Title: Tools for Easier Analysis of Meteorological Fields
Description: Many useful functions and extensions for dealing
with meteorological data in the tidy data framework. Extends 'ggplot2'
for better plotting of scalar and vector fields and provides commonly
used analysis methods in the atmospheric sciences.
Author: Elio Campitelli [cre, aut] (<https://orcid.org/0000-0002-7742-9230>)
Maintainer: Elio Campitelli <elio.campitelli@cima.fcen.uba.ar>
Diff between metR versions 0.4.0 dated 2019-07-08 and 0.5.0 dated 2019-11-12
DESCRIPTION | 8 MD5 | 41 ++-- NAMESPACE | 1 NEWS.md | 28 ++- R/Derivate.R | 49 ++++- R/EOF_methods.R | 22 ++ R/GetSMNData.R | 22 ++ R/Impute2D.R | 5 R/ReadNetCDF.R | 90 ++++++---- R/cross.R | 25 ++ R/geom_arrow.R | 7 R/geom_streamline.R | 15 + R/geom_text_contour.R | 8 R/helpfunctions.R | 14 - inst/doc/Visualization-tools.html | 296 +++++++++++++++++---------------- inst/doc/Working-with-data.html | 338 +++++++++++++++++++------------------- man/Derivate.Rd | 10 - man/GetSMNData.Rd | 7 man/ReadNetCDF.Rd | 6 man/denormalize.Rd |only man/figures/logo.png |binary man/is.cross.Rd | 8 22 files changed, 591 insertions(+), 409 deletions(-)
Title: Retrieve and Analyze Clinical Trials in Public Registers
Description: Provides functions for querying, retrieving and analysing
protocol- and results-related information on clinical trials from
two public registers, the European Union Clinical Trials Register
(EUCTR, <https://www.clinicaltrialsregister.eu/>) and
ClinicalTrials.gov (CTGOV, <https://clinicaltrials.gov/>). The
information is transformed and then stored in a database (nodbi).
Functions are provided for accessing and analysing the locally
stored information on the clinical trials, as well as for
identifying duplicate records. The package is motivated by the need
for aggregating and trend-analysing the design, conduct and outcomes
across clinical trials.
Author: Ralf Herold [aut, cre] (<https://orcid.org/0000-0002-8148-6748>)
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 1.0.1 dated 2019-10-23 and 1.1 dated 2019-11-12
DESCRIPTION | 14 +++---- MD5 | 38 +++++++++---------- NEWS.md | 23 +++++++++++ R/main.R | 49 +++++++++++++++--------- R/utils.R | 54 +++++++++++++++------------ README.md | 4 +- exec/euctr2json.sh | 47 +++++++++++++++-------- inst/tinytest/test_ctrdata_mongo_remote_ro.R | 2 - man/ctrLoadQueryIntoDb.Rd | 19 +++++++-- man/ctrLoadQueryIntoDbCtgov.Rd | 16 ++++++-- man/ctrLoadQueryIntoDbEuctr.Rd | 16 ++++++-- man/ctrOpenSearchPagesInBrowser.Rd | 3 - man/ctrRerunQuery.Rd | 10 +++-- man/ctrdata.Rd | 1 man/dbCTRAnnotateQueryRecords.Rd | 10 ++++- man/dbCTRLoadJSONFiles.Rd | 5 ++ man/dbFindIdsUniqueTrials.Rd | 10 +++-- man/dbGetFieldsIntoDf.Rd | 3 - man/dfFindUniqueEuctrRecord.Rd | 7 ++- man/dfMergeTwoVariablesRelevel.Rd | 3 - 20 files changed, 217 insertions(+), 117 deletions(-)
Title: Encapsulated Classes with Reference Semantics
Description: Creates classes with reference semantics, similar to R's built-in
reference classes. Compared to reference classes, R6 classes are simpler
and lighter-weight, and they are not built on S4 classes so they do not
require the methods package. These classes allow public and private
members, and they support inheritance, even when the classes are defined in
different packages.
Author: Winston Chang [aut, cre]
Maintainer: Winston Chang <winston@stdout.org>
Diff between R6 versions 2.4.0 dated 2019-02-14 and 2.4.1 dated 2019-11-12
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 5 +++++ R/clone.R | 30 +++++++++++++++++------------- R/new.R | 26 ++++++++++++++++++++------ R/r6_class.R | 1 + tests/testthat/test-nonportable.R | 9 ++++----- tests/testthat/test-s3-methods.R | 19 +++++++++++++++++++ 8 files changed, 76 insertions(+), 34 deletions(-)
Title: Methods for Calculating 'EQ-5D' Utility Index Scores
Description: EQ-5D is a popular health related quality of life instrument used
in the clinical and economic evaluation of health care. Developed by the
EuroQol group <https://www.euroqol.org>, the instrument consists of two
components: health state description and evaluation. For the description
component a subject self-rates their health in terms of five dimensions;
mobility, self-care, usual activities, pain/discomfort, and
anxiety/depression using either a three-level (EQ-5D-3L,
<https://www.euroqol.org/eq-5d-instruments/eq-5d-3l-about>) or a five-level
(EQ-5D-5L, <https://www.euroqol.org/eq-5d-instruments/eq-5d-5l-about>)
scale. Frequently the scores on these five dimensions are converted to a
single utility index using country specific value sets, which can be used
in the clinical and economic evaluation of health care as well as in
population health surveys. The eq5d package provides methods to calculate
index scores from a subject's dimension scores. 25 TTO and 11 VAS EQ-5D-3L value
sets including those for countries in Szende et al (2007)
<doi:10.1007/1-4020-5511-0> and Szende et al (2014)
<doi:10.1007/978-94-007-7596-1>, 18 EQ-5D-5L EQ-VT value sets from the EuroQol
website, and the EQ-5D-5L crosswalk value sets developed by van Hout et al. (2012)
<doi:10.1016/j.jval.2012.02.008> are included. Additionally, a shiny web tool is
included to enable the calculation and visualisation of EQ-5D index values via a
web browser using EQ-5D dimension scores stored in CSV or Excel files.
