Title: Tidy Up and Test XPath Queries on HTML and XML Content
Description: HTML documents can be beautiful and pristine. They can also be
wretched, evil, malformed demon-spawn. Now, you can tidy up that HTML and XHTML
before processing it with your favorite angle-bracket crunching tools, going beyond
the limited tidying that 'libxml2' affords in the 'XML' and 'xml2' packages and
taming even the ugliest HTML code generated by the likes of Google Docs and Microsoft
Word. It's also possible to use the functions provided to format or "pretty print"
HTML content as it is being tidied. Utilities are also included that make it
possible to view formatted and "pretty printed" HTML/XML
content from HTML/XML document objects, nodes, node sets and plain character HTML/XML
using 'vkbeautify' (by Vadim Kiryukhin) and 'highlight.js' (by Ivan Sagalaev).
Also (optionally) enables filtering of nodes via XPath or viewing an HTML/XML document
in "tree" view using 'XMLDisplay' (by Lev Muchnik). See
<https://github.com/vkiryukhin/vkBeautify> and
<http://www.levmuchnik.net/Content/ProgrammingTips/WEB/XMLDisplay/DisplayXMLFileWithJavascript.html>
for more information about 'vkbeautify' and 'XMLDisplay', respectively.
Author: Bob Rudis [aut, cre],
Dave Raggett [ctb, aut] (Original HTML Tidy library),
Charles Reitzel [ctb, aut] (Modern HTML Tidy library),
Björn Höhrmann [ctb, aut] (HTML5 Support),
Kenton Russell [aut, ctb] (xml-viewer integration),
Vadim Kiryukhin [ctb, cph] (vkbeautify library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
Lev Muchnik [ctb, cph] (xml-viewer library)
Maintainer: Bob Rudis <bob@rud.is>
Diff between htmltidy versions 0.4.0 dated 2017-09-29 and 0.5.0 dated 2019-10-03
htmltidy-0.4.0/htmltidy/README.md |only htmltidy-0.4.0/htmltidy/inst/htmlwidgets/lib/xml-viewer/package.json |only htmltidy-0.4.0/htmltidy/inst/htmlwidgets/lib/xml-viewer/treewdgt.css |only htmltidy-0.4.0/htmltidy/inst/htmlwidgets/lib/xml-viewer/xml-viewer.js |only htmltidy-0.5.0/htmltidy/DESCRIPTION | 22 - htmltidy-0.5.0/htmltidy/MD5 | 40 +- htmltidy-0.5.0/htmltidy/R/xmltreeview.R | 11 htmltidy-0.5.0/htmltidy/inst/COPYRIGHTS | 19 - htmltidy-0.5.0/htmltidy/inst/htmlwidgets/lib/jquery |only htmltidy-0.5.0/htmltidy/inst/htmlwidgets/lib/xml-viewer/LICENSE |only htmltidy-0.5.0/htmltidy/inst/htmlwidgets/lib/xml-viewer/README.md | 40 -- htmltidy-0.5.0/htmltidy/inst/htmlwidgets/lib/xml-viewer/XMLDisplay.css |only htmltidy-0.5.0/htmltidy/inst/htmlwidgets/lib/xml-viewer/XMLDisplay.js |only htmltidy-0.5.0/htmltidy/inst/htmlwidgets/lib/xml-viewer/add.png |only htmltidy-0.5.0/htmltidy/inst/htmlwidgets/lib/xml-viewer/bullet_arrow_down.png |only htmltidy-0.5.0/htmltidy/inst/htmlwidgets/lib/xml-viewer/bullet_arrow_up.png |only htmltidy-0.5.0/htmltidy/inst/htmlwidgets/lib/xml-viewer/callout.gif |only htmltidy-0.5.0/htmltidy/inst/htmlwidgets/lib/xml-viewer/draghandle.gif |only htmltidy-0.5.0/htmltidy/inst/htmlwidgets/lib/xml-viewer/exclamation.png |only htmltidy-0.5.0/htmltidy/inst/htmlwidgets/lib/xml-viewer/loader.gif |only htmltidy-0.5.0/htmltidy/inst/htmlwidgets/lib/xml-viewer/magnifier.png |only htmltidy-0.5.0/htmltidy/inst/htmlwidgets/lib/xml-viewer/minus.gif |only htmltidy-0.5.0/htmltidy/inst/htmlwidgets/lib/xml-viewer/plus.gif |only htmltidy-0.5.0/htmltidy/inst/htmlwidgets/lib/xml-viewer/xonomy.css |only htmltidy-0.5.0/htmltidy/inst/htmlwidgets/lib/xml-viewer/xonomy.js |only htmltidy-0.5.0/htmltidy/inst/htmlwidgets/xmltreeview.js | 22 + htmltidy-0.5.0/htmltidy/inst/htmlwidgets/xmltreeview.yaml | 10 htmltidy-0.5.0/htmltidy/man/tidy_html.Rd | 23 - htmltidy-0.5.0/htmltidy/man/xml_tree_view.Rd | 17 - htmltidy-0.5.0/htmltidy/src/language.c | 144 +++++----- htmltidy-0.5.0/htmltidy/src/tidyplatform.h | 6 31 files changed, 192 insertions(+), 162 deletions(-)
Title: Bayesian Applied Regression Modeling via Stan
Description: Estimates previously compiled regression models using the 'rstan'
package, which provides the R interface to the Stan C++ library for Bayesian
estimation. Users specify models via the customary R syntax with a formula and
data.frame plus some additional arguments for priors.
Author: Jonah Gabry [aut],
Imad Ali [ctb],
Sam Brilleman [ctb],
Jacqueline Buros Novik [ctb] (R/stan_jm.R),
AstraZeneca [ctb] (R/stan_jm.R),
Trustees of Columbia University [cph],
Simon Wood [cph] (R/stan_gamm4.R),
R Core Deveopment Team [cph] (R/stan_aov.R),
Douglas Bates [cph] (R/pp_data.R),
Martin Maechler [cph] (R/pp_data.R),
Ben Bolker [cph] (R/pp_data.R),
Steve Walker [cph] (R/pp_data.R),
Brian Ripley [cph] (R/stan_aov.R, R/stan_polr.R),
William Venables [cph] (R/stan_polr.R),
Paul-Christian Burkner [cph] (R/misc.R),
Ben Goodrich [cre, aut]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstanarm versions 2.18.2 dated 2018-11-10 and 2.19.2 dated 2019-10-03
rstanarm-2.18.2/rstanarm/inst/doc/children/SETTINGS-loo.txt |only rstanarm-2.18.2/rstanarm/inst/doc/children/SETTINGS-rstan.txt |only rstanarm-2.18.2/rstanarm/man/print.kfold.Rd |only rstanarm-2.18.2/rstanarm/vignettes/children/SETTINGS-loo.txt |only rstanarm-2.18.2/rstanarm/vignettes/children/SETTINGS-rstan.txt |only rstanarm-2.19.2/rstanarm/DESCRIPTION | 22 rstanarm-2.19.2/rstanarm/MD5 | 291 ++-- rstanarm-2.19.2/rstanarm/NAMESPACE | 25 rstanarm-2.19.2/rstanarm/NEWS.md | 9 rstanarm-2.19.2/rstanarm/R/bayes_R2.R | 142 + rstanarm-2.19.2/rstanarm/R/doc-adapt_delta.R | 17 rstanarm-2.19.2/rstanarm/R/doc-rstanarm-package.R | 12 rstanarm-2.19.2/rstanarm/R/jm_data_block.R | 8 rstanarm-2.19.2/rstanarm/R/log_lik.R | 5 rstanarm-2.19.2/rstanarm/R/loo-kfold.R |only rstanarm-2.19.2/rstanarm/R/loo-prediction.R | 2 rstanarm-2.19.2/rstanarm/R/loo.R | 632 ++++---- rstanarm-2.19.2/rstanarm/R/misc.R | 85 - rstanarm-2.19.2/rstanarm/R/plots.R | 32 rstanarm-2.19.2/rstanarm/R/posterior_interval.R | 2 rstanarm-2.19.2/rstanarm/R/posterior_linpred.R | 2 rstanarm-2.19.2/rstanarm/R/posterior_predict.R | 9 rstanarm-2.19.2/rstanarm/R/posterior_vs_prior.R | 1 rstanarm-2.19.2/rstanarm/R/pp_check.R | 5 rstanarm-2.19.2/rstanarm/R/print-and-summary.R | 230 +-- rstanarm-2.19.2/rstanarm/R/prior_summary.R | 154 +- rstanarm-2.19.2/rstanarm/R/priors.R | 2 rstanarm-2.19.2/rstanarm/R/stan_betareg.R | 10 rstanarm-2.19.2/rstanarm/R/stan_betareg.fit.R | 12 rstanarm-2.19.2/rstanarm/R/stan_biglm.fit.R | 96 + rstanarm-2.19.2/rstanarm/R/stan_gamm4.R | 12 rstanarm-2.19.2/rstanarm/R/stan_glm.R | 16 rstanarm-2.19.2/rstanarm/R/stan_glm.fit.R | 187 ++ rstanarm-2.19.2/rstanarm/R/stan_glmer.R | 44 rstanarm-2.19.2/rstanarm/R/stan_jm.R | 2 rstanarm-2.19.2/rstanarm/R/stan_jm.fit.R | 5 rstanarm-2.19.2/rstanarm/R/stan_lm.fit.R | 29 rstanarm-2.19.2/rstanarm/R/stan_nlmer.R | 13 rstanarm-2.19.2/rstanarm/R/stan_polr.R | 3 rstanarm-2.19.2/rstanarm/R/stanmvreg-methods.R | 6 rstanarm-2.19.2/rstanarm/R/stanreg-methods.R | 129 + rstanarm-2.19.2/rstanarm/R/stanreg.R | 2 rstanarm-2.19.2/rstanarm/R/stanreg_list.R | 282 +++ rstanarm-2.19.2/rstanarm/R/zzz.R | 5 rstanarm-2.19.2/rstanarm/build/vignette.rds |binary rstanarm-2.19.2/rstanarm/inst/doc/aov.R | 5 rstanarm-2.19.2/rstanarm/inst/doc/aov.Rmd | 9 rstanarm-2.19.2/rstanarm/inst/doc/aov.html | 307 +++- rstanarm-2.19.2/rstanarm/inst/doc/betareg.R | 12 rstanarm-2.19.2/rstanarm/inst/doc/betareg.Rmd | 16 rstanarm-2.19.2/rstanarm/inst/doc/betareg.html | 390 ++++- rstanarm-2.19.2/rstanarm/inst/doc/binomial.R | 41 rstanarm-2.19.2/rstanarm/inst/doc/binomial.Rmd | 47 rstanarm-2.19.2/rstanarm/inst/doc/binomial.html | 413 ++++- rstanarm-2.19.2/rstanarm/inst/doc/children/SETTINGS-gg.txt | 3 rstanarm-2.19.2/rstanarm/inst/doc/continuous.R | 20 rstanarm-2.19.2/rstanarm/inst/doc/continuous.Rmd | 24 rstanarm-2.19.2/rstanarm/inst/doc/continuous.html | 462 ++++-- rstanarm-2.19.2/rstanarm/inst/doc/count.R | 24 rstanarm-2.19.2/rstanarm/inst/doc/count.Rmd | 39 rstanarm-2.19.2/rstanarm/inst/doc/count.html | 346 +++- rstanarm-2.19.2/rstanarm/inst/doc/glmer.R | 12 rstanarm-2.19.2/rstanarm/inst/doc/glmer.Rmd | 30 rstanarm-2.19.2/rstanarm/inst/doc/glmer.html | 368 ++++- rstanarm-2.19.2/rstanarm/inst/doc/interaction.rda |only rstanarm-2.19.2/rstanarm/inst/doc/jm.Rmd | 5 rstanarm-2.19.2/rstanarm/inst/doc/jm.html | 470 ++++-- rstanarm-2.19.2/rstanarm/inst/doc/lm.R | 27 rstanarm-2.19.2/rstanarm/inst/doc/lm.Rmd | 34 rstanarm-2.19.2/rstanarm/inst/doc/lm.html | 343 +++- rstanarm-2.19.2/rstanarm/inst/doc/mrp-files |only rstanarm-2.19.2/rstanarm/inst/doc/mrp.R |only rstanarm-2.19.2/rstanarm/inst/doc/mrp.Rmd |only rstanarm-2.19.2/rstanarm/inst/doc/mrp.bib |only rstanarm-2.19.2/rstanarm/inst/doc/mrp.html |only rstanarm-2.19.2/rstanarm/inst/doc/mrp_sim.rda |only rstanarm-2.19.2/rstanarm/inst/doc/plot_data.rda |only rstanarm-2.19.2/rstanarm/inst/doc/polr.R | 7 rstanarm-2.19.2/rstanarm/inst/doc/polr.Rmd | 11 rstanarm-2.19.2/rstanarm/inst/doc/polr.html | 329 +++- rstanarm-2.19.2/rstanarm/inst/doc/pooling.R | 2 rstanarm-2.19.2/rstanarm/inst/doc/pooling.Rmd | 6 rstanarm-2.19.2/rstanarm/inst/doc/pooling.html | 714 ++++++---- rstanarm-2.19.2/rstanarm/inst/doc/preference_by_state.rda |only rstanarm-2.19.2/rstanarm/inst/doc/priors.R | 13 rstanarm-2.19.2/rstanarm/inst/doc/priors.Rmd | 4 rstanarm-2.19.2/rstanarm/inst/doc/priors.html | 385 ++++- rstanarm-2.19.2/rstanarm/inst/doc/rstanarm.R | 12 rstanarm-2.19.2/rstanarm/inst/doc/rstanarm.Rmd | 27 rstanarm-2.19.2/rstanarm/inst/doc/rstanarm.html | 422 ++++- rstanarm-2.19.2/rstanarm/inst/doc/sample_alt.rda |only rstanarm-2.19.2/rstanarm/inst/doc/state_plot_data.rda |only rstanarm-2.19.2/rstanarm/inst/doc/summary_by_poststrat_var.rda |only rstanarm-2.19.2/rstanarm/man/QR-argument.Rd | 4 rstanarm-2.19.2/rstanarm/man/adapt_delta.Rd | 21 rstanarm-2.19.2/rstanarm/man/bayes_R2.stanreg.Rd | 45 rstanarm-2.19.2/rstanarm/man/kfold.stanreg.Rd |only rstanarm-2.19.2/rstanarm/man/launch_shinystan.stanreg.Rd | 10 rstanarm-2.19.2/rstanarm/man/loo.stanreg.Rd | 260 +-- rstanarm-2.19.2/rstanarm/man/loo_predict.stanreg.Rd | 10 rstanarm-2.19.2/rstanarm/man/plot.stanreg.Rd | 13 rstanarm-2.19.2/rstanarm/man/posterior_vs_prior.Rd | 10 rstanarm-2.19.2/rstanarm/man/pp_check.stanreg.Rd | 10 rstanarm-2.19.2/rstanarm/man/print.stanreg.Rd | 14 rstanarm-2.19.2/rstanarm/man/priors.Rd | 6 rstanarm-2.19.2/rstanarm/man/rstanarm-package.Rd | 14 rstanarm-2.19.2/rstanarm/man/stan_biglm.Rd | 15 rstanarm-2.19.2/rstanarm/man/stan_glm.Rd | 14 rstanarm-2.19.2/rstanarm/man/stan_glmer.Rd | 8 rstanarm-2.19.2/rstanarm/man/stan_jm.Rd | 2 rstanarm-2.19.2/rstanarm/man/stanreg-methods.Rd | 14 rstanarm-2.19.2/rstanarm/man/stanreg_list.Rd | 29 rstanarm-2.19.2/rstanarm/man/summary.stanreg.Rd | 14 rstanarm-2.19.2/rstanarm/src/stan_files/bernoulli.stan | 57 rstanarm-2.19.2/rstanarm/src/stan_files/binomial.stan | 28 rstanarm-2.19.2/rstanarm/src/stan_files/continuous.stan | 209 +- rstanarm-2.19.2/rstanarm/src/stan_files/count.stan | 81 - rstanarm-2.19.2/rstanarm/src/stan_files/lm.stan | 14 rstanarm-2.19.2/rstanarm/src/stan_files/model/assoc_evaluate.stan | 229 +-- rstanarm-2.19.2/rstanarm/src/stan_files/polr.stan | 20 rstanarm-2.19.2/rstanarm/tests/testthat.R | 6 rstanarm-2.19.2/rstanarm/tests/testthat/helpers/expect_equivalent_loo.R | 2 rstanarm-2.19.2/rstanarm/tests/testthat/stan_files/bernoulli.stan | 57 rstanarm-2.19.2/rstanarm/tests/testthat/stan_files/binomial.stan | 28 rstanarm-2.19.2/rstanarm/tests/testthat/stan_files/continuous.stan | 209 +- rstanarm-2.19.2/rstanarm/tests/testthat/stan_files/count.stan | 81 - rstanarm-2.19.2/rstanarm/tests/testthat/stan_files/lm.stan | 14 rstanarm-2.19.2/rstanarm/tests/testthat/stan_files/model/assoc_evaluate.stan | 229 +-- rstanarm-2.19.2/rstanarm/tests/testthat/stan_files/polr.stan | 20 rstanarm-2.19.2/rstanarm/tests/testthat/test_loo.R | 126 - rstanarm-2.19.2/rstanarm/tests/testthat/test_misc.R | 21 rstanarm-2.19.2/rstanarm/tests/testthat/test_stan_functions.R | 15 rstanarm-2.19.2/rstanarm/tests/testthat/test_stan_glm.R | 20 rstanarm-2.19.2/rstanarm/tests/testthat/test_stan_glmer.R | 35 rstanarm-2.19.2/rstanarm/tests/testthat/test_stan_mvmer.R | 10 rstanarm-2.19.2/rstanarm/vignettes/aov.Rmd | 9 rstanarm-2.19.2/rstanarm/vignettes/betareg.Rmd | 16 rstanarm-2.19.2/rstanarm/vignettes/binomial.Rmd | 47 rstanarm-2.19.2/rstanarm/vignettes/children/SETTINGS-gg.txt | 3 rstanarm-2.19.2/rstanarm/vignettes/continuous.Rmd | 24 rstanarm-2.19.2/rstanarm/vignettes/count.Rmd | 39 rstanarm-2.19.2/rstanarm/vignettes/glmer.Rmd | 30 rstanarm-2.19.2/rstanarm/vignettes/jm.Rmd | 5 rstanarm-2.19.2/rstanarm/vignettes/lm.Rmd | 34 rstanarm-2.19.2/rstanarm/vignettes/mrp-files |only rstanarm-2.19.2/rstanarm/vignettes/mrp.Rmd |only rstanarm-2.19.2/rstanarm/vignettes/polr.Rmd | 11 rstanarm-2.19.2/rstanarm/vignettes/pooling.Rmd | 6 rstanarm-2.19.2/rstanarm/vignettes/priors.Rmd | 4 rstanarm-2.19.2/rstanarm/vignettes/rstanarm.Rmd | 27 150 files changed, 6857 insertions(+), 3341 deletions(-)
Title: Reproducible Research Tools
Description: Reproducible research tools automates the creation of an analysis directory structure and work flow. There are R markdown
skeletons which encapsulate typical analytic work flow steps. Functions will create appropriate modules which may
pass data from one step to another.
Author: Brian Fannin [aut, cre]
Maintainer: Brian Fannin <captain@pirategrunt.com>
Diff between represtools versions 0.1.2 dated 2016-08-30 and 0.1.3 dated 2019-10-03
represtools-0.1.2/represtools/inst/templates/rstudio.Rproj |only represtools-0.1.3/represtools/DESCRIPTION | 15 +- represtools-0.1.3/represtools/MD5 | 37 ++--- represtools-0.1.3/represtools/README.md | 4 represtools-0.1.3/represtools/build/vignette.rds |binary represtools-0.1.3/represtools/inst/doc/represtools.html | 71 +++++++--- represtools-0.1.3/represtools/man/Analyze.Rd | 1 represtools-0.1.3/represtools/man/Cook.Rd | 1 represtools-0.1.3/represtools/man/DescribeObjects.Rd | 1 represtools-0.1.3/represtools/man/Gather.Rd | 1 represtools-0.1.3/represtools/man/GetSQL.Rd | 1 represtools-0.1.3/represtools/man/ListObjects.Rd | 1 represtools-0.1.3/represtools/man/LoadObjects.Rd | 1 represtools-0.1.3/represtools/man/Make.Rd | 1 represtools-0.1.3/represtools/man/NamesToObjects.Rd | 1 represtools-0.1.3/represtools/man/NewResearch.Rd | 1 represtools-0.1.3/represtools/man/OutputFile.Rd | 1 represtools-0.1.3/represtools/man/Present.Rd | 1 represtools-0.1.3/represtools/man/represtools.Rd | 1 represtools-0.1.3/represtools/tests/testthat/testNewAnalysis.R | 5 20 files changed, 78 insertions(+), 67 deletions(-)
Title: Read SDMX-XML Data
Description: Read Statistical Data and Metadata Exchange (SDMX) XML data.
This the main transmission format used in official statistics. Data can be imported from
local SDMX-ML files or a SDMX web-service and will be read in 'as is' into a dataframe object.
The 'RapidXML' C++ library <http://rapidxml.sourceforge.net> is used to parse the XML data.
