 5 - R/properties.R | 7 + R/quick-functions.R | 3 R/zzz.R | 7 + README.md | 89 ++++++++++---------- inst/doc/design-principles.html | 4 inst/doc/huxreg.html | 4 inst/doc/huxtable.html | 47 +++++------ inst/doc/themes.html | 10 +- man/extract-methods.Rd | 27 +++--- man/font.Rd | 7 + man/huxtable-options.Rd | 4 tests/testthat/bookdown-test.log | 4 tests/testthat/file179bc39585594.log |only tests/testthat/file179bc46ef1b9c.log |only tests/testthat/fontspec-test.Rmd |only tests/testthat/huxreg.log | 4 tests/testthat/huxtable.log | 4 tests/testthat/table-tester-2.log | 6 - tests/testthat/temp-artefacts |only tests/testthat/test-manipulation-helpers.R |only tests/testthat/test-object-manipulation.R | 123 +++-------------------------- tests/testthat/test-yy-end-to-end.R | 9 ++ tests/testthat/themes.log | 4 30 files changed, 236 insertions(+), 271 deletions(-)
Title: Gaussian-Based Visualization of Gaussian and Non-Gaussian
Model-Based Clustering
Description: Gaussian-Based Visualization of Gaussian and Non-Gaussian Model-Based Clustering done on any type of data. Visualization is based on the probabilities of classification.
Author: Christophe Biernacki [aut],
Matthieu Marbac [aut, cre],
Vincent Vandewalle [aut]
Maintainer: Matthieu Marbac <matthieu.marbac@gmail.com>
Diff between ClusVis versions 1.1.0 dated 2018-04-19 and 1.2.0 dated 2019-06-24
DESCRIPTION | 16 +++----- MD5 | 22 +++++------ R/clusvis.R | 90 ++++++++++++++++++++++++++++++++++++--------- R/clusvismixmod.R | 35 +++++++++++++++++ R/clusvisvarsellcm.R | 6 +-- R/plot.R | 43 +++++++++++---------- data/congress.rda |binary man/ClusVis-package.Rd | 32 +++++++++++++--- man/clusvis.Rd | 53 ++++++++++++++++++++++---- man/clusvisMixmod.Rd | 35 +++++++++++++++++ man/clusvisVarSelLCM.Rd | 6 +-- man/plotDensityClusVisu.Rd | 41 ++++++++++++-------- 12 files changed, 283 insertions(+), 96 deletions(-)
Title: Apply Statistical Post-Processing to Improve Sea Ice Predictions
Description: Tools for correcting biases and calibrating sea ice predictions obtained from dynamic ensemble models. Implements and extends Director et al. (2017) <doi:10.1175/JCLI-D-17-0185.1> This package depends on the 'ncdf4' and 'rgeos' R packages. These packages require installing externally from R Unidata's 'NetCDF' library and Geometry Engine - Open Source ('GEOS'). (See the 'rgeos' and 'ncdf4' packages for details.)