Author: Fraser Morton [aut, cre],
Jagtar Singh Nijjar [aut]
Maintainer: Fraser Morton <fraser.morton@glasgow.ac.uk>
Diff between eq5d versions 0.3.0 dated 2019-09-13 and 0.4.0 dated 2019-11-12
DESCRIPTION | 10 +-- MD5 | 46 +++++++++-------- NEWS.md | 13 ++++- R/data.R | 28 +++++++--- R/eq5d.R | 26 +++++++--- R/eq5d3l.R | 45 ++++++++++++++++- README.md | 35 +++++++++---- data/tto.RData |binary data/vt.RData |binary inst/doc/eq5d.R | 13 ++++- inst/doc/eq5d.Rmd | 17 +++++- inst/doc/eq5d.html | 42 +++++++++++----- inst/shiny/server.R | 48 +++++++++++++----- inst/shiny/ui.R | 22 +++++--- inst/shiny/www/images/shiny_app_excel_scores.png |only man/TTO.Rd | 18 +++++-- man/VAS.Rd | 4 - man/VT.Rd | 10 ++- man/eq5d-package.Rd | 4 - man/eq5d.Rd | 11 +++- man/figures/shiny_app_excel_scores.png |only tests/testthat/test-eq5d.R | 13 ++++- tests/testthat/test-eq5d3l.R | 59 +++++++++++++++++++---- tests/testthat/test-eq5d5l.R | 30 +++++++++-- vignettes/eq5d.Rmd | 17 +++++- 25 files changed, 383 insertions(+), 128 deletions(-)
Title: Tools for Analyzing Factorial Experiments
Description: Offers a helping hand to psychologists and other behavioral scientists who routinely deal with experimental data from factorial experiments. It includes several functions to format output from other R functions according to the style guidelines of the APA (American Psychological Association). This formatted output can be copied directly into manuscripts to facilitate data reporting. These features are backed up by a toolkit of several small helper functions, e.g., offering out-of-the-box outlier removal. The package lends its name to Georg "Schorsch" Schuessler, ingenious technician at the Department of Psychology III, University of Wuerzburg. For details on the implemented methods, see Roland Pfister and Markus Janczyk (2016) <doi: 10.20982/tqmp.12.2.p147>.
Author: Roland Pfister, Markus Janczyk
Maintainer: Roland Pfister <roland.pfister@psychologie.uni-wuerzburg.de>
Diff between schoRsch versions 1.6 dated 2019-05-02 and 1.7 dated 2019-11-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/anova_out.R | 8 ++++---- man/schoRsch.Rd | 5 +++-- 4 files changed, 14 insertions(+), 13 deletions(-)
Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Aron Atkins [ctb],
Aaron Wolen [ctb],
Ashley Manton [ctb],
Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>),
Ben Baumer [ctb],
Brian Diggs [ctb],
Brian Zhang [ctb],
Cassio Pereira [ctb],
Christophe Dervieux [ctb],
David Hugh-Jones [ctb],
David Robinson [ctb],
Doug Hemken [ctb],
Duncan Murdoch [ctb],
Elio Campitelli [ctb],
Emily Riederer [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Forest Fang [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Garrick Aden-Buie [ctb],
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Hao Zhu [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Hiroaki Yutani [ctb],
Ian Lyttle [ctb],
Hodges Daniel [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jason Punyon [ctb],
Javier Luraschi [ctb],
Jeff Arnold [ctb],
Jenny Bryan [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
John Muschelli [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Jonathan Sidi [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kaiyin Zhong [ctb],
Kamil Slowikowski [ctb],
Karl Forner [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Lorenz Walthert [ctb],
Lucas Gallindo [ctb],
Marius Hofert [ctb],
Martin Modrák [ctb],
Michael Chirico [ctb],
Michael Friendly [ctb],
Michal Bojanowski [ctb],
Michel Kuhlmann [ctb],