Author: Matthew de Queljoe [aut, cre],
Marcin Kalicinski [ctb, cph] (Author of RapidXML library),
Emmanuel Blondel [ctb, cph] (<https://orcid.org/0000-0002-5870-5762>,
SDMX-ML test files),
SDMX org [ctb, cph] (SDMX-ML test files)
Maintainer: Matthew de Queljoe <matthew.dequeljoe@gmail.com>
Diff between readsdmx versions 0.2.2 dated 2019-02-01 and 0.3.0 dated 2019-10-03
DESCRIPTION | 12 - MD5 | 40 +++- NEWS.md | 35 ++-- R/readsdmx.R | 6 README.md | 19 +- inst/extdata/codelist_2.0.xml | 14 + inst/extdata/compact_2.0_BIS.xml |only inst/extdata/cross_sectional_2.0.xml |only inst/extdata/generic_ecb_exr_rg_flat.xml |only inst/extdata/generic_ecb_exr_rg_ts.xml |only inst/extdata/generic_ecb_exr_rg_ts_gf.xml |only inst/extdata/generic_ecb_exr_rg_xs.xml |only inst/extdata/insee_ssd.xml |only inst/extdata/utility_2.0.xml |only man/read_sdmx.Rd | 9 - src/compactdata.h | 144 +++++++---------- src/cross_sectionaldata.h |only src/datamessage.h | 165 +++++++++++-------- src/genericdata.h | 252 ++++++++++++++---------------- src/readsdmx.cpp | 41 ++-- src/structuredata.h | 122 +++++++------- src/utilitydata.h |only tests/testthat/test_compact.R | 34 +++- tests/testthat/test_cross_sectional.R |only tests/testthat/test_generic.R | 36 ++++ tests/testthat/test_structure.R | 13 + tests/testthat/test_utility.R |only 27 files changed, 538 insertions(+), 404 deletions(-)
Title: Kaplan-Meier Plot with 'ggplot2'
Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jskm versions 0.3.6 dated 2019-09-04 and 0.3.7 dated 2019-10-03
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NEWS.md | 4 ++++ R/jskm.R | 14 ++++++++++---- R/svyjskm.R | 14 ++++++++++---- inst/doc/jskm.html | 8 ++++---- man/figures/README-unnamed-chunk-1-1.png |binary man/figures/README-unnamed-chunk-1-2.png |binary man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-3-2.png |binary man/figures/README-unnamed-chunk-3-3.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-4-2.png |binary 14 files changed, 45 insertions(+), 29 deletions(-)
Title: Serialize R Objects to JSON, JavaScript Object Notation
Description: This is a package that allows conversion to and from
data in Javascript object notation (JSON) format.
This allows R objects to be inserted into Javascript/ECMAScript/ActionScript code
and allows R programmers to read and convert JSON content to R objects.
This is an alternative to rjson package. Originally, that was too slow for converting large R objects to JSON
and was not extensible. rjson's performance is now similar to this package, and perhaps slightly faster in some cases.
This package uses methods and is readily extensible by defining methods for different classes,
vectorized operations, and C code and callbacks to R functions for deserializing JSON objects to R.
The two packages intentionally share the same basic interface. This package (RJSONIO) has many additional
options to allow customizing the generation and processing of JSON content.
This package uses libjson rather than implementing yet another JSON parser. The aim is to support
other general projects by building on their work, providing feedback and benefit from their ongoing development.
Author: Duncan Temple Lang [aut, cre] (<https://orcid.org/0000-0003-0159-1546>),
Jonathan Wallace [aut] (aka ninja9578, author of included libjson
sources)
Maintainer: ORPHANED
Diff between RJSONIO versions 1.3-1.2 dated 2019-06-04 and 1.3-1.3 dated 2019-10-03
DESCRIPTION | 6 ++--- MD5 | 6 ++--- src/libjson/Source/JSONValidator.cpp | 40 +++++++++++++++++------------------ src/libjson/Source/JSONWorker.cpp | 8 +++---- 4 files changed, 30 insertions(+), 30 deletions(-)
Title: Transformation Trees and Forests
Description: Recursive partytioning of transformation models with
corresponding random forest for conditional transformation models
as described in 'Transformation Forests' (Hothorn and Zeileis, 2017, <arXiv:1701.02110>)
and 'Top-Down Transformation Choice' (Hothorn, 2018, <DOI:10.1177/1471082X17748081>).
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between trtf versions 0.3-5 dated 2019-02-04 and 0.3-6 dated 2019-10-03
DESCRIPTION | 9 +- MD5 | 33 ++++++--- R/methods.R | 4 - R/trees_forests.R | 60 +++++++++++++----- inst/NEWS.Rd | 14 ++++ inst/ordinal_forests |only inst/survival_forests/predictive/tr_data_simulation.R | 3 inst/survival_forests/prognostic/data_simulation.R | 3 man/traforest.Rd | 12 +++ man/trafotree.Rd | 10 +++ tests/GBSG2-Ex.R | 2 tests/regtest-traforest.R | 2 tests/regtest-trafotree.R | 2 13 files changed, 122 insertions(+), 32 deletions(-)
Title: Analyzing Real-Time Quantitative PCR Data
Description: Calculates the amplification efficiency and curves from real-time
quantitative PCR (Polymerase Chain Reaction) data. Estimates the relative
expression from PCR data using the double delta CT and the standard curve
methods Livak & Schmittgen (2001) <doi:10.1006/meth.2001.1262>. Tests for
statistical significance using two-group tests and linear regression
Yuan et al. (2006) <doi: 10.1186/1471-2105-7-85>.
Author: Mahmoud Ahmed [aut, cre] (<https://orcid.org/0000-0002-4377-6541>)
Maintainer: Mahmoud Ahmed <mahmoud.s.fahmy@students.kasralainy.edu.eg>
Diff between pcr versions 1.1.2 dated 2018-07-24 and 1.2.0 dated 2019-10-03
DESCRIPTION | 17 - MD5 | 75 ++-- NAMESPACE | 20 - NEWS.md | 11 R/analyses_fun.R | 358 ++++++++++++--------- R/assessment_fun.R | 116 ++++--- R/helper_fun.R | 571 ++++++++--------------------------- R/pcr.R | 23 - R/plotting_fun.R | 107 +++--- R/testing_fun.R | 247 +++++++++------ README.md | 15 inst/CITATION |only inst/doc/qpcr_analysis.R | 38 +- inst/doc/qpcr_analysis.Rmd | 40 +- inst/doc/qpcr_analysis.html | 86 ++--- man/dot-pcr_amount.Rd |only man/dot-pcr_average.Rd |only man/dot-pcr_cv.Rd |only man/dot-pcr_error.Rd |only man/dot-pcr_intercept.Rd |only man/dot-pcr_normalize.Rd |only man/dot-pcr_plot_analyze.Rd |only man/dot-pcr_plot_assess.Rd |only man/dot-pcr_relative.Rd |only man/dot-pcr_rsquared.Rd |only man/dot-pcr_sd.Rd |only man/dot-pcr_slope.Rd |only man/pcr.Rd | 8 man/pcr_analyze.Rd | 8 man/pcr_assess.Rd | 10 man/pcr_curve.Rd | 11 man/pcr_dct.Rd | 12 man/pcr_ddct.Rd | 43 +- man/pcr_efficiency.Rd | 33 +- man/pcr_lm.Rd | 21 - man/pcr_standard.Rd | 15 man/pcr_test.Rd | 21 - man/pcr_ttest.Rd | 16 man/pcr_wilcox.Rd | 17 - tests/testthat/test_analyses_fun.R | 306 +++++------------- tests/testthat/test_assessment_fun.R | 18 - tests/testthat/test_helper_fun.R | 114 ++---- tests/testthat/test_plotting_fun.R | 19 - tests/testthat/test_testing_fun.R | 95 +++++ vignettes/qpcr_analysis.Rmd | 40 +- 45 files changed, 1151 insertions(+), 1380 deletions(-)
Title: Talking to 'Docker' and 'Singularity' Containers
Description: Provides a unified interface to interact with 'docker' and 'singularity' containers.
You can execute a command inside a container, mount a volume or copy a file.
Author: Robrecht Cannoodt [aut] (<https://orcid.org/0000-0003-3641-729X>,
rcannood),
Wouter Saelens [aut, cre] (<https://orcid.org/0000-0002-7114-6248>,
zouter)
Maintainer: Wouter Saelens <wouter.saelens@gmail.com>
Diff between babelwhale versions 1.0.0 dated 2019-07-09 and 1.0.1 dated 2019-10-03
babelwhale-1.0.0/babelwhale/inst |only babelwhale-1.0.1/babelwhale/DESCRIPTION | 6 +- babelwhale-1.0.1/babelwhale/MD5 | 16 +++---- babelwhale-1.0.1/babelwhale/NEWS.md |only babelwhale-1.0.1/babelwhale/R/config_default.R | 2 babelwhale-1.0.1/babelwhale/R/run.R | 1 babelwhale-1.0.1/babelwhale/README.md | 21 +++++----- babelwhale-1.0.1/babelwhale/tests/testthat/test-config_default.R |only babelwhale-1.0.1/babelwhale/tests/testthat/test-copy_file.R | 2 babelwhale-1.0.1/babelwhale/tests/testthat/test-run_docker.R | 7 ++- 10 files changed, 30 insertions(+), 25 deletions(-)
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Butler A and Satija R (2017) <doi:10.1101/164889> for more details.
Author: Rahul Satija [aut] (<https://orcid.org/0000-0001-9448-8833>),
Andrew Butler [aut] (<https://orcid.org/0000-0003-3608-0463>),
Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>),
Tim Stuart [aut] (<https://orcid.org/0000-0002-3044-0897>),
Jeff Farrell [ctb],
Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>),
Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>),
Patrick Roelli [ctb],
Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>)
Maintainer: Paul Hoffman <nygcSatijalab@nygenome.org>
Diff between Seurat versions 3.1.0 dated 2019-08-20 and 3.1.1 dated 2019-10-03
DESCRIPTION | 15 +- MD5 | 36 +++-- NAMESPACE | 8 + NEWS.md | 20 ++- R/convenience.R | 7 - R/data.R | 47 +++++++ R/dimensional_reduction.R | 16 ++ R/integration.R | 6 R/objects.R | 185 +++++++++++++++++++++++------- R/preprocessing.R | 26 +++- R/utilities.R | 251 ++++++++++++++++++++++++++++++++++++++++- README.md | 2 data/cc.genes.updated.2019.rda |only man/AddModuleScore.Rd | 9 + man/RegroupIdents.Rd |only man/RunUMAP.Rd | 16 +- man/UpdateSymbolList.Rd |only man/cc.genes.Rd | 2 man/cc.genes.updated.2019.Rd |only man/h5ad.Rd | 10 + man/pbmc_small.Rd | 2 21 files changed, 559 insertions(+), 99 deletions(-)
Title: Partitioning Hierarchical Diversity and Differentiation Across
Metrics and Scales, from Genes to Ecosystems
Description: Miscellaneous R functions for calculating and decomposing hierarchical diversity metrics, including hierarchical allele richness, hierarchical exponential Shannon entropy (true diversity of order q=1), hierarchical heterozygosity and genetic differentiation (Jaccard dissimilarity, Delta D,Fst and Jost's D). In addition,a new approach to identify population structure based on the homogeneity of multivariate variances of Shannon differentiation is presented. This package allows you to analyse spatial structured genetic data or species data under a unifying framework (Gaggiotti, O. E. et al, 2018, Evol Appl, 11:1176-1193; <DOI:10.1111/eva.12593>), which partitions diversity and differentiation into any hierarchical levels. It helps you easily structure and format your data. In summary,it implements the analyses of true diversity profiles (q=0,1,2), hierarchical diversities and differentiation decomposition, visualization of population structure, as well as the estimation of correlation between geographic distance and genetic differentiation.