Author: Hannah M. Director, Adrian E. Raftery, and Cecilia M. Bitz
Maintainer: Hannah M. Director <direch@uw.edu>
Diff between IceCast versions 1.2.0 dated 2017-08-16 and 2.1.0 dated 2019-06-24
IceCast-1.2.0/IceCast/data/datalist |only IceCast-1.2.0/IceCast/data/emFeb19811982.RData |only IceCast-1.2.0/IceCast/data/emFeb2012.RData |only IceCast-1.2.0/IceCast/data/maps198102_201102.rda |only IceCast-1.2.0/IceCast/data/obsFeb19811982.rda |only IceCast-1.2.0/IceCast/data/obsFeb2012.rda |only IceCast-1.2.0/IceCast/data/regionInfo.RData |only IceCast-1.2.0/IceCast/data/sampleMappedPoints_region1.RData |only IceCast-1.2.0/IceCast/man/allRegions.Rd |only IceCast-1.2.0/IceCast/man/anyIntersect.Rd |only IceCast-1.2.0/IceCast/man/bgWater.Rd |only IceCast-1.2.0/IceCast/man/checkIntersect.Rd |only IceCast-1.2.0/IceCast/man/contourShift.Rd |only IceCast-1.2.0/IceCast/man/convToGrid.Rd |only IceCast-1.2.0/IceCast/man/createMapping.Rd |only IceCast-1.2.0/IceCast/man/emFeb19811982.Rd |only IceCast-1.2.0/IceCast/man/emFeb2012.Rd |only IceCast-1.2.0/IceCast/man/extractCoords.Rd |only IceCast-1.2.0/IceCast/man/findHoles.Rd |only IceCast-1.2.0/IceCast/man/getArea.Rd |only IceCast-1.2.0/IceCast/man/getCoords.Rd |only IceCast-1.2.0/IceCast/man/getDist.Rd |only IceCast-1.2.0/IceCast/man/getInd.Rd |only IceCast-1.2.0/IceCast/man/getInitMonth.Rd |only IceCast-1.2.0/IceCast/man/getMap.Rd |only IceCast-1.2.0/IceCast/man/getRegion.Rd |only IceCast-1.2.0/IceCast/man/intLine.Rd |only IceCast-1.2.0/IceCast/man/keepLine.Rd |only IceCast-1.2.0/IceCast/man/keepPoly.Rd |only IceCast-1.2.0/IceCast/man/landMat.Rd |only IceCast-1.2.0/IceCast/man/makePolygons.Rd |only IceCast-1.2.0/IceCast/man/obsFeb19811982.Rd |only IceCast-1.2.0/IceCast/man/obsFeb2012.Rd |only IceCast-1.2.0/IceCast/man/quickRun.Rd |only IceCast-1.2.0/IceCast/man/readBootstrap.Rd |only IceCast-1.2.0/IceCast/man/readMonthlyBS.Rd |only IceCast-1.2.0/IceCast/man/regionInfo.Rd |only IceCast-1.2.0/IceCast/man/rmHoles.Rd |only IceCast-1.2.0/IceCast/man/untwistSec.Rd |only IceCast-2.1.0/IceCast/DESCRIPTION | 19 IceCast-2.1.0/IceCast/MD5 | 197 ++- IceCast-2.1.0/IceCast/NAMESPACE | 54 IceCast-2.1.0/IceCast/R/MCF.R |only IceCast-2.1.0/IceCast/R/RcppExports.R |only IceCast-2.1.0/IceCast/R/biasCorrect.R | 403 ++----- IceCast-2.1.0/IceCast/R/fitContours.R |only IceCast-2.1.0/IceCast/R/genContours.R |only IceCast-2.1.0/IceCast/R/genPolys.R |only IceCast-2.1.0/IceCast/R/geodesicAreas.R | 145 +- IceCast-2.1.0/IceCast/R/importExport.R | 175 +-- IceCast-2.1.0/IceCast/R/mappings.R | 675 ++++-------- IceCast-2.1.0/IceCast/R/misc.R | 416 ++++--- IceCast-2.1.0/IceCast/R/polygons.R | 82 - IceCast-2.1.0/IceCast/R/readBootstrap.R | 110 + IceCast-2.1.0/IceCast/R/regionInformation.R | 80 + IceCast-2.1.0/IceCast/R/selfIntersections.R | 178 +-- IceCast-2.1.0/IceCast/R/storedResults.R | 539 ++++++--- IceCast-2.1.0/IceCast/README.md |only IceCast-2.1.0/IceCast/build/vignette.rds |binary IceCast-2.1.0/IceCast/data/allRegions.rda |binary IceCast-2.1.0/IceCast/data/bgWater.rda |binary IceCast-2.1.0/IceCast/data/clim_9_2005_2007.rda |only IceCast-2.1.0/IceCast/data/clim_9_2008.rda |only