Miller Patrick [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Niels Richard Hansen [ctb],
Noam Ross [ctb],
Obada Mahdi [ctb],
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Robert Krzyzanowski [ctb],
Romain Francois [ctb],
Ruaridh Williamson [ctb],
Scott Kostyshak [ctb],
Sebastian Meyer [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Sylvain Rousseau [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tim Mastny [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Zachary Foster [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between knitr versions 1.25 dated 2019-09-18 and 1.26 dated 2019-11-12
DESCRIPTION | 8 +-- MD5 | 94 +++++++++++++++++++++---------------------- R/citation.R | 69 +++++++++++++++++++++---------- R/defaults.R | 12 ++++- R/output.R | 5 -- R/utils.R | 12 +++++ inst/doc/datatables.R | 6 +- inst/doc/docco-classic.R | 10 ++-- inst/doc/docco-classic.html | 6 +- inst/doc/docco-linear.R | 8 +-- inst/doc/docco-linear.html | 6 +- inst/doc/knit_expand.R | 34 +++++++-------- inst/doc/knit_expand.html | 4 - inst/doc/knit_print.R | 36 ++++++++-------- inst/doc/knit_print.html | 12 ++--- inst/doc/knitr-html.R | 8 +-- inst/doc/knitr-html.html | 2 inst/doc/knitr-intro.R | 6 +- inst/doc/knitr-intro.html | 12 ++--- inst/doc/knitr-markdown.R | 12 ++--- inst/doc/knitr-markdown.html | 8 +-- inst/doc/knitr-refcard.pdf |binary man/Sweave2knitr.Rd | 3 - man/cache_engines.Rd | 2 man/combine_words.Rd | 3 - man/fig_chunk.Rd | 3 - man/include_graphics.Rd | 4 - man/kable.Rd | 5 +- man/knit.Rd | 4 - man/knit2html.Rd | 4 - man/knit2pandoc.Rd | 5 +- man/knit2pdf.Rd | 4 - man/knit2wp.Rd | 6 +- man/knit_code.Rd | 2 man/knit_engines.Rd | 2 man/knit_hooks.Rd | 2 man/knit_patterns.Rd | 2 man/load_cache.Rd | 4 - man/opts_chunk.Rd | 2 man/opts_hooks.Rd | 2 man/opts_knit.Rd | 2 man/opts_template.Rd | 2 man/output_hooks.Rd | 3 - man/read_chunk.Rd | 5 +- man/spin.Rd | 9 ++-- man/stitch.Rd | 5 +- man/write_bib.Rd | 34 ++++++--------- tests/testit/test-closure.R | 5 ++ 48 files changed, 273 insertions(+), 221 deletions(-)
Title: Enhanced Help to Enable "Docstring"-Comments in Users Functions
Description: By overloading the R help() function, this package allows users to use "docstring" style comments within their own defined functions.
Author: Marcelo Ponce [aut, cre]
Maintainer: Marcelo Ponce <mponce@scinet.utoronto.ca>
Diff between ehelp versions 1.0 dated 2019-10-18 and 1.1 dated 2019-11-12
ehelp-1.0/ehelp/R/ehelp-NOobj.R |only ehelp-1.0/ehelp/R/ehelp-obj.R |only ehelp-1.1/ehelp/DESCRIPTION | 6 - ehelp-1.1/ehelp/MD5 | 31 +++++--- ehelp-1.1/ehelp/NEWS | 1 ehelp-1.1/ehelp/R/ehelp-defns.R |only ehelp-1.1/ehelp/R/ehelp-utils.R |only ehelp-1.1/ehelp/R/ehelp.R | 105 ++++++++++++++-------------- ehelp-1.1/ehelp/README.md | 65 +++++++++++++++-- ehelp-1.1/ehelp/inst/doc/eHelp.html | 48 ++++++++++-- ehelp-1.1/ehelp/man/ehelp.Rd | 50 ++++--------- ehelp-1.1/ehelp/man/ehelp.palette.Rd |only ehelp-1.1/ehelp/man/format.defns.Rd |only ehelp-1.1/ehelp/man/help.Rd | 44 ----------- ehelp-1.1/ehelp/man/print.Rd | 2 ehelp-1.1/ehelp/man/print.ehelp.Rd | 8 +- ehelp-1.1/ehelp/man/processOutput.Rd |only ehelp-1.1/ehelp/man/write.Fncorpus.Rd |only ehelp-1.1/ehelp/man/write.Info.Rd |only ehelp-1.1/ehelp/man/write.ehelp.Rd |only ehelp-1.1/ehelp/man/write.fmt.Rd |only ehelp-1.1/ehelp/tests/testthat/test-ehelp.R | 11 +- 22 files changed, 209 insertions(+), 162 deletions(-)
Title: Models for Data from Unmarked Animals
Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates.