Author: Xinghu Qin
Maintainer: Xinghu Qin <qinxinghu@gmail.com>
Diff between HierDpart versions 0.3.5 dated 2019-02-13 and 0.5.0 dated 2019-10-03
HierDpart-0.3.5/HierDpart/R/HierAr.R |only HierDpart-0.3.5/HierDpart/R/HierHe.R |only HierDpart-0.3.5/HierDpart/R/plot.aggegates.R |only HierDpart-0.3.5/HierDpart/README.md |only HierDpart-0.5.0/HierDpart/DESCRIPTION | 14 HierDpart-0.5.0/HierDpart/MD5 | 27 HierDpart-0.5.0/HierDpart/NAMESPACE | 7 HierDpart-0.5.0/HierDpart/R/HierAr_updated.R |only HierDpart-0.5.0/HierDpart/R/HierDjost.R |only HierDpart-0.5.0/HierDpart/R/HierFst.R | 2 HierDpart-0.5.0/HierDpart/R/HierHe_updated.R |only HierDpart-0.5.0/HierDpart/R/HierJd.R |only HierDpart-0.5.0/HierDpart/R/plot.aggregates.R |only HierDpart-0.5.0/HierDpart/R/pwDeltaD.R |only HierDpart-0.5.0/HierDpart/inst/doc/HierDpart.html | 680 +++++++++++++++------- HierDpart-0.5.0/HierDpart/inst/extdata/Island |only HierDpart-0.5.0/HierDpart/inst/extdata/Island.txt |only HierDpart-0.5.0/HierDpart/man/HierAr.Rd | 2 HierDpart-0.5.0/HierDpart/man/HierDjost.Rd |only HierDpart-0.5.0/HierDpart/man/HierHe.Rd | 6 HierDpart-0.5.0/HierDpart/man/HierJd.Rd |only HierDpart-0.5.0/HierDpart/man/pwDeltaD.Rd |only 22 files changed, 510 insertions(+), 228 deletions(-)
Title: Tools for Working with Geohashes
Description: Tools for working with Gustavo Niemeyer's geohash coordinate system, including API for interacting with other common R GIS libraries.
Author: Michael Chirico [aut, cre],
Dmitry Shkolnik [ctb]
Maintainer: Michael Chirico <MichaelChirico4@gmail.com>
Diff between geohashTools versions 0.2.4 dated 2019-08-26 and 0.3.0 dated 2019-10-03
geohashTools-0.2.4/geohashTools/R/RcppExports.R |only geohashTools-0.2.4/geohashTools/src/RcppExports.cpp |only geohashTools-0.2.4/geohashTools/src/geohash.cpp |only geohashTools-0.3.0/geohashTools/DESCRIPTION | 18 geohashTools-0.3.0/geohashTools/LICENSE | 375 +++++++++- geohashTools-0.3.0/geohashTools/MD5 | 43 - geohashTools-0.3.0/geohashTools/NAMESPACE | 1 geohashTools-0.3.0/geohashTools/NEWS.md | 32 geohashTools-0.3.0/geohashTools/R/gh_decode.R | 22 geohashTools-0.3.0/geohashTools/R/gh_encode.R | 6 geohashTools-0.3.0/geohashTools/R/gh_neighbors.R | 6 geohashTools-0.3.0/geohashTools/R/gis_tools.R | 24 geohashTools-0.3.0/geohashTools/R/onLoad.R | 6 geohashTools-0.3.0/geohashTools/README.md | 141 ++- geohashTools-0.3.0/geohashTools/man/gh_decode.Rd | 3 geohashTools-0.3.0/geohashTools/man/gh_encode.Rd | 3 geohashTools-0.3.0/geohashTools/man/gh_neighbors.Rd | 5 geohashTools-0.3.0/geohashTools/man/utils.Rd | 3 geohashTools-0.3.0/geohashTools/src/geohash.c |only geohashTools-0.3.0/geohashTools/src/geohash.h | 74 + geohashTools-0.3.0/geohashTools/src/init.c |only geohashTools-0.3.0/geohashTools/tests/testthat/test-decode.R | 5 geohashTools-0.3.0/geohashTools/tests/testthat/test-encode.R | 32 geohashTools-0.3.0/geohashTools/tests/testthat/test-gis-tools.R | 69 + geohashTools-0.3.0/geohashTools/tests/testthat/test-neighbors.R | 50 - 25 files changed, 714 insertions(+), 204 deletions(-)
Title: Simultaneous Enrichment Analysis
Description: SEA performs simultaneous feature-set testing for (gen)omics data. It tests the unified null hypothesis and controls the family-wise error rate for all possible pathways. The unified null hypothesis is defined as: "The proportion of true features in the set is less than or equal to a threshold." Family-wise error rate control is provided through use of closed testing with Simes test. There are some practical functions to play around with the pathways of interest.
Author: Mitra Ebrahimpoor
Maintainer: Mitra Ebrahimpoor<m.ebrahimpoor@lumc.nl>
Diff between rSEA versions 1.0.1 dated 2019-02-21 and 2.0.0 dated 2019-10-03
rSEA-1.0.1/rSEA/R/sea.test-function.R |only rSEA-1.0.1/rSEA/R/sea.top-function.R |only rSEA-1.0.1/rSEA/R/set.test-function.R |only rSEA-1.0.1/rSEA/R/sysdata.rda |only rSEA-1.0.1/rSEA/R/tdphat-function.R |only rSEA-1.0.1/rSEA/man/sea.test-function.Rd |only rSEA-1.0.1/rSEA/man/sea.top-function.Rd |only rSEA-1.0.1/rSEA/man/set.test-function.Rd |only rSEA-1.0.1/rSEA/man/tdphat-function.Rd |only rSEA-2.0.0/rSEA/DESCRIPTION | 13 +++++++------ rSEA-2.0.0/rSEA/MD5 | 23 +++++++++++------------ rSEA-2.0.0/rSEA/NAMESPACE | 11 ++++++++--- rSEA-2.0.0/rSEA/R/sea.R |only rSEA-2.0.0/rSEA/R/settdp.R |only rSEA-2.0.0/rSEA/R/settest.R |only rSEA-2.0.0/rSEA/R/topsea.R |only rSEA-2.0.0/rSEA/man/SEA.Rd |only rSEA-2.0.0/rSEA/man/rSEA-package.Rd | 13 +++++-------- rSEA-2.0.0/rSEA/man/setTDP.Rd |only rSEA-2.0.0/rSEA/man/setTest.Rd |only rSEA-2.0.0/rSEA/man/topSEA.Rd |only 21 files changed, 31 insertions(+), 29 deletions(-)
Title: Object Pooling
Description: Enables the creation of object pools, which make it less
computationally expensive to fetch a new object. Currently the
only supported pooled objects are 'DBI' connections.
Author: Joe Cheng [aut, cre],
Barbara Borges [aut],
RStudio [cph]
Maintainer: Joe Cheng <joe@rstudio.com>
Diff between pool versions 0.1.4.2 dated 2019-01-07 and 0.1.4.3 dated 2019-10-03
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/scheduler.R | 9 +++++++-- tests/testthat/test-create-destroy.R | 22 ++++++++++++++++++---- 5 files changed, 37 insertions(+), 13 deletions(-)
Title: Common Functionality for the 'dynverse' Packages
Description: Provides common functionality for the 'dynverse' packages.
'dynverse' is created to support the development, execution, and benchmarking of trajectory inference methods.
For more information, check out <https://dynverse.org>.
Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>,
rcannood),
Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>, zouter)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between dynutils versions 1.0.3 dated 2019-05-02 and 1.0.4 dated 2019-10-03
dynutils-1.0.3/dynutils/inst/NEWS |only dynutils-1.0.3/dynutils/inst/NEWS.md |only dynutils-1.0.3/dynutils/man/update_news.Rd |only dynutils-1.0.4/dynutils/DESCRIPTION | 8 +- dynutils-1.0.4/dynutils/MD5 | 30 +++++------ dynutils-1.0.4/dynutils/NAMESPACE | 1 dynutils-1.0.4/dynutils/NEWS.md |only dynutils-1.0.4/dynutils/R/development.R | 3 - dynutils-1.0.4/dynutils/R/news.R | 38 ++------------ dynutils-1.0.4/dynutils/R/package.R | 7 +- dynutils-1.0.4/dynutils/README.md | 28 ++++------ dynutils-1.0.4/dynutils/build/vignette.rds |binary dynutils-1.0.4/dynutils/inst/doc/functionality.R | 2 dynutils-1.0.4/dynutils/inst/doc/functionality.Rmd | 5 - dynutils-1.0.4/dynutils/inst/doc/functionality.html | 54 ++++++++++---------- dynutils-1.0.4/dynutils/man/dynutils.Rd | 7 +- dynutils-1.0.4/dynutils/tests/testthat/test-news.R | 16 ----- dynutils-1.0.4/dynutils/vignettes/functionality.Rmd | 5 - 18 files changed, 80 insertions(+), 124 deletions(-)
Title: Cross-Validation for Model Selection
Description: Cross-validate one or multiple regression and classification models
and get relevant evaluation metrics in a tidy format. Validate the
best model on a test set and compare it to a baseline evaluation.
Alternatively, evaluate predictions from an external model. Currently
supports regression and classification (binary and multiclass).
Described in chp. 5 of Jeyaraman, B. P., Olsen, L. R.,
& Wambugu M. (2019, ISBN: 9781838550134).