IceCast-2.1.0/IceCast/data/ecmwf_binMonth9.rda |only IceCast-2.1.0/IceCast/data/full.rda |only IceCast-2.1.0/IceCast/data/land.rda |binary IceCast-2.1.0/IceCast/data/landMat.rda |binary IceCast-2.1.0/IceCast/data/map_curr_1.rda |only IceCast-2.1.0/IceCast/data/maps199309_200709.rda |only IceCast-2.1.0/IceCast/data/merged.rda |only IceCast-2.1.0/IceCast/data/obsSep2006_2007.rda |only IceCast-2.1.0/IceCast/data/obsSep2008.rda |only IceCast-2.1.0/IceCast/data/obs_9_2005_2007.rda |only IceCast-2.1.0/IceCast/data/obs_9_2008.rda |only IceCast-2.1.0/IceCast/data/obs_maps.rda |only IceCast-2.1.0/IceCast/data/pars_1.rda |only IceCast-2.1.0/IceCast/data/ppe_9_2005_2007.rda |only IceCast-2.1.0/IceCast/data/ppe_9_2008.rda |only IceCast-2.1.0/IceCast/data/pred_maps.rda |only IceCast-2.1.0/IceCast/data/prop_area.rda |only IceCast-2.1.0/IceCast/data/reg_info.rda |only IceCast-2.1.0/IceCast/data/sampleMappedPoints_region5.rda |only IceCast-2.1.0/IceCast/data/sipSep2006_2007.rda |only IceCast-2.1.0/IceCast/data/sipSep2008.rda |only IceCast-2.1.0/IceCast/inst/doc/FitAndGenerateContours.R |only IceCast-2.1.0/IceCast/inst/doc/FitAndGenerateContours.Rmd |only IceCast-2.1.0/IceCast/inst/doc/FitAndGenerateContours.html |only IceCast-2.1.0/IceCast/inst/doc/MixtureContourForecasts.R |only IceCast-2.1.0/IceCast/inst/doc/MixtureContourForecasts.Rmd |only IceCast-2.1.0/IceCast/inst/doc/MixtureContourForecasts.html |only IceCast-2.1.0/IceCast/inst/doc/biasCorrectDemo.R | 148 +- IceCast-2.1.0/IceCast/inst/doc/biasCorrectDemo.Rmd | 383 ++++-- IceCast-2.1.0/IceCast/inst/doc/biasCorrectDemo.html | 276 ++-- IceCast-2.1.0/IceCast/man/RunMCMC.Rd |only IceCast-2.1.0/IceCast/man/all_regions.Rd |only IceCast-2.1.0/IceCast/man/any_intersect.Rd |only IceCast-2.1.0/IceCast/man/bg_water.Rd |only IceCast-2.1.0/IceCast/man/bound_info.Rd |only IceCast-2.1.0/IceCast/man/calc_pars.Rd |only IceCast-2.1.0/IceCast/man/censor.Rd |only IceCast-2.1.0/IceCast/man/check_intersect.Rd |only IceCast-2.1.0/IceCast/man/clim_9_2005_2007.Rd |only IceCast-2.1.0/IceCast/man/clim_9_2008.Rd |only IceCast-2.1.0/IceCast/man/cond_prob.Rd |only IceCast-2.1.0/IceCast/man/contig_zero.Rd |only IceCast-2.1.0/IceCast/man/contour_shift.Rd |only IceCast-2.1.0/IceCast/man/conv_to_grid.Rd |only IceCast-2.1.0/IceCast/man/create_mapping.Rd |only IceCast-2.1.0/IceCast/man/discrep.Rd | 63 - IceCast-2.1.0/IceCast/man/dist_mat.Rd |only IceCast-2.1.0/IceCast/man/ecmwf_bin.Rd |only IceCast-2.1.0/IceCast/man/extract_coords.Rd |only IceCast-2.1.0/IceCast/man/find_trans.Rd |only IceCast-2.1.0/IceCast/man/fit_cont_pars.Rd |only IceCast-2.1.0/IceCast/man/fit_weights.Rd |only IceCast-2.1.0/IceCast/man/full.Rd |only IceCast-2.1.0/IceCast/man/gen_cont.Rd |only IceCast-2.1.0/IceCast/man/get_area.Rd |only IceCast-2.1.0/IceCast/man/get_coords.Rd |only IceCast-2.1.0/IceCast/man/get_dist.Rd |only IceCast-2.1.0/IceCast/man/get_ind.Rd |only IceCast-2.1.0/IceCast/man/get_init_month.Rd |only IceCast-2.1.0/IceCast/man/get_map.Rd |only IceCast-2.1.0/IceCast/man/get_region.Rd |only IceCast-2.1.0/IceCast/man/indiv_poly.Rd |only IceCast-2.1.0/IceCast/man/int_line.Rd |only IceCast-2.1.0/IceCast/man/inter_start_line.Rd |only IceCast-2.1.0/IceCast/man/interp_new_pts.Rd |only IceCast-2.1.0/IceCast/man/keep_line.Rd |only IceCast-2.1.0/IceCast/man/keep_poly.Rd |only IceCast-2.1.0/IceCast/man/land.Rd | 38 IceCast-2.1.0/IceCast/man/land_mat.Rd |only IceCast-2.1.0/IceCast/man/make_polygons.Rd |only IceCast-2.1.0/IceCast/man/map_curr_1.Rd |only IceCast-2.1.0/IceCast/man/mapxy.Rd | 23 IceCast-2.1.0/IceCast/man/merge_conts.Rd |only IceCast-2.1.0/IceCast/man/merged.Rd |only IceCast-2.1.0/IceCast/man/obsSep2006_2007.Rd |only IceCast-2.1.0/IceCast/man/obsSep2008.Rd |only IceCast-2.1.0/IceCast/man/obs_9_2005_2007.Rd |only IceCast-2.1.0/IceCast/man/obs_9_2008.Rd |only IceCast-2.1.0/IceCast/man/obs_maps.Rd |only IceCast-2.1.0/IceCast/man/pars_1.Rd |only IceCast-2.1.0/IceCast/man/ppe_9_2005_2007.Rd |only IceCast-2.1.0/IceCast/man/ppe_9_2008.Rd |only IceCast-2.1.0/IceCast/man/pred_maps.Rd |only IceCast-2.1.0/IceCast/man/prob_map.Rd |only IceCast-2.1.0/IceCast/man/prop_area.Rd |only IceCast-2.1.0/IceCast/man/pt_line_inter.Rd |only IceCast-2.1.0/IceCast/man/quick_run.Rd |only IceCast-2.1.0/IceCast/man/read_bootstrap.Rd |only IceCast-2.1.0/IceCast/man/read_monthly_BS.Rd |only IceCast-2.1.0/IceCast/man/reg_info.Rd |only IceCast-2.1.0/IceCast/man/rm_holes.Rd |only IceCast-2.1.0/IceCast/man/sec_to_interp.Rd |only IceCast-2.1.0/IceCast/man/sipSep2006_2007.Rd |only IceCast-2.1.0/IceCast/man/sipSep2008.Rd |only IceCast-2.1.0/IceCast/man/spatialCollEx.Rd | 4 IceCast-2.1.0/IceCast/man/to_fit.Rd |only IceCast-2.1.0/IceCast/man/train_ind.Rd |only IceCast-2.1.0/IceCast/man/ts_adj_mu.Rd |only IceCast-2.1.0/IceCast/man/untwist.Rd | 11 IceCast-2.1.0/IceCast/man/untwist_sec.Rd |only IceCast-2.1.0/IceCast/man/wght_mod.Rd |only IceCast-2.1.0/IceCast/man/y_obs.Rd |only IceCast-2.1.0/IceCast/src |only IceCast-2.1.0/IceCast/vignettes/FitAndGenerateContours.Rmd |only IceCast-2.1.0/IceCast/vignettes/MixtureContourForecasts.Rmd |only IceCast-2.1.0/IceCast/vignettes/biasCorrectDemo.Rmd | 383 ++++-- 169 files changed, 2427 insertions(+), 1975 deletions(-)
Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre],
Edward L. Ionides [aut],
Carles Breto [aut],
Stephen P. Ellner [ctb],
Matthew J. Ferrari [ctb],
Bruce E. Kendall [ctb],
Michael Lavine [ctb],
Dao Nguyen [ctb],
Daniel C. Reuman [ctb],
Helen Wearing [ctb],
Simon N. Wood [ctb],
Sebastian Funk [ctb],
Steven G. Johnson [ctb],
Eamon O'Dea [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 2.1 dated 2019-06-03 and 2.2 dated 2019-06-24
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- R/dacca.R | 7 +------ R/ou2.R | 9 +-------- R/parameter_trans.R | 3 +++ R/plot.R | 2 +- R/probe_match.R | 15 ++++++++++++++- R/proposals.R | 2 +- R/ricker.R | 6 +----- R/runif_design.R | 2 +- R/spect_match.R | 14 +++++++++++++- inst/NEWS | 8 ++++++++ inst/NEWS.Rd | 6 ++++++ man/dacca.Rd | 9 ++++----- man/ou2.Rd | 11 +++++------ man/parameter_trans.Rd | 3 +++ man/plot.Rd | 11 ++++++++++- man/ricker.Rd | 9 ++++----- 18 files changed, 97 insertions(+), 62 deletions(-)
Title: New Plots Based on 'ggplot2' and Functions to Create Regular
Shapes
Description: An extension to 'ggplot2' with miscellaneous functions. It contains