Author: Ian Fiske, Richard Chandler, David Miller, Andy Royle, Marc Kery, Jeff Hostetler, Rebecca Hutchinson, Adam Smith, Ken Kellner
Maintainer: Andy Royle <aroyle@usgs.gov>
Diff between unmarked versions 0.12-3 dated 2019-02-05 and 0.13-0 dated 2019-11-12
DESCRIPTION | 13 MD5 | 380 - NAMESPACE | 119 NEWS | 244 R/boot.R | 1113 ++-- R/classes.R | 122 R/colext.R | 604 +- R/distsamp.R | 658 +- R/gdistsamp.R | 926 +-- R/getDesign.R | 2281 ++++----- R/gmultmix.R | 395 - R/gpcount.R | 350 - R/mapInfo.R | 30 R/multinomPois.R | 220 R/occu.R | 224 R/occuFP.R | 284 - R/occuMS.R |only R/occuMulti.R | 266 - R/occuPEN.R | 640 +- R/occuRN.R | 220 R/occuTTD.R |only R/pcount.R | 298 - R/pcount.spHDS.R | 284 - R/pcountOpen.R | 536 +- R/piFun.R |only R/ranef.R | 1832 +++---- R/unmarkedCrossVal.R |only R/unmarkedEstimate.R | 533 +- R/unmarkedFit.R | 7855 ++++++++++++++++--------------- R/unmarkedFitList.R | 593 +- R/unmarkedFrame.R | 2562 +++++----- R/unmarkedLinComb.R | 330 - R/utils.R | 1527 +++--- R/vif.R |only build/vignette.rds |binary inst/CITATION | 40 inst/bench/bench.occu.R | 80 inst/bench/bench.pcount.R | 94 inst/bench/bench.pcountOpen.R | 106 inst/csv/alfl.capRecap.csv | 102 inst/csv/alfl.csv | 198 inst/csv/alflCovs.csv | 102 inst/csv/distdata.csv | 50 inst/csv/frog2001pcru.csv | 676 +- inst/csv/frog2001pfer.csv | 676 +- inst/csv/widewt.csv | 476 - inst/doc/cap-recap.R | 440 - inst/doc/cap-recap.Rnw | 1484 ++--- inst/doc/cap-recap.pdf |binary inst/doc/colext.R | 670 +- inst/doc/colext.Rnw | 2858 +++++------ inst/doc/colext.pdf |binary inst/doc/distsamp.R | 292 - inst/doc/distsamp.Rnw | 804 +-- inst/doc/distsamp.pdf |binary inst/doc/spp-dist.R | 322 - inst/doc/spp-dist.Rnw | 802 +-- inst/doc/spp-dist.pdf |binary inst/doc/unmarked.R | 222 inst/doc/unmarked.Rnw | 524 +- inst/doc/unmarked.pdf |binary inst/unitTests/runTests.R | 196 inst/unitTests/runit.colext.R | 150 inst/unitTests/runit.crossVal.R |only inst/unitTests/runit.distsamp.r | 286 - inst/unitTests/runit.format.R | 86 inst/unitTests/runit.gdistsamp.R | 442 + inst/unitTests/runit.gmultmix.R | 157 inst/unitTests/runit.gpcount.R | 54 inst/unitTests/runit.modSel.R | 124 inst/unitTests/runit.multinomPois.R | 145 inst/unitTests/runit.nonparboot.R | 322 - inst/unitTests/runit.occu.R | 334 - inst/unitTests/runit.occuFP.R |only inst/unitTests/runit.occuMS.R |only inst/unitTests/runit.occuMulti.R | 422 + inst/unitTests/runit.occuPEN.R | 314 - inst/unitTests/runit.occuRN.R |only inst/unitTests/runit.occuTTD.R |only inst/unitTests/runit.parboot.R | 426 - inst/unitTests/runit.pcount.R | 74 inst/unitTests/runit.pcount.spHDS.R | 52 inst/unitTests/runit.pcountOpen.R | 800 +-- inst/unitTests/runit.pifun.R |only inst/unitTests/runit.predict.R | 372 - inst/unitTests/runit.ranef.R | 1076 ++-- inst/unitTests/runit.unmarkedFrame.R | 167 inst/unitTests/runit.unmarkedMultFrame.R | 588 +- inst/unitTests/runit.utils.R | 406 - inst/unitTests/runit.vif.R |only inst/unitTests/sim.colext.R | 506 - inst/unitTests/sim.distsamp.R | 766 +-- inst/unitTests/sim.gdistsamp.R | 808 +-- inst/unitTests/sim.gmultmix.R | 750 +- inst/unitTests/sim.gpcount.R | 298 - inst/unitTests/sim.pcount.R | 116 inst/unitTests/sim.pcountOpen.r | 1974 +++---- inst/unitTests/sim.ranef.R | 1036 ++-- man/SE-methods.Rd | 32 man/SSE.Rd | 40 man/Switzerland.Rd | 114 man/backTransform-methods.rd | 100 man/birds.Rd | 82 man/coef-methods.Rd | 66 man/colext.Rd | 290 - man/computeMPLElambdas.Rd | 98 man/confint-methods.Rd | 60 man/crossVal.Rd |only man/crossbill.Rd | 174 man/cruz.Rd | 130 man/csvToUMF.Rd | 102 man/detFuns.Rd | 116 man/distsamp.Rd | 360 - man/extract-methods.Rd | 186 man/fitList.Rd | 92 man/fitted-methods.Rd | 84 man/formatDistData.Rd | 164 man/formatMult.Rd | 34 man/formatWideLong.Rd | 128 man/frogs.Rd | 96 man/gdistsamp.Rd | 336 - man/getB-methods.Rd | 22 man/getFP-methods.Rd | 20 man/getP-methods.Rd | 56 man/gf.Rd | 52 man/gmultmix.Rd | 328 - man/gpcount.Rd | 308 - man/imputeMissing.Rd | 106 man/issj.Rd | 92 man/jay.Rd | 160 man/lambda2psi.Rd | 52 man/linearComb-methods.Rd | 64 man/linetran.Rd | 76 man/mallard.Rd | 60 man/masspcru.Rd | 72 man/modSel.Rd | 120 man/multinomPois.Rd | 206 man/nonparboot-methods.Rd | 171 man/occu.Rd | 222 man/occuFP.Rd | 248 man/occuMS.Rd |only