Author: Ludvig Renbo Olsen [aut, cre],
Benjamin Hugh Zachariae [aut]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between cvms versions 0.3.0 dated 2019-09-29 and 0.3.1 dated 2019-10-03
DESCRIPTION | 6 MD5 | 55 +++--- NAMESPACE | 1 NEWS.md | 7 R/baseline_binomial.R | 39 +++- R/baseline_multinomial.R | 2 R/basics_cross_validate_list.R | 6 R/basics_model_fn.R | 2 R/basics_update_model_specifics.R | 4 R/basics_validate_list.R | 10 - R/binomial_classification_eval.R | 2 R/binomial_eval.R | 14 - R/create_boxplot.R | 2 R/cross_validate_fn.R | 43 ++--- R/cross_validate_fn_single.R | 12 + R/custom_cross_validate_list.R | 10 - R/custom_model_fn.R | 262 ++------------------------------ R/custom_run_predict_fn.R |only R/evaluate.R | 2 R/extract_model_effects.R | 6 R/helpers.R | 44 +++-- R/linear_regression_eval.R | 14 - R/nesting_predictions.R | 6 R/run_model_fitting.R | 13 - R/validate_fn_single.R | 2 build/cvms.pdf |binary man/cross_validate_fn.Rd | 45 ++--- tests/testthat/test_cross_validate_fn.R | 74 ++++++--- tests/testthat/test_metrics.R | 24 +- 29 files changed, 277 insertions(+), 430 deletions(-)
Title: Robust Regression with Data Driven Tuning Parameter
Description: Data driven approach for robust regression estimation in homoscedastic and heteroscedastic context. See Wang et al. (2007), <doi:10.1198/106186007X180156> regarding homoscedastic framework.
Author: You-Gan Wang, Benoit Liquet, Aurelien Callens and Na Wang.
Maintainer: You-Gan Wang <you-gan.wang@qut.edu.au>
Diff between rlmDataDriven versions 0.3.0 dated 2019-05-17 and 0.4.0 dated 2019-10-03
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Interface to Geometry Engine - Open Source ('GEOS')
Description: Interface to Geometry Engine - Open Source ('GEOS') using the C 'API' for topology operations on geometries. The 'GEOS' library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on 'CRAN'. ('rgeos' >= 0.5-1): Up to and including 'GEOS' 3.7.1, topological operations succeeded with some invalid geometries for which the same operations fail from and including 'GEOS' 3.7.2. The 'checkValidity=' argument defaults and structure have been changed, from default FALSE to integer default '0L' for 'GEOS' < 3.7.2 (no check), '1L' 'GEOS' >= 3.7.2 (check and warn). A value of '2L' is also provided that may be used, assigned globally using 'set_RGEOS_CheckValidity(2L)', or locally using the 'checkValidity=2L' argument, to attempt zero-width buffer repair if invalid geometries are found. The previous default (FALSE, now '0L') is fastest and used for 'GEOS' < 3.7.2, but will not warn users of possible problems before the failure of topological operations that previously succeeded.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Colin Rundel [aut],
Edzer Pebesma [ctb],
Rainer Stuetz [ctb],
Karl Ove Hufthammer [ctb],
Patrick Giraudoux [ctb],
Martin Davis [cph, ctb],
Sandro Santilli [cph, ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgeos versions 0.5-1 dated 2019-08-05 and 0.5-2 dated 2019-10-03
ChangeLog | 18 ++++++++++++++++++ DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- R/rgeos_predicate_binary.R | 17 ++++++++++++----- configure | 37 +++++++++++++++++-------------------- configure.ac | 16 ++++++++-------- inst/ChangeLog | 18 ++++++++++++++++++ inst/SVN_VERSION | 2 +- man/pred-binary-gIntersects.Rd | 14 ++++++++++++++ 9 files changed, 101 insertions(+), 47 deletions(-)
Title: Systematic Conservation Prioritization in R
Description: Conservation prioritization using integer
programming techniques. To solve large-scale problems, users
should install the 'gurobi' optimizer
(available from <http://www.gurobi.com/>).
Author: Jeffrey O Hanson [aut],
Richard Schuster [aut, cre],
Nina Morrell [aut],
Matthew Strimas-Mackey [aut],
Matthew E Watts [aut],
Peter Arcese [aut],
Joseph Bennett [aut],
Hugh P Possingham [aut]
Maintainer: Richard Schuster <richard.schuster@glel.carleton.ca>
Diff between prioritizr versions 4.1.3 dated 2019-09-06 and 4.1.4 dated 2019-10-03
DESCRIPTION | 6 - MD5 | 36 ++++----- R/add_locked_in_constraints.R | 1 R/fast_extract.R | 2 R/rij_matrix.R | 13 ++- README.md | 10 +- inst/doc/gurobi_installation.html | 8 +- inst/doc/prioritizr.html | 2 inst/doc/publication_record.Rmd | 15 ++-- inst/doc/publication_record.html | 15 ++-- inst/doc/saltspring.html | 2 inst/doc/tasmania.html | 122 ++++++++++++++++----------------- inst/doc/zones.html | 12 +-- man/add_locked_in_constraints.Rd | 1 man/fast_extract.Rd | 2 man/rij_matrix.Rd | 6 + tests/testthat/test_replacement_cost.R | 2 vignettes/publication_record.Rmd | 15 ++-- vignettes/references.bib | 2 19 files changed, 143 insertions(+), 129 deletions(-)
Title: Sensitivity Analysis of Neural Networks
Description: Analysis functions to quantify inputs importance in neural network models.
Functions are available for calculating and plotting the inputs importance and obtaining
the activation function of each neuron layer and its derivatives. The importance of a given
input is defined as the distribution of the derivatives of the output with respect to that
input in each training data point.
Author: José Portela González [aut],
Antonio Muñoz San Roque [aut],
Jaime Pizarroso Gonzalo [ctb, cre]
Maintainer: Jaime Pizarroso Gonzalo <jpizarroso@alu.comillas.edu>
Diff between NeuralSens versions 0.0.8 dated 2019-09-28 and 0.0.9 dated 2019-10-03
DESCRIPTION | 6 - MD5 | 24 +++---- R/ActFunc.R | 57 +++++++++++++++--- R/NeuralSens-package.R | 2 R/SensAnalysisMLP.R | 145 +++++++++++++++++++++++++++++++++-------------- R/SensTimePlot.R | 2 R/SensitivityPlots.R | 2 R/data.R | 51 ++++++++++------ data/syntheticdata.rdata |binary man/NeuralSens.Rd | 2 man/SensAnalysisMLP.Rd | 35 +++++------ man/SensTimePlot.Rd | 2 man/syntheticdata.Rd | 51 ++++++++++------ 13 files changed, 253 insertions(+), 126 deletions(-)
Title: A Shiny Application for Automatic Measurements of Tree-Ring
Widths on Digital Images
Description: Use morphological image processing and edge detection algorithms to automatically measure tree ring widths on digital images. Users can also manually mark tree rings on species with complex anatomical structures. The arcs of inner-rings and angles of successive inclined ring boundaries are used to correct ring-width series. The package provides a Shiny-based application, allowing R beginners to easily analyze tree ring images and export ring-width series in standard file formats.
Author: Jingning Shi [aut, cre],
Wei Xiang [aut]
Maintainer: Jingning Shi <snow940220@bjfu.edu.cn>
Diff between MtreeRing versions 1.4.1 dated 2019-09-23 and 1.4.2 dated 2019-10-03
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 3 +++ R/ring_app_launch.R | 7 ++++--- man/ring_app_launch.Rd | 7 ++++--- 5 files changed, 18 insertions(+), 13 deletions(-)
Title: Joint Models for Longitudinal Measurements and Competing Risks
Failure Time Data
Description: Fit joint models of continuous or ordinal longitudinal data and time-to-event data with competing risks. For a detailed information, see Robert Elashoff, Gang li and Ning Li (2016, ISBN:9781439807828) ; Robert M. Elashoff,Gang Li and Ning Li (2008) <doi:10.1111/j.1541-0420.2007.00952.x> ; Ning Li, Robert Elashoff, Gang Li and Jeffrey Saver (2010) <doi:10.1002/sim.3798> .