two groups of functions: Functions in the first group draw 'ggplot2' - based plots: gg_shading_bar() draws barplot
with shading colors in each bar. geom_rect_cm(), geom_circle_cm() and geom_ellipse_cm() draw rectangles, circles
and ellipses with centimeter as their unit. Thus their sizes do not change when the coordinate system or the aspect ratio
changes. annotation_transparent_text() draws labels with transparent texts. annotation_shading_polygon() draws irregular
polygons with shading colors. Functions in the second group generate coordinates for regular shapes and make linear transformations.
Author: Jiang Wu [aut, cre] (from Capital Normal University)
Maintainer: Jiang Wu <textidea@sina.com>
Diff between plothelper versions 0.1.2 dated 2019-06-09 and 0.1.3 dated 2019-06-24
DESCRIPTION | 11 ++- MD5 | 26 +++++---- NAMESPACE | 3 + R/annotation_shading_polygon.R | 106 ++++++++++++++++++++++++++----------- R/annotation_transparent_text.R | 84 +++++++++++++++++++---------- R/ellipsexy.R | 7 ++ R/enlarge_raster.R |only R/geom_ellipse_cm.R | 2 R/image_composite2.R |only R/resize_to_standard.R |only man/annotation_shading_polygon.Rd | 36 +++++++++--- man/annotation_transparent_text.Rd | 25 ++++++-- man/ellipsexy.Rd | 7 ++ man/enlarge_raster.Rd |only man/geom_ellipse_cm.Rd | 2 man/image_composite2.Rd |only man/resize_to_standard.Rd |only 17 files changed, 218 insertions(+), 91 deletions(-)
Title: Programming with Big Data -- Scalable Linear Algebra Packages
Description: Utilizing scalable linear algebra packages mainly
including 'BLACS', 'PBLAS', and 'ScaLAPACK' in double precision via
'pbdMPI' based on 'ScaLAPACK' version 2.0.2.
Author: Wei-Chen Chen [aut, cre],
Drew Schmidt [aut],
George Ostrouchov [aut],
Pragneshkumar Patel [aut],
Brian Ripley [ctb] (Solaris & Mac)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdSLAP versions 0.2-5 dated 2019-04-08 and 0.2-6 dated 2019-06-24
pbdSLAP-0.2-5/pbdSLAP/inst/LAPACK_LICENSE.txt |only pbdSLAP-0.2-5/pbdSLAP/src/LAPACK |only pbdSLAP-0.2-6/pbdSLAP/ChangeLog | 3 +++ pbdSLAP-0.2-6/pbdSLAP/DESCRIPTION | 11 +++++------ pbdSLAP-0.2-6/pbdSLAP/MD5 | 17 ++++++----------- pbdSLAP-0.2-6/pbdSLAP/R/get_conf.r |only pbdSLAP-0.2-6/pbdSLAP/inst/doc/pbdSLAP-guide.pdf |binary pbdSLAP-0.2-6/pbdSLAP/src/Makevars.in | 2 -- pbdSLAP-0.2-6/pbdSLAP/src/Makevars.win | 2 -- 9 files changed, 14 insertions(+), 21 deletions(-)
Title: Integro-Difference Equation Spatio-Temporal Models
Description: The Integro-Difference Equation model is a linear, dynamical model used to model
phenomena that evolve in space and in time; see, for example, Cressie and Wikle (2011,
ISBN:978-0-471-69274-4) or Dewar et al. (2009) <doi:10.1109/TSP.2008.2005091>. At the
heart of the model is the kernel, which dictates how the process evolves from one time
point to the next. Both process and parameter reduction are used to facilitate computation,
and spatially-varying kernels are allowed. Data used to estimate the parameters are assumed
to be readings of the process corrupted by Gaussian measurement error. Parameters are fitted
by maximum likelihood, and estimation is carried out using an evolution algorithm.