man/occuMulti.Rd | 451 - man/occuPEN.Rd | 254 - man/occuPEN_CV.Rd | 270 - man/occuRN.Rd | 172 man/occuTTD.Rd |only man/ovendata.Rd | 66 man/parboot.Rd | 164 man/pcount.Rd | 258 - man/pcount.spHDS.Rd | 250 man/pcountOpen.Rd | 488 - man/piFuns.Rd | 128 man/pointtran.Rd | 70 man/predict-methods.Rd | 70 man/ranef-methods.Rd | 304 - man/sight2perpdist.Rd | 64 man/simulate-methods.Rd | 90 man/unmarked-package.Rd | 524 +- man/unmarkedEstimate-class.Rd | 86 man/unmarkedEstimateList-class.Rd | 34 man/unmarkedFit-class.Rd | 435 - man/unmarkedFitList-class.rd | 132 man/unmarkedFrame-class.Rd | 326 - man/unmarkedFrame.Rd | 198 man/unmarkedFrameDS.Rd | 148 man/unmarkedFrameMPois.Rd | 229 man/unmarkedFrameOccu.Rd | 142 man/unmarkedFrameOccuFP.Rd | 120 man/unmarkedFrameOccuMS.Rd |only man/unmarkedFrameOccuMulti.Rd | 122 man/unmarkedFrameOccuTTD.Rd |only man/unmarkedFramePCO.Rd | 232 man/unmarkedFramePCount.Rd | 130 man/unmarkedMultFrame.Rd | 327 - man/unmarkedRanef-class.Rd | 150 man/vcov-methods.Rd | 30 man/vif.Rd |only src/detfuns.cpp | 77 src/detfuns.h | 58 src/get_mlogit.cpp |only src/get_mlogit.h |only src/init.c | 18 src/nll_distsamp.cpp | 54 src/nll_distsamp.h | 4 src/nll_gdistsamp.cpp |only src/nll_gdistsamp.h |only src/nll_gmultmix.cpp |only src/nll_gmultmix.h |only src/nll_multinomPois.cpp |only src/nll_multinomPois.h |only src/nll_occu.cpp | 18 src/nll_occu.h | 2 src/nll_occuMS.cpp |only src/nll_occuMS.h |only src/nll_occuMulti.cpp | 2 src/nll_occuRN.cpp |only src/nll_occuRN.h |only src/nll_occuTTD.cpp |only src/nll_occuTTD.h |only src/pifun.cpp |only src/pifun.h |only vignettes/cap-recap.Rnw | 1484 ++--- vignettes/colext.Rnw | 2858 +++++------ vignettes/distsamp.Rnw | 804 +-- vignettes/ecology.bst | 2918 +++++------ vignettes/spp-dist.Rnw | 802 +-- vignettes/unmarked.Rnw | 524 +- vignettes/unmarked.bib | 640 +- 208 files changed, 36935 insertions(+), 34815 deletions(-)
Title: 'rquery' for 'data.table'
Description: Implements the 'rquery' piped Codd-style query algebra using 'data.table'. This allows
for a high-speed in memory implementation of Codd-style data manipulation tools.
Author: John Mount [aut, cre],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between rqdatatable versions 1.2.3 dated 2019-10-24 and 1.2.4 dated 2019-11-12
DESCRIPTION | 12 ++-- MD5 | 17 +++--- NEWS.md | 7 ++ R/relop_project.R | 15 +++++ build/vignette.rds |binary inst/doc/GroupedSampling.html | 40 +++++++-------- inst/doc/R_mapping.html | 14 ++--- inst/doc/logisticexample.html | 79 ++++++++++++++---------------- inst/unit_tests/test_degenerate_project.R |only inst/unit_tests/test_relop_drop_columns.R | 1 10 files changed, 101 insertions(+), 84 deletions(-)
Title: Extract Features from Images
Description: Synthesize images into characteristic features for time-series analysis or machine learning applications. The package was originally intended for monitoring volcanic eruptions in video data by highlighting and extracting regions above the vent associated with plume activity. However, the functions within are general and have wide applications for image processing, analyzing, filtering, and plotting.
Author: Alex J.C. Witsil
Maintainer: Alex J.C. Witsil <alexjcwitsil@gmail.com>
Diff between imagefx versions 0.2.0 dated 2019-09-13 and 0.3.0 dated 2019-11-12
DESCRIPTION | 8 ++++---- MD5 | 14 ++++++++++++-- NAMESPACE | 3 ++- R/amp.sig.r |only R/cor.mat.r |only R/gen.eg.img.list.r |only R/shift.vec.r |only R/sig.extract.r |only man/amp.sig.Rd |only man/cor.mat.Rd |only man/gen.eg.img.list.Rd |only man/shift.vec.Rd |only man/sig.extract.Rd |only 13 files changed, 18 insertions(+), 7 deletions(-)
Title: Case-Control Analysis of Multi-Allelic Loci
Description: Data sets and functions for chi-squared Hardy-Weinberg and case-control association tests of highly polymorphic genetic data [e.g., human leukocyte antigen (HLA) data]. Performs association tests at multiple levels of polymorphism (haplotype, locus and HLA amino-acids) as described in Pappas DJ, Marin W, Hollenbach JA, Mack SJ (2016) <doi:10.1016/j.humimm.2015.12.006>. Combines rare variants to a common class to account for sparse cells in tables as described by Hollenbach JA, Mack SJ, Thomson G, Gourraud PA (2012) <doi:10.1007/978-1-61779-842-9_14>.