Author: Hong Wang<wh@csu.edu.cn>, Ning Li<nli@biomath.ucla.edu> and Gang Li<vli@ucla.edu>
Maintainer: Hong Wang <wh@csu.edu.cn>
Diff between JMcmprsk versions 0.9.4 dated 2019-05-17 and 0.9.6 dated 2019-10-03
DESCRIPTION | 8 ++-- MD5 | 40 ++++++++++++-------- NAMESPACE | 4 ++ R/RcppExports.R | 83 +++++++++++++++++++++++++++++++++++++++++++ R/jmc.R | 10 +++-- R/jmc_long.R |only R/jmo.R | 2 - R/jmo_long.R |only R/logLik.JMcmprsk.R | 2 - build/vignette.rds |binary configure | 14 +++---- inst/doc/JMcmprsk.R | 2 - inst/doc/JMcmprsk.Rmd | 4 +- inst/doc/JMcmprsk.html | 6 +-- inst/extdata/fvc621_y.txt | 2 - inst/extdata/rawfvc621_y.txt |only inst/extdata/test.txt |only man/SimDataC.Rd |only man/SimDataO.Rd |only man/jmc.Rd | 6 +-- man/jmc_long.Rd |only man/jmo_long.Rd |only src/RcppExports.cpp | 45 +++++++++++++++++++++++ src/SimDataC.cpp |only src/SimDataO.cpp |only vignettes/JMcmprsk.Rmd | 4 +- 26 files changed, 188 insertions(+), 44 deletions(-)
Title: Extension of `data.frame`
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Author: Matt Dowle [aut, cre],
Arun Srinivasan [aut],
Jan Gorecki [ctb],
Michael Chirico [ctb],
Pasha Stetsenko [ctb],
Tom Short [ctb],
Steve Lianoglou [ctb],
Eduard Antonyan [ctb],
Markus Bonsch [ctb],
Hugh Parsonage [ctb],
Scott Ritchie [ctb],
Kun Ren [ctb],
Xianying Tan [ctb],
Rick Saporta [ctb],
Otto Seiskari [ctb],
Xianghui Dong [ctb],
Michel Lang [ctb],
Watal Iwasaki [ctb],
Seth Wenchel [ctb],
Karl Broman [ctb],
Tobias Schmidt [ctb],
David Arenburg [ctb],
Ethan Smith [ctb],
Francois Cocquemas [ctb],
Matthieu Gomez [ctb],
Philippe Chataignon [ctb],
Declan Groves [ctb],
Daniel Possenriede [ctb],
Felipe Parages [ctb],
Denes Toth [ctb],
Mus Yaramaz-David [ctb],
Ayappan Perumal [ctb],
James Sams [ctb],
Martin Morgan [ctb],
Michael Quinn [ctb],
@javrucebo [ctb],
@marc-outins [ctb],
Roy Storey [ctb],
Manish Saraswat [ctb],
Morgan Jacob [ctb],
Michael Schubmehl [ctb]
Maintainer: Matt Dowle <mattjdowle@gmail.com>
Diff between data.table versions 1.12.2 dated 2019-04-07 and 1.12.4 dated 2019-10-03
data.table-1.12.2/data.table/man/first.Rd |only data.table-1.12.2/data.table/src/froll.h |only data.table-1.12.2/data.table/src/frollR.h |only data.table-1.12.4/data.table/DESCRIPTION | 24 data.table-1.12.4/data.table/MD5 | 295 data.table-1.12.4/data.table/NAMESPACE | 35 data.table-1.12.4/data.table/NEWS.md | 600 - data.table-1.12.4/data.table/R/IDateTime.R | 200 data.table-1.12.4/data.table/R/as.data.table.R | 210 data.table-1.12.4/data.table/R/between.R | 71 data.table-1.12.4/data.table/R/bmerge.R | 269 data.table-1.12.4/data.table/R/cedta.R | 13 data.table-1.12.4/data.table/R/data.table.R | 1476 +- data.table-1.12.4/data.table/R/duplicated.R | 73 data.table-1.12.4/data.table/R/fcast.R | 99 data.table-1.12.4/data.table/R/fmelt.R | 22 data.table-1.12.4/data.table/R/foverlaps.R | 35 data.table-1.12.4/data.table/R/frank.R | 12 data.table-1.12.4/data.table/R/fread.R | 240 data.table-1.12.4/data.table/R/froll.R | 18 data.table-1.12.4/data.table/R/fwrite.R | 56 data.table-1.12.4/data.table/R/getdots.R | 2 data.table-1.12.4/data.table/R/groupingsets.R | 36 data.table-1.12.4/data.table/R/last.R | 48 data.table-1.12.4/data.table/R/like.R | 22 data.table-1.12.4/data.table/R/merge.R | 17 data.table-1.12.4/data.table/R/onAttach.R | 18 data.table-1.12.4/data.table/R/onLoad.R | 40 data.table-1.12.4/data.table/R/openmp-utils.R | 4 data.table-1.12.4/data.table/R/print.data.table.R | 42 data.table-1.12.4/data.table/R/setkey.R | 310 data.table-1.12.4/data.table/R/setops.R | 50 data.table-1.12.4/data.table/R/shift.R | 18 data.table-1.12.4/data.table/R/tables.R | 22 data.table-1.12.4/data.table/R/test.data.table.R | 165 data.table-1.12.4/data.table/R/timetaken.R | 2 data.table-1.12.4/data.table/R/transpose.R | 36 data.table-1.12.4/data.table/R/uniqlist.R | 10 data.table-1.12.4/data.table/R/utils.R | 94 data.table-1.12.4/data.table/R/wrappers.R |only data.table-1.12.4/data.table/R/xts.R | 11 data.table-1.12.4/data.table/build/vignette.rds |binary data.table-1.12.4/data.table/inst/doc/datatable-benchmarking.Rmd | 2 data.table-1.12.4/data.table/inst/doc/datatable-benchmarking.html | 15 data.table-1.12.4/data.table/inst/doc/datatable-faq.Rmd | 7 data.table-1.12.4/data.table/inst/doc/datatable-faq.html | 24 data.table-1.12.4/data.table/inst/doc/datatable-importing.Rmd | 30 data.table-1.12.4/data.table/inst/doc/datatable-importing.html | 35 data.table-1.12.4/data.table/inst/doc/datatable-intro.Rmd | 4 data.table-1.12.4/data.table/inst/doc/datatable-intro.html | 17 data.table-1.12.4/data.table/inst/doc/datatable-keys-fast-subset.Rmd | 54 data.table-1.12.4/data.table/inst/doc/datatable-keys-fast-subset.html | 195 data.table-1.12.4/data.table/inst/doc/datatable-reference-semantics.html | 13 data.table-1.12.4/data.table/inst/doc/datatable-reshape.Rmd | 42 data.table-1.12.4/data.table/inst/doc/datatable-reshape.html | 81 data.table-1.12.4/data.table/inst/doc/datatable-sd-usage.R |only data.table-1.12.4/data.table/inst/doc/datatable-sd-usage.Rmd |only data.table-1.12.4/data.table/inst/doc/datatable-sd-usage.html |only data.table-1.12.4/data.table/inst/doc/datatable-secondary-indices-and-auto-indexing.html | 41 data.table-1.12.4/data.table/inst/tests/csvy |only data.table-1.12.4/data.table/inst/tests/froll.Rraw | 806 - data.table-1.12.4/data.table/inst/tests/issue_3400_fread.txt |only data.table-1.12.4/data.table/inst/tests/nafill.Rraw |only data.table-1.12.4/data.table/inst/tests/noquote.csv.gz |only data.table-1.12.4/data.table/inst/tests/other.Rraw | 39 data.table-1.12.4/data.table/inst/tests/tests.Rraw | 5707 +++++++--- data.table-1.12.4/data.table/inst/tests/types.Rraw |only data.table-1.12.4/data.table/man/IDateTime.Rd | 11 data.table-1.12.4/data.table/man/J.Rd | 48 data.table-1.12.4/data.table/man/as.data.table.Rd | 10 data.table-1.12.4/data.table/man/as.data.table.xts.Rd | 5 data.table-1.12.4/data.table/man/assign.Rd | 15 data.table-1.12.4/data.table/man/between.Rd | 11 data.table-1.12.4/data.table/man/coalesce.Rd |only data.table-1.12.4/data.table/man/data.table-class.Rd | 2 data.table-1.12.4/data.table/man/data.table.Rd | 39 data.table-1.12.4/data.table/man/dcast.data.table.Rd | 52 data.table-1.12.4/data.table/man/fifelse.Rd |only data.table-1.12.4/data.table/man/foverlaps.Rd | 4 data.table-1.12.4/data.table/man/frank.Rd | 2 data.table-1.12.4/data.table/man/fread.Rd | 207 data.table-1.12.4/data.table/man/froll.Rd | 90 data.table-1.12.4/data.table/man/fwrite.Rd | 31 data.table-1.12.4/data.table/man/last.Rd | 44 data.table-1.12.4/data.table/man/last.updated.Rd |only data.table-1.12.4/data.table/man/like.Rd | 27 data.table-1.12.4/data.table/man/melt.data.table.Rd | 9 data.table-1.12.4/data.table/man/merge.Rd | 2 data.table-1.12.4/data.table/man/nafill.Rd |only data.table-1.12.4/data.table/man/openmp-utils.Rd | 18 data.table-1.12.4/data.table/man/patterns.Rd | 2 data.table-1.12.4/data.table/man/print.data.table.Rd | 4 data.table-1.12.4/data.table/man/set2key.Rd | 1 data.table-1.12.4/data.table/man/setattr.Rd | 6 data.table-1.12.4/data.table/man/setkey.Rd | 15 data.table-1.12.4/data.table/man/special-symbols.Rd | 11 data.table-1.12.4/data.table/man/test.Rd |only data.table-1.12.4/data.table/man/test.data.table.Rd | 19 data.table-1.12.4/data.table/man/transform.data.table.Rd | 2 data.table-1.12.4/data.table/man/transpose.Rd | 5 data.table-1.12.4/data.table/man/truelength.Rd | 13 data.table-1.12.4/data.table/src/Makevars | 2 data.table-1.12.4/data.table/src/assign.c | 904 - data.table-1.12.4/data.table/src/between.c | 223 data.table-1.12.4/data.table/src/bmerge.c | 115 data.table-1.12.4/data.table/src/chmatch.c | 62 data.table-1.12.4/data.table/src/cj.c |only data.table-1.12.4/data.table/src/coalesce.c |only data.table-1.12.4/data.table/src/data.table.h | 89 data.table-1.12.4/data.table/src/dogroups.c | 265 data.table-1.12.4/data.table/src/fastmean.c | 14 data.table-1.12.4/data.table/src/fcast.c | 81 data.table-1.12.4/data.table/src/fifelse.c |only data.table-1.12.4/data.table/src/fmelt.c | 286 data.table-1.12.4/data.table/src/forder.c | 112 data.table-1.12.4/data.table/src/frank.c | 91 data.table-1.12.4/data.table/src/fread.c | 117 data.table-1.12.4/data.table/src/freadR.c | 369 data.table-1.12.4/data.table/src/freadR.h | 2 data.table-1.12.4/data.table/src/froll.c | 466 data.table-1.12.4/data.table/src/frollR.c | 237 data.table-1.12.4/data.table/src/frolladaptive.c | 383 data.table-1.12.4/data.table/src/fwrite.c | 490 data.table-1.12.4/data.table/src/fwrite.h | 63 data.table-1.12.4/data.table/src/fwriteR.c | 85 data.table-1.12.4/data.table/src/gsumm.c | 598 - data.table-1.12.4/data.table/src/ijoin.c | 17 data.table-1.12.4/data.table/src/init.c | 74 data.table-1.12.4/data.table/src/myomp.h | 1 data.table-1.12.4/data.table/src/nafill.c |only data.table-1.12.4/data.table/src/nqrecreateindices.c | 24 data.table-1.12.4/data.table/src/openmp-utils.c | 30 data.table-1.12.4/data.table/src/quickselect.c | 143 data.table-1.12.4/data.table/src/rbindlist.c | 120 data.table-1.12.4/data.table/src/reorder.c | 60 data.table-1.12.4/data.table/src/shift.c | 27 data.table-1.12.4/data.table/src/subset.c | 5 data.table-1.12.4/data.table/src/transpose.c | 134 data.table-1.12.4/data.table/src/types.c |only data.table-1.12.4/data.table/src/types.h | 19 data.table-1.12.4/data.table/src/uniqlist.c | 130 data.table-1.12.4/data.table/src/utils.c |only data.table-1.12.4/data.table/src/vecseq.c | 28 data.table-1.12.4/data.table/src/wrappers.c | 43 data.table-1.12.4/data.table/tests/main.R | 5 data.table-1.12.4/data.table/tests/nafill.R |only data.table-1.12.4/data.table/tests/other.R |only data.table-1.12.4/data.table/tests/types.R |only data.table-1.12.4/data.table/vignettes/Pitching.RData |only data.table-1.12.4/data.table/vignettes/Teams.RData |only data.table-1.12.4/data.table/vignettes/datatable-benchmarking.Rmd | 2 data.table-1.12.4/data.table/vignettes/datatable-faq.Rmd | 7 data.table-1.12.4/data.table/vignettes/datatable-importing.Rmd | 30 data.table-1.12.4/data.table/vignettes/datatable-intro.Rmd | 4 data.table-1.12.4/data.table/vignettes/datatable-keys-fast-subset.Rmd | 54 data.table-1.12.4/data.table/vignettes/datatable-reshape.Rmd | 42 data.table-1.12.4/data.table/vignettes/datatable-sd-usage.Rmd |only data.table-1.12.4/data.table/vignettes/plots |only 158 files changed, 11685 insertions(+), 6880 deletions(-)
Title: Imputation for Proteomics
Description: Functions to analyse missing value mechanisms and to impute data sets in the context of bottom-up MS-based proteomics.