Author: Andrew Zammit-Mangion [aut, cre]
Maintainer: Andrew Zammit-Mangion <andrewzm@gmail.com>
Diff between IDE versions 0.2.0 dated 2018-08-07 and 0.3.0 dated 2019-06-24
DESCRIPTION | 10 MD5 | 8 R/IDEfunctions.R | 1595 ++++++++++++++++++++++++------------------------- inst/doc/IDE_intro.pdf | 243 +++---- man/IDE.Rd | 4 5 files changed, 944 insertions(+), 916 deletions(-)
Title: Creating Groups from Data
Description: Subsetting methods for balanced cross-validation, time series windowing,
and general grouping and splitting of data.
Author: Ludvig Renbo Olsen [aut, cre]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between groupdata2 versions 1.0.0 dated 2017-10-21 and 1.1.0 dated 2019-06-24
DESCRIPTION | 17 MD5 | 123 NAMESPACE | 9 NEWS.md | 46 R/create_num_col_groups.R |only R/differs_from_previous.R |only R/extract_folds_colnames.R |only R/find_missing_starts.R | 8 R/find_starts.R | 126 R/fold.R | 549 ++ R/group.R | 47 R/group_factor.R | 19 R/helpers.R | 264 + R/l_methods.R | 1 R/numerical_balancing.R |only R/package_info.R | 16 R/partition.R | 286 - R/primes_remainder.R | 2 R/rearrange.R |only R/sampling.R |only R/sampling_methods.R |only R/splitters.R | 10 R/splt.R | 12 R/staircase_methods.R | 4 R/staircase_remainder.R | 2 README.md | 373 + build/vignette.rds |binary inst/doc/automatic_groups_with_groupdata2.R | 4 inst/doc/automatic_groups_with_groupdata2.Rmd | 18 inst/doc/automatic_groups_with_groupdata2.html | 489 +- inst/doc/cross-validation_with_groupdata2.R | 24 inst/doc/cross-validation_with_groupdata2.Rmd | 100 inst/doc/cross-validation_with_groupdata2.html | 1087 ++-- inst/doc/description_of_groupdata2.R | 255 + inst/doc/description_of_groupdata2.Rmd | 704 ++- inst/doc/description_of_groupdata2.html | 4569 +++++++++++++++----- inst/doc/introduction_to_groupdata2.Rmd | 14 inst/doc/introduction_to_groupdata2.html | 229 - inst/doc/time_series_with_groupdata2.R | 13 inst/doc/time_series_with_groupdata2.Rmd | 23 inst/doc/time_series_with_groupdata2.html | 525 +- man/balance.Rd |only man/differs_from_previous.Rd |only man/downsample.Rd |only man/find_missing_starts.Rd | 15 man/find_starts.Rd | 26 man/fold.Rd | 281 - man/grapes-primes-grapes.Rd | 2 man/grapes-staircase-grapes.Rd | 2 man/group.Rd | 33 man/group_factor.Rd | 17 man/groupdata2.Rd | 18 man/partition.Rd | 161 man/rearrange.Rd |only man/splt.Rd | 22 man/upsample.Rd |only tests/testthat/test_balance.R |only tests/testthat/test_differs_from_previous.R |only tests/testthat/test_find_starts.R | 4 tests/testthat/test_fold.R | 408 + tests/testthat/test_group.R | 2 tests/testthat/test_handling_identical_columns.R |only tests/testthat/test_numerically_balanced_grouping.R |only tests/testthat/test_partition.R | 223 tests/testthat/test_rearrange.R |only tests/testthat/test_sampling_methods.R |only tests/testthat/test_utilities.R |only vignettes/automatic_groups_with_groupdata2.Rmd | 18 vignettes/cross-validation_with_groupdata2.Rmd | 100 vignettes/description_of_groupdata2.Rmd | 704 ++- vignettes/introduction_to_groupdata2.Rmd | 14 vignettes/time_series_with_groupdata2.Rmd | 23 72 files changed, 9268 insertions(+), 2773 deletions(-)
Title: Draw Gene Arrow Maps in 'ggplot2'
Description: Provides a 'ggplot2' geom and helper functions for drawing gene
arrow maps.