Author: Derek Pappas <dpappas@chori.org>, Steve Mack <sjmack@chori.org>, Jill
Hollenbach <Jill.Hollenbach@ucsf.edu>
Maintainer: Steve Mack <sjmack@chori.org>
Diff between BIGDAWG versions 2.1 dated 2018-02-08 and 2.3 dated 2019-11-12
DESCRIPTION | 14 - MD5 | 50 ++-- NEWS | 463 +++++++++++++++++++------------------------ R/A.R | 1 R/A_ExonPtnAlign_functions.R | 4 R/BIGDAWG.R | 23 +- R/ErrLog.R | 2 R/GL2TAB.R | 1 R/GLSconvert.R | 2 R/H_wrapper_MC.R | 2 R/check_functions.R | 30 ++ R/sysdata.rda |binary build/vignette.rds |binary inst/doc/BIGDAWG.Rmd | 6 inst/doc/BIGDAWG.html | 223 +++++++++++++++++++- inst/doc/GLSconvert.Rmd | 2 inst/doc/GLSconvert.html | 214 ++++++++++++++++++- man/A.wrapper.Rd | 4 man/BIGDAWG.Rd | 10 man/Check.Data.Rd | 4 man/Check.Params.GLS.Rd | 3 man/Check.Params.Rd | 4 man/H.MC.wrapper.Rd | 4 man/L.wrapper.Rd | 3 vignettes/BIGDAWG.Rmd | 6 vignettes/GLSconvert.Rmd | 2 26 files changed, 713 insertions(+), 364 deletions(-)
Title: Import Data in the JCAMP-DX Format
Description: Import data written in the JCAMP-DX format. This is an instrument-independent format used in the field of spectroscopy. Examples include IR, NMR, and Raman spectroscopy. See the vignette for background and supported formats. The official JCAMP-DX site is <http://www.jcamp-dx.org/>.
Author: Bryan A. Hanson [aut, cre] (<https://orcid.org/0000-0003-3536-8246>)
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between readJDX versions 0.3.250 dated 2018-10-15 and 0.4.29 dated 2019-11-12
readJDX-0.3.250/readJDX/NEWS |only readJDX-0.3.250/readJDX/R/decompressJDXxyy.R |only readJDX-0.3.250/readJDX/R/findDataTables.R |only readJDX-0.3.250/readJDX/R/getJDXcompression.R |only readJDX-0.3.250/readJDX/R/processDataTable.R |only readJDX-0.4.29/readJDX/DESCRIPTION | 16 readJDX-0.4.29/readJDX/MD5 | 64 +- readJDX-0.4.29/readJDX/NAMESPACE | 2 readJDX-0.4.29/readJDX/NEWS.md |only readJDX-0.4.29/readJDX/R/HelperFunctions.R |only readJDX-0.4.29/readJDX/R/deDIF.R | 160 +---- readJDX-0.4.29/readJDX/R/decompLines.R |only readJDX-0.4.29/readJDX/R/decompressXYY.R |only readJDX-0.4.29/readJDX/R/extractParams.R | 417 +++++++-------- readJDX-0.4.29/readJDX/R/findVariableLists.R |only readJDX-0.4.29/readJDX/R/getComp.R |only readJDX-0.4.29/readJDX/R/insertDUPs.R | 134 ++--- readJDX-0.4.29/readJDX/R/onAttach.R |only readJDX-0.4.29/readJDX/R/processVariableLIst.R |only readJDX-0.4.29/readJDX/R/readJDX.R | 482 ++++++++++-------- readJDX-0.4.29/readJDX/R/repDUPs.R | 129 ++-- readJDX-0.4.29/readJDX/R/sinkall.R |only readJDX-0.4.29/readJDX/R/unDIF.R | 121 ++-- readJDX-0.4.29/readJDX/R/unSQZ.R | 56 +- readJDX-0.4.29/readJDX/R/yValueCheck.R |only readJDX-0.4.29/readJDX/build/vignette.rds |binary readJDX-0.4.29/readJDX/inst/doc/GuideToVignettes.R |only readJDX-0.4.29/readJDX/inst/doc/GuideToVignettes.Rmd |only readJDX-0.4.29/readJDX/inst/doc/GuideToVignettes.pdf |only readJDX-0.4.29/readJDX/inst/doc/MiniDIFDUP_1.R |only readJDX-0.4.29/readJDX/inst/doc/MiniDIFDUP_1.Rnw |only readJDX-0.4.29/readJDX/inst/doc/MiniDIFDUP_1.pdf |only readJDX-0.4.29/readJDX/inst/doc/MiniDIFDUP_2.Rnw |only readJDX-0.4.29/readJDX/inst/doc/MiniDIFDUP_2.pdf |only readJDX-0.4.29/readJDX/inst/doc/ProgramFlow.R |only readJDX-0.4.29/readJDX/inst/doc/ProgramFlow.Rmd |only readJDX-0.4.29/readJDX/inst/doc/ProgramFlow.pdf |only readJDX-0.4.29/readJDX/inst/doc/readJDX.R | 8 readJDX-0.4.29/readJDX/inst/doc/readJDX.Rmd | 40 - readJDX-0.4.29/readJDX/inst/doc/readJDX.pdf |binary readJDX-0.4.29/readJDX/inst/extdata/MiniDIFDUP.JDX |only readJDX-0.4.29/readJDX/inst/extdata/isasspc1.dx |only readJDX-0.4.29/readJDX/man/decompLines.Rd |only readJDX-0.4.29/readJDX/man/readJDX.Rd | 160 ++++- readJDX-0.4.29/readJDX/man/sinkall.Rd |only readJDX-0.4.29/readJDX/vignettes/GuideToVignettes.Rmd |only readJDX-0.4.29/readJDX/vignettes/MiniDIFDUP_1.Rnw |only readJDX-0.4.29/readJDX/vignettes/MiniDIFDUP_2.Rnw |only readJDX-0.4.29/readJDX/vignettes/ProgramFlow.Rmd |only readJDX-0.4.29/readJDX/vignettes/readJDX.Rmd | 40 - 50 files changed, 952 insertions(+), 877 deletions(-)
Title: Read and Write 'FreeSurfer' Neuroimaging File Formats
Description: Provides functions to read and write data from neuroimaging files in 'FreeSurfer' <http://freesurfer.net/> binary formats. This includes the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file format. Contains a brain surface mesh, given by a list of vertices and a list of faces.