Author: Quentin Giai Gianetto
Maintainer: Quentin Giai Gianetto <quentin2g@yahoo.fr>
Diff between imp4p versions 0.7 dated 2018-08-10 and 0.8 dated 2019-10-03
DESCRIPTION | 6 MD5 | 50 +++--- R/estim_mix.R | 324 ++++++++++++++++-------------------------- R/impute_mi.R | 12 - R/impute_mix.R | 18 +- R/impute_mle.R | 18 +- R/mi_mix.R | 42 +---- R/prob_mcar.R | 53 ++---- R/prob_mcar_tab.R | 12 - man/estim_mix.Rd | 31 ---- man/fast_apply_nb_na.Rd | 10 + man/fast_apply_nb_not_na.Rd | 6 man/fast_apply_sd_na_rm_T.Rd | 6 man/fast_apply_sum_na_rm_T.Rd | 5 man/fast_sim.Rd | 2 man/impute_mi.Rd | 8 - man/impute_mix.Rd | 13 - man/impute_mle.Rd | 4 man/mi_mix.Rd | 2 man/miss_total_process.Rd | 3 man/pi_mcar_karpievitch.Rd | 9 - man/pi_mcar_logit.Rd | 9 - man/pi_mcar_probit.Rd | 9 - man/prob_mcar.Rd | 17 +- man/proba_mcar_tab.Rd | 7 src/fast_sim.cpp | 70 +++------ 26 files changed, 305 insertions(+), 441 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-10-02 0.2.4
Title: A Simple Router for HTTP and WebSocket Requests
Description: In order to make sure that web request ends up in the correct
handler function a router is often used. 'routr' is a package implementing a
simple but powerful routing functionality for R based servers. It is a fully
functional 'fiery' plugin, but can also be used with other 'httpuv' based
servers.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>)
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between routr versions 0.3.0 dated 2017-10-26 and 0.4.0 dated 2019-10-03
routr-0.3.0/routr/man/figures/routr_logo.png |only routr-0.4.0/routr/DESCRIPTION | 25 +++-- routr-0.4.0/routr/MD5 | 20 ++-- routr-0.4.0/routr/NEWS.md | 9 ++ routr-0.4.0/routr/R/route.R | 45 +++++++++- routr-0.4.0/routr/R/routr-package.R |only routr-0.4.0/routr/README.md | 116 +++++++++++++++++++++----- routr-0.4.0/routr/man/Route.Rd | 8 + routr-0.4.0/routr/man/figures/logo.png |only routr-0.4.0/routr/man/ressource_route.Rd | 1 routr-0.4.0/routr/man/routr-package.Rd |only routr-0.4.0/routr/man/sizelimit_route.Rd | 1 routr-0.4.0/routr/tests/testthat/test-route.R | 33 +++++++ 13 files changed, 216 insertions(+), 42 deletions(-)
Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt
Maintainer: Roeland Kindt <R.KINDT@CGIAR.ORG>
Diff between BiodiversityR versions 2.11-2 dated 2019-06-29 and 2.11-3 dated 2019-10-03
DESCRIPTION | 8 +- MD5 | 22 +++--- NAMESPACE | 1 R/ensemble.VIF.R | 92 +++++++++++++++++++++++++++ R/ensemble.calibrate.models.R | 138 ++++++++++++++++++++++++++++++++++++++++- R/ensemble.calibrate.weights.R | 69 +++++++++++++++++--- R/ensemble.evaluate.R |only R/ensemble.mean.R | 2 R/ensemble.threshold.R | 2 inst/ChangeLog | 39 +++++++++++ man/ensemble.Rd | 7 ++ man/ensemble.evaluate.Rd |only man/importancevalue.Rd | 18 +++++ 13 files changed, 372 insertions(+), 26 deletions(-)
Title: Whole Genome Average Interval Mapping for QTL Detection and
Estimation using ASReml-R
Description: A computationally efficient whole genome approach to detecting and estimating significant QTL in linkage maps using the flexible linear mixed modelling functionality of ASReml-R.
Author: Julian Taylor <julian.taylor@adelaide.edu.au> and Ari Verbyla <ari.verbyla@csiro.au>
Maintainer: Julian Taylor <julian.taylor@adelaide.edu.au>
Diff between wgaim versions 2.0-0 dated 2019-08-28 and 2.0-1 dated 2019-10-03
wgaim-2.0-0/wgaim/R/wgaim15.R |only wgaim-2.0-1/wgaim/DESCRIPTION | 8 +-- wgaim-2.0-1/wgaim/MD5 | 14 +++--- wgaim-2.0-1/wgaim/R/wgaim16.R |only wgaim-2.0-1/wgaim/inst/NEWS.Rd | 19 +++++---- wgaim-2.0-1/wgaim/inst/doc/wgaim_intro.Rmd | 2 wgaim-2.0-1/wgaim/inst/doc/wgaim_intro.html | 58 ++++++++++++++-------------- wgaim-2.0-1/wgaim/vignettes/intro.bib | 4 - wgaim-2.0-1/wgaim/vignettes/wgaim_intro.Rmd | 2 9 files changed, 56 insertions(+), 51 deletions(-)
Title: Statistical Tests for Assessing Trinormal ROC Data
Description: Several statistical test functions as well as a function for exploratory data analysis to investigate classifiers allocating individuals to one of three disjoint and ordered classes. In a single classifier assessment the discriminatory power is compared to classification by chance. In a comparison of two classifiers the null hypothesis corresponds to equal discriminatory power of the two classifiers.
Author: Samuel Noll [aut],
Reinhard Furrer [ctb, cre],
Benjamin Reiser [ctb],
Christos T. Nakas [ctb]
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>
Diff between trinROC versions 0.3 dated 2019-05-28 and 0.3.1 dated 2019-10-03
DESCRIPTION | 6 MD5 | 8 build/vignette.rds |binary tests/testthat/test_trinROC.R | 2 vignettes/trinROC_vignette.html | 1106 ++++++++++++++++++---------------------- 5 files changed, 525 insertions(+), 597 deletions(-)
Title: Spatial Analysis and Modelling Utilities
Description: Utilities to support spatial data manipulation, query, sampling
and modelling. Functions include models for species population density, download
utilities for climate and global deforestation spatial products, spatial
smoothing, multivariate separability, point process model for creating pseudo-
absences and sub-sampling, polygon and point-distance landscape metrics,
auto-logistic model, sampling models, cluster optimization, statistical
exploratory tools and raster-based metrics.
Author: Jeffrey S. Evans [aut, cre],
Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between spatialEco versions 1.2-0 dated 2019-07-24 and 1.2-1 dated 2019-10-03
spatialEco-1.2-0/spatialEco/NEWS |only spatialEco-1.2-1/spatialEco/DESCRIPTION | 16 +- spatialEco-1.2-1/spatialEco/MD5 | 50 +++++-- spatialEco-1.2-1/spatialEco/NAMESPACE | 7 + spatialEco-1.2-1/spatialEco/R/annulus.matrix.R |only spatialEco-1.2-1/spatialEco/R/bearing.distance.R | 2 spatialEco-1.2-1/spatialEco/R/effect.size.R | 1 spatialEco-1.2-1/spatialEco/R/insert.values.R | 2 spatialEco-1.2-1/spatialEco/R/knn.R |only spatialEco-1.2-1/spatialEco/R/parse.bits.R |only spatialEco-1.2-1/spatialEco/R/polyPerimeter.R | 2 spatialEco-1.2-1/spatialEco/R/random.raster.R |only spatialEco-1.2-1/spatialEco/R/raster.kendall.R | 105 ++++++---------- spatialEco-1.2-1/spatialEco/R/raster.modifed.ttest.R |only spatialEco-1.2-1/spatialEco/R/se.news.R |only spatialEco-1.2-1/spatialEco/R/sg.smooth.R | 17 ++ spatialEco-1.2-1/spatialEco/R/shift.R |only spatialEco-1.2-1/spatialEco/R/sieve.R |only spatialEco-1.2-1/spatialEco/R/smooth.time.series.R | 21 ++- spatialEco-1.2-1/spatialEco/R/subsample.distance.R | 103 ++++++++------- spatialEco-1.2-1/spatialEco/R/trasp.R | 2 spatialEco-1.2-1/spatialEco/R/zonal.stats.R | 26 +-- spatialEco-1.2-1/spatialEco/R/zzz.R |only spatialEco-1.2-1/spatialEco/inst/NEWS |only spatialEco-1.2-1/spatialEco/man/annulus.matrix.Rd |only spatialEco-1.2-1/spatialEco/man/knn.Rd |only spatialEco-1.2-1/spatialEco/man/parse.bits.Rd |only spatialEco-1.2-1/spatialEco/man/random.raster.Rd |only spatialEco-1.2-1/spatialEco/man/raster.kendall.Rd | 51 ++----- spatialEco-1.2-1/spatialEco/man/raster.modifed.ttest.Rd |only spatialEco-1.2-1/spatialEco/man/se.news.Rd |only spatialEco-1.2-1/spatialEco/man/sg.smooth.Rd | 15 ++ spatialEco-1.2-1/spatialEco/man/shift.Rd |only spatialEco-1.2-1/spatialEco/man/smooth.time.series.Rd | 21 ++- spatialEco-1.2-1/spatialEco/man/subsample.distance.Rd | 58 ++++---- 35 files changed, 271 insertions(+), 228 deletions(-)
Title: Bridge Between 'R' and 'Scala' with Callbacks
Description: 'Scala' <http://www.scala-lang.org/> is embedded in 'R' and callbacks from 'Scala' to 'R' are available. Support is provided to write 'R' packages that access 'Scala'. After installation, please run 'rscala::scalaConfig()'.
Author: David B. Dahl [aut, cre]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between rscala versions 3.2.15 dated 2019-07-09 and 3.2.16 dated 2019-10-03
DESCRIPTION | 8 ++-- MD5 | 40 ++++++++++---------- NAMESPACE | 1 NEWS | 7 +++ R/INTERNAL-protocol.R | 5 +- R/scala.R | 78 ++++++++++++++++++++++++++++++---------- R/scalaConfig.R | 6 +-- R/scalaJARs.R | 73 ++----------------------------------- R/sysdata.rda |binary README.md | 2 - inst/data-raw/urls.txt | 51 +++++++++++--------------- inst/doc/rscala.R | 6 +-- inst/doc/rscala.Rnw | 25 ++++++------ inst/doc/rscala.pdf |binary inst/java/scala-2.11/rscala.jar |binary inst/java/scala-2.12/rscala.jar |binary inst/java/scala-2.13/rscala.jar |binary java/rscala-source.jar |binary man/scala.Rd | 8 ++-- man/scalaJARs.Rd | 9 +--- vignettes/rscala.Rnw | 25 ++++++------ 21 files changed, 159 insertions(+), 185 deletions(-)
Title: Permits *apply() Style Dispatch for 'HPC'
Description: Function of apply style using 'MPI' provides better 'HPC' environment on R.