Author: David Wilkins [aut, cre],
Zachary Kurtz [ctb]
Maintainer: David Wilkins <david@wilkox.org>
Diff between gggenes versions 0.3.2 dated 2018-11-07 and 0.4.0 dated 2019-06-24
DESCRIPTION | 21 +- MD5 | 78 ++++++--- NAMESPACE | 3 NEWS.md | 28 ++- R/data.R | 12 + R/geom_gene_arrow.R | 44 ++--- R/geom_gene_label.R | 47 ++--- R/geom_subgene_arrow.R |only R/geom_subgene_label.R |only R/make_alignment_dummies.R | 23 +- R/theme_genes.R | 8 - README.md | 135 +++++++++++------ build/vignette.rds |binary data/example_genes.rda |binary data/example_subgenes.rda |only inst/doc/introduction-to-gggenes.R | 25 +++ inst/doc/introduction-to-gggenes.Rmd | 67 +++++++- inst/doc/introduction-to-gggenes.html | 189 +++++++++++++++--------- man/example_genes.Rd | 20 +- man/figures/README-geom_gene_arrow-1.png |binary man/figures/README-labelled_genes-1.png |binary man/figures/README-make_alignment_dummies-1.png |binary man/figures/README-reversing_direction-1.png |binary man/figures/README-subgene_labels-1.png |only man/figures/README-subgenes-1.png |only man/figures/README-theme_genes-1.png |binary man/geom_gene_arrow.Rd | 53 +++--- man/geom_gene_label.Rd | 43 ++--- man/geom_subgene_arrow.Rd |only man/geom_subgene_label.Rd |only man/gggenes.Rd | 6 man/make_alignment_dummies.Rd | 25 +-- man/theme_genes.Rd | 8 - tests/figs |only tests/testthat/test-geom_gene_arrow.R | 26 +-- tests/testthat/test-geom_gene_label.R | 25 --- tests/testthat/test-geom_subgene_arrow.R |only tests/testthat/test-geom_subgene_label.R |only tests/testthat/test-make_alignment_dummies.R | 39 +--- tests/testthat/test-plots.R |only tests/testthat/test-theme_genes.R | 25 --- vignettes/introduction-to-gggenes.Rmd | 67 +++++++- 42 files changed, 625 insertions(+), 392 deletions(-)
Title: Color Calculations with Emphasis on Spectral Data
Description: Calculate with spectral properties of light sources, materials, cameras, eyes, and scanners.
Build complex systems from simpler parts using a spectral product algebra. For light sources,
compute CCT, CRI, and SSI. For object colors, compute optimal colors and Logvinenko coordinates.
Work with the standard CIE illuminants and color matching functions, and read spectra from
text files, including CGATS files. Estimate a spectrum from its response. A user guide and 9 vignettes are included.