Author: Tim Schäfer [aut, cre] (<https://orcid.org/0000-0002-3683-8070>)
Maintainer: Tim Schäfer <ts+code@rcmd.org>
Diff between freesurferformats versions 0.1.4 dated 2019-11-06 and 0.1.5 dated 2019-11-12
DESCRIPTION | 6 ++--- MD5 | 41 ++++++++++++++++++----------------- NAMESPACE | 2 + R/read_fs_annot.R | 16 ++++++------- R/read_fs_curv.R | 4 +-- R/read_fs_label.R | 9 +++++-- R/read_fs_mgh.R | 12 +++++----- R/read_fs_surface.R | 2 - R/write_fs_label.R |only R/write_fs_mgh.R | 8 +++--- R/write_fs_surface.R | 8 +++--- man/guess.filename.is.gzipped.Rd | 4 +-- man/read.fs.annot.Rd | 4 +-- man/read.fs.curv.Rd | 4 +-- man/read.fs.label.Rd | 13 +++++++++-- man/read.fs.mgh.Rd | 8 +++--- man/read.fs.surface.Rd | 2 - man/readcolortable.Rd | 6 ++--- man/readcolortable_oldformat.Rd | 6 ++--- man/write.fs.label.Rd |only man/write.fs.mgh.Rd | 8 +++--- man/write.fs.surface.Rd | 8 +++--- tests/testthat/test-write-fs-label.R |only 23 files changed, 95 insertions(+), 76 deletions(-)
More information about freesurferformats at CRAN
Permanent link
Title: Functions for Tabular Reporting
Description: Create pretty tables for 'HTML', 'Microsoft Word' and 'Microsoft PowerPoint' documents.
Functions are provided to let users create tables, modify and format their content.
It extends package 'officer' that does not contain any feature for customized tabular reporting
and can be used within R markdown documents.
Author: David Gohel [aut, cre],
Quentin Fazilleau [ctb],
Maxim Nazarov [ctb] (rmarkdown for docx output),
Titouan Robert [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between flextable versions 0.5.5 dated 2019-06-25 and 0.5.6 dated 2019-11-12
DESCRIPTION | 6 - MD5 | 100 ++++++++++++++++---------------- NAMESPACE | 10 ++- NEWS | 17 +++++ R/01_fpstruct.R | 13 ++-- R/05_content.R | 125 +++++++++++++++++++++++++++++++++++++--- R/as_flextable.R | 12 ++- R/body_add_flextable.R | 1 R/display.R | 7 -- R/flextable_sizes.R | 24 +++++-- R/formatters.R | 52 ++++++++++++---- R/ph_with_flextable.R | 61 +++++-------------- R/printers.R | 75 ++++++++++++++++-------- R/proc_freq.R | 92 ++++++++++++++++++++++++----- R/styles.R | 9 -- R/tabpart_format.R | 4 - R/tabpart_mains.R | 8 ++ R/themes.R | 10 +-- README.md | 4 - build/vignette.rds |binary inst/doc/display.html | 62 ++++++++++++++----- inst/doc/format.html | 58 +++++++++++++----- inst/doc/layout.html | 84 +++++++++++++++++--------- inst/doc/overview.html | 40 ++++++++++-- inst/doc/selectors.html | 44 ++++++++++---- inst/web_1.0.0/tabwid.css | 25 +++++++- man/as_b.Rd | 3 man/as_bracket.Rd | 3 man/as_chunk.Rd | 3 man/as_flextable.Rd | 6 + man/as_i.Rd | 3 man/as_image.Rd | 3 man/as_sub.Rd | 3 man/as_sup.Rd | 3 man/colformat_char.Rd | 9 +- man/colformat_int.Rd | 9 +- man/colformat_lgl.Rd | 10 ++- man/colformat_num.Rd | 10 ++- man/font.Rd | 8 -- man/hyperlink_text.Rd | 3 man/knit_print.flextable.Rd | 13 ++++ man/linerange.Rd | 3 man/lollipop.Rd |only man/minibar.Rd | 3 man/ph_with.flextable.Rd | 14 +++- man/ph_with_flextable.Rd | 20 ------ man/proc_freq.Rd | 20 ++++++ man/save_as_image.Rd | 9 ++ man/theme_alafoli.Rd | 4 - man/theme_booktabs.Rd | 2 tests/testthat/test-images.R | 1 tests/testthat/test-proc-freq.R |only 52 files changed, 777 insertions(+), 331 deletions(-)
Title: A Wrapper of the JavaScript Library 'DataTables'
Description: Data objects in R can be rendered as HTML tables using the
JavaScript library 'DataTables' (typically via R Markdown or Shiny). The
'DataTables' library has been included in this R package. The package name
'DT' is an abbreviation of 'DataTables'.