And this package supports long vector, can deal with slightly big data.
Author: Junji NAKANO <nakanoj@ism.ac.jp> and Ei-ji Nakama <nakama@ki.rim.or.jp>
Maintainer: Ei-ji Nakama <nakama@ki.rim.or.jp>
Diff between Rhpc versions 0.18-204 dated 2018-07-24 and 0.19-276 dated 2019-10-03
ChangeLog | 4 ++++ DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- configure | 45 +++++++++++++++++++++++---------------------- configure.ac | 5 +++-- src/Makevars.win | 12 ++++++------ src/RhpcMPI.c | 14 +++++++------- src/worker/Makefile.win | 12 ++++++------ src/worker/RhpcWorker.c | 7 +++++++ src/worker/fakemaster.c | 2 +- 10 files changed, 71 insertions(+), 58 deletions(-)
Title: Random Forests Model Selection and Performance Evaluation
Description: Utilities for Random Forest model selection, class balance
correction, significance test, cross validation and partial dependency
plots.
Author: Jeffrey S. Evans [cre, aut],
Melanie A. Murphy [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between rfUtilities versions 2.1-4 dated 2018-12-17 and 2.1-5 dated 2019-10-03
rfUtilities-2.1-4/rfUtilities/NEWS |only rfUtilities-2.1-5/rfUtilities/DESCRIPTION | 12 - rfUtilities-2.1-5/rfUtilities/MD5 | 24 +-- rfUtilities-2.1-5/rfUtilities/NAMESPACE | 1 rfUtilities-2.1-5/rfUtilities/R/logLoss.R | 19 +- rfUtilities-2.1-5/rfUtilities/R/plot.rf.cv.R | 5 rfUtilities-2.1-5/rfUtilities/R/print.rf.cv.R | 4 rfUtilities-2.1-5/rfUtilities/R/rf.crossValidation.R | 106 +++++++++------- rfUtilities-2.1-5/rfUtilities/R/rfu.news.R |only rfUtilities-2.1-5/rfUtilities/R/summary.rf.cv.R | 2 rfUtilities-2.1-5/rfUtilities/inst/NEWS |only rfUtilities-2.1-5/rfUtilities/man/logLoss.Rd | 24 +-- rfUtilities-2.1-5/rfUtilities/man/plot.rf.cv.Rd | 5 rfUtilities-2.1-5/rfUtilities/man/rf.crossValidation.Rd | 18 +- rfUtilities-2.1-5/rfUtilities/man/rfu.news.Rd |only 15 files changed, 134 insertions(+), 86 deletions(-)
Title: Automatic Shift Detection using a Phylogenetic EM
Description: Implementation of the automatic shift detection method for
Brownian Motion (BM) or Ornstein–Uhlenbeck (OU) models of trait evolution on
phylogenies. Some tools to handle equivalent shifts configurations are also
available. See Bastide et al. (2017) <doi:10.1111/rssb.12206> and
Bastide et al. (2018) <doi:10.1093/sysbio/syy005>.
Author: Paul Bastide [aut, cre],
Mahendra Mariadassou [ctb]
Maintainer: Paul Bastide <paul.bastide@m4x.org>
Diff between PhylogeneticEM versions 1.2.1 dated 2018-09-11 and 1.3.0 dated 2019-10-03
PhylogeneticEM-1.2.1/PhylogeneticEM/man/impute.data.Rphylopars.Rd |only PhylogeneticEM-1.3.0/PhylogeneticEM/DESCRIPTION | 22 PhylogeneticEM-1.3.0/PhylogeneticEM/MD5 | 57 - PhylogeneticEM-1.3.0/PhylogeneticEM/NEWS.md | 14 PhylogeneticEM-1.3.0/PhylogeneticEM/R/estimateEM.R | 151 +- PhylogeneticEM-1.3.0/PhylogeneticEM/R/generic_functions.R | 18 PhylogeneticEM-1.3.0/PhylogeneticEM/R/init_EM.R | 197 +-- PhylogeneticEM-1.3.0/PhylogeneticEM/R/partitionsNumber.R | 2 PhylogeneticEM-1.3.0/PhylogeneticEM/R/plot_functions.R | 14 PhylogeneticEM-1.3.0/PhylogeneticEM/R/shutoff.R | 66 - PhylogeneticEM-1.3.0/PhylogeneticEM/build/vignette.rds |binary PhylogeneticEM-1.3.0/PhylogeneticEM/inst/CITATION | 4 PhylogeneticEM-1.3.0/PhylogeneticEM/inst/doc/monkeys.html | 521 +++++++--- PhylogeneticEM-1.3.0/PhylogeneticEM/inst/doc/tutorial.html | 477 ++++++--- PhylogeneticEM-1.3.0/PhylogeneticEM/man/PhyloEM.Rd | 19 PhylogeneticEM-1.3.0/PhylogeneticEM/man/check_range_alpha.Rd | 2 PhylogeneticEM-1.3.0/PhylogeneticEM/man/estimateEM.Rd | 16 PhylogeneticEM-1.3.0/PhylogeneticEM/man/find_rotation.Rd | 4 PhylogeneticEM-1.3.0/PhylogeneticEM/man/init.EM.lasso.Rd | 3 PhylogeneticEM-1.3.0/PhylogeneticEM/man/init.alpha.gamma.estimation.Rd | 2 PhylogeneticEM-1.3.0/PhylogeneticEM/man/merge_rotations.Rd | 2 PhylogeneticEM-1.3.0/PhylogeneticEM/man/plot.PhyloEM.Rd | 9 PhylogeneticEM-1.3.0/PhylogeneticEM/man/plot_criterion.Rd | 2 PhylogeneticEM-1.3.0/PhylogeneticEM/tests/testthat/test-core-log_likelihood.R | 2 PhylogeneticEM-1.3.0/PhylogeneticEM/tests/testthat/test-independent_multivariate.R | 6 PhylogeneticEM-1.3.0/PhylogeneticEM/tests/testthat/test-shifts-model_selection.R | 2 PhylogeneticEM-1.3.0/PhylogeneticEM/tests/testthat/test-upward_downward.R | 26 PhylogeneticEM-1.3.0/PhylogeneticEM/tests/testthat/test-utilities-handling_parameters.R | 2 PhylogeneticEM-1.3.0/PhylogeneticEM/tests/testthat/test-utilities-impute-traits.R | 2 PhylogeneticEM-1.3.0/PhylogeneticEM/tests/testthat/test-utilities-rotations.R | 16 30 files changed, 1066 insertions(+), 592 deletions(-)
More information about PhylogeneticEM at CRAN
Permanent link
Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services
<https://aws.amazon.com>. The functions handle building, signing, and
sending requests, and receiving responses. They are designed to help build
higher-level interfaces to individual services, such as Simple Storage
Service (S3).
Author: David Kretch [aut, cre],
Adam Banker [aut],
Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>
Diff between paws.common versions 0.2.1 dated 2019-09-21 and 0.2.2 dated 2019-10-03
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- NEWS.md | 6 ++++++ R/handlers_rest.R | 10 +++++++--- R/xmlutil.R | 3 ++- tests/testthat/test_handlers_rest.R |only tests/testthat/test_handlers_restxml.R | 28 +++++++++++++++++++++++++--- 7 files changed, 49 insertions(+), 15 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 4.6.1 dated 2019-08-06 and 4.7.0 dated 2019-10-03
DESCRIPTION | 6 MD5 | 115 +++++-- NAMESPACE | 1 NEWS.md | 13 R/get-set-convenience.R | 55 +++ R/huxreg.R | 10 R/manipulation.R | 97 ++++-- R/zzz.R | 49 ++- build/vignette.rds |binary data/jams.rda |binary inst/doc/design-principles.html | 5 inst/doc/huxreg.html | 27 + inst/doc/huxtable.html | 48 +-- inst/doc/themes.html | 11 man/add_rows.Rd | 19 - man/huxtable-FAQ.Rd | 4 man/huxtable-options.Rd | 2 man/huxtable-package.Rd | 47 ++- man/insert_column.Rd | 48 ++- man/jams.Rd | 2 man/merge_cells.Rd | 3 man/merge_repeated_rows.Rd |only tests/testthat/bookdown-test.log | 447 ++++++++++++++-------------- tests/testthat/huxreg.log | 451 ++++++++++++++--------------- tests/testthat/huxtable.aux |only tests/testthat/huxtable.log | 437 +++++++++++++--------------- tests/testthat/libs |only tests/testthat/table-tester-2.log | 414 +++++++++++++------------- tests/testthat/test-huxreg.R | 2 tests/testthat/test-manipulation-helpers.R | 12 tests/testthat/test-print.R | 2 tests/testthat/test-set-interface.R | 38 ++ tests/testthat/themes.log | 437 +++++++++++++--------------- 33 files changed, 1545 insertions(+), 1257 deletions(-)
Title: Spatial Graph-Theoretic Genetic Gravity Modelling
Description: Implementation of spatial graph-theoretic genetic gravity models.
The model framework is applicable for other types of spatial flow questions.
Includes functions for constructing spatial graphs, sampling and summarizing
associated raster variables and building unconstrained and singly constrained
gravity models.
Author: Jeffrey S. Evans [aut, cre],
Melanie Murphy [aut]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between GeNetIt versions 0.1-1 dated 2017-07-31 and 0.1-2 dated 2019-10-03
DESCRIPTION | 16 +++-- MD5 | 38 +++++++------ NAMESPACE | 4 + R/area.graph.statistics.R | 68 +++-------------------- R/build.node.data.R | 14 +++- R/compare.models.R |only R/flow.R |only R/graph.statistics.R | 124 ++++++++++++++++++++++++++++++------------- R/gravity.R | 19 ++++-- R/gravity.es.R |only R/knn.graph.R | 27 +++++---- R/ralu.site-data.R | 2 data/dps.rda |binary inst/NEWS | 13 +++- man/area.graph.statistics.Rd | 45 ++------------- man/build.node.data.Rd | 14 +++- man/compare.models.Rd |only man/flow.Rd |only man/graph.statistics.Rd | 50 ++++++++++++----- man/gravity.Rd | 21 +++++-- man/gravity.es.Rd |only man/knn.graph.Rd | 16 ++--- man/ralu.site.Rd | 2 23 files changed, 259 insertions(+), 214 deletions(-)