Author: Glenn Davis [aut, cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between colorSpec versions 0.9-1 dated 2019-05-31 and 1.0-1 dated 2019-06-24
colorSpec-0.9-1/colorSpec/inst/doc/Thumbs.db |only colorSpec-0.9-1/colorSpec/inst/doc/proofs.txt |only colorSpec-1.0-1/colorSpec/DESCRIPTION | 14 colorSpec-1.0-1/colorSpec/MD5 | 64 colorSpec-1.0-1/colorSpec/NAMESPACE | 9 colorSpec-1.0-1/colorSpec/NEWS.md | 10 colorSpec-1.0-1/colorSpec/R/colorSpec.comp.R | 623 ++++- colorSpec-1.0-1/colorSpec/R/colorSpec.interpolate.R | 2 colorSpec-1.0-1/colorSpec/R/colorSpec.metrics.R |only colorSpec-1.0-1/colorSpec/R/colorSpec.ops.R | 8 colorSpec-1.0-1/colorSpec/R/colorSpec.optimal.R | 407 +++ colorSpec-1.0-1/colorSpec/R/datasets.R | 2 colorSpec-1.0-1/colorSpec/R/transitions.R |only colorSpec-1.0-1/colorSpec/R/utils.R | 73 colorSpec-1.0-1/colorSpec/R/zonogon.R | 199 + colorSpec-1.0-1/colorSpec/R/zonogon3.R |only colorSpec-1.0-1/colorSpec/R/zonohedron.R | 1905 +++++++++++++--- colorSpec-1.0-1/colorSpec/build/vignette.rds |binary colorSpec-1.0-1/colorSpec/inst/CITATION | 4 colorSpec-1.0-1/colorSpec/inst/doc/blueflame.pdf |binary colorSpec-1.0-1/colorSpec/inst/doc/colorSpec-guide.Rmd | 53 colorSpec-1.0-1/colorSpec/inst/doc/colorSpec-guide.html | 55 colorSpec-1.0-1/colorSpec/inst/doc/convexity.R |only colorSpec-1.0-1/colorSpec/inst/doc/convexity.pdf |only colorSpec-1.0-1/colorSpec/inst/doc/convexity.rnw |only colorSpec-1.0-1/colorSpec/inst/doc/emulation.pdf |binary colorSpec-1.0-1/colorSpec/inst/doc/gallery.pdf |binary colorSpec-1.0-1/colorSpec/inst/doc/inversion.pdf |binary colorSpec-1.0-1/colorSpec/inst/doc/lens-aging.pdf |binary colorSpec-1.0-1/colorSpec/inst/doc/optimals.pdf |binary colorSpec-1.0-1/colorSpec/inst/doc/phenolred.html | 27 colorSpec-1.0-1/colorSpec/inst/doc/photoncounting.html | 6 colorSpec-1.0-1/colorSpec/man/bandSpectra.Rd |only colorSpec-1.0-1/colorSpec/man/canonicalOptimalColors.Rd |only colorSpec-1.0-1/colorSpec/man/responsivityMetrics.Rd |only colorSpec-1.0-1/colorSpec/tests/test-bands.R |only colorSpec-1.0-1/colorSpec/vignettes/bibliography.bib | 19 colorSpec-1.0-1/colorSpec/vignettes/colorSpec-guide.Rmd | 53 colorSpec-1.0-1/colorSpec/vignettes/convexity.rnw |only colorSpec-1.0-1/colorSpec/vignettes/framed.sty |only 40 files changed, 3082 insertions(+), 451 deletions(-)
Title: Modern Nonparametric Tools for Two-Sample Quantile and
Distribution Comparisons
Description: Allows practitioners to determine (i) if two univariate distributions (which can be continuous, discrete, or even mixed) are equal, (ii) how two distributions differ (shape differences, e.g., location, scale, etc.), and (iii) where two distributions differ (at which quantiles), all using nonparametric LP statistics. The primary reference is Jungreis, D. (2019, Technical Report).
Author: David Jungreis, Subhadeep Mukhopadhyay
Maintainer: David Jungreis <dbjungreis@gmail.com>
Diff between QDComparison versions 2.0 dated 2018-10-30 and 3.0 dated 2019-06-24
DESCRIPTION | 11 +- MD5 | 34 ++++---- R/LP.QDC.R | 169 +++++++++++++++++++++----------------------- R/LP.XY.R | 57 +++++++------- R/LP.smooth.R | 33 +++++--- R/QDC.Permute.R | 41 +++++----- R/QTE.Out.R | 137 ++++++++++++++++------------------- R/eLP.poly.R | 11 +- R/seqle.R | 20 ++--- data/Depression.rda |binary data/Earnings1978.rda |binary data/Fundraising.rda |binary data/Microfinance.rda |binary data/NMES.rda |binary man/LP.QDC.Rd | 26 +++--- man/LP.XY.Rd | 20 ++--- man/QDComparison-package.Rd | 10 +- man/eLP.poly.Rd | 4 - 18 files changed, 285 insertions(+), 288 deletions(-)