Author: Yihui Xie [aut, cre],
Joe Cheng [aut],
Xianying Tan [aut],
JJ Allaire [ctb],
Maximilian Girlich [ctb],
Greg Freedman Ellis [ctb],
Johannes Rauh [ctb],
jQuery contributors [ctb, cph] (jQuery in htmlwidgets/lib),
SpryMedia Limited [ctb, cph] (DataTables in htmlwidgets/lib),
Brian Reavis [ctb, cph] (selectize.js in htmlwidgets/lib),
Leon Gersen [ctb, cph] (noUiSlider in htmlwidgets/lib),
Bartek Szopka [ctb, cph] (jquery.highlight.js in htmlwidgets/lib),
RStudio Inc [cph]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between DT versions 0.9 dated 2019-09-17 and 0.10 dated 2019-11-12
DESCRIPTION | 8 +-- MD5 | 8 +-- R/format.R | 4 + inst/doc/DT.html | 84 ++++++++++++++++++++++++++++++++++++----- inst/htmlwidgets/datatables.js | 2 5 files changed, 87 insertions(+), 19 deletions(-)
Title: Pattern Heterogeneity via Distributional Differences Across
Contingency Tables
Description: Statistical hypothesis testing of pattern heterogeneity via
differences in underlying distributions across two or more contingency
tables. Three tests are included: the comparative chi-squared test
(Song et al, 2014) <doi:10.1093/nar/gku086> (Zhang et al, 2015)
<doi:10.1093/nar/gkv358>, the Sharma-Song test, and the heterogeneity test.
Under the null hypothesis that row and column variables are statistically
independent and joint distributions are equal, their test statistics all
follow an asymptotically chi-squared distribution. These options test for
heterogeneous patterns that differ in either the first order (marginal) or
the second order (joint distribution deviation from product of marginals).
Second-order differences may reveal more fundamental changes than
first-order differences across heterogeneous patterns.
Author: Ruby Sharma [aut],
Joe Song [aut, cre] (<https://orcid.org/0000-0002-6883-6547>)
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between DiffXTables versions 0.0.1 dated 2019-11-04 and 0.0.2 dated 2019-11-12
DESCRIPTION | 31 ++++++++++-------- MD5 | 22 ++++++------- NEWS | 16 +++++++++ R/CPChisq.R | 4 +- R/Sharma-Song.R | 38 +++++++++++++--------- R/heterogeneity.R | 2 - README.md | 9 +++-- inst/CITATION | 15 +++------ inst/doc/DiffXTables.Rmd | 14 ++------ inst/doc/DiffXTables.html | 63 +++++++++++++++----------------------- tests/testthat/test_DiffXTables.R | 55 +++++++++++++++++++++++++++++++++ vignettes/DiffXTables.Rmd | 14 ++------ 12 files changed, 171 insertions(+), 112 deletions(-)
Title: Test Set for Differential Equations
Description: Solvers and test set for stiff and non-stiff differential equations, and
differential algebraic equations.
'Mazzia, F., Cash, J.R. and K. Soetaert, 2012. DOI: 10.1016/j.cam.2012.03.014'.
Author: Karline Soetaert [aut, cre],
Jeff Cash [aut],
Francesca Mazzia [aut],
Ernst Hairer [ctb] (files dopri8.f, dopri6.f),
Gerard Wanner [ctb] (files dopri8.f, dopri6.f),
T. Abdulla [ctb] (file mebdfi.f),
Cecilia Magherini [ctb] (files bimd.f, bimda.f),
Luigi Brugnano [ctb] (files bimd.f, bimda.f),
Cleve Moler [ctb] (file bimda.f)
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between deTestSet versions 1.1.6 dated 2019-08-21 and 1.1.7 dated 2019-11-12
DESCRIPTION | 37 +++++++++++++++++++++++++++---------- MD5 | 4 ++-- inst/doc/deTestSet.pdf |binary 3 files changed, 29 insertions(+), 12 deletions(-)
Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
JJ Allaire [ctb],
Albert Kim [ctb],
Alessandro Samuel-Rosa [ctb],
Andrzej Oles [ctb],
Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>),
Aust Frederik [ctb] (<https://orcid.org/0000-0003-4900-788X>),
Bastiaan Quast [ctb],
Ben Marwick [ctb],
Chester Ismay [ctb],
Christophe Dervieux [ctb],
Clifton Franklund [ctb],
Daniel Emaasit [ctb],
David Shuman [ctb],
Dean Attali [ctb],
Drew Tyre [ctb],
Ellis Valentiner [ctb],
Frans van Dunne [ctb],
Hadley Wickham [ctb],
Jeff Allen [ctb],
Jennifer Bryan [ctb],
Jonathan McPhers [ctb],
JooYoung Seo [ctb] (<https://orcid.org/0000-0002-4064-6012>),
Junwen Huang [ctb],
Kevin Cheung [ctb],
Kevin Ushey [ctb],
Kim Seonghyun [ctb],
Kirill Muller [ctb],
Luciano Selzer [ctb],
Matthew Lincoln [ctb],
Maximilian Held [ctb],
Michael Sachs [ctb],
Michal Bojanowski [ctb],
Noam Ross [ctb],
Peter Hickey [ctb],
Romain Lesur [ctb] (<https://orcid.org/0000-0002-0721-5595>),
Sahir Bhatnagar [ctb],
Steve Simpson [ctb],
Thierry Onkelinx [ctb] (<https://orcid.org/0000-0001-8804-4216>),
Vincent Fulco [ctb],
Yixuan Qiu [ctb],
Zhuoer Dong [ctb],
RStudio Inc [cph],
Bartek Szopka [ctb] (The jQuery Highlight plugin),
Zeno Rocha [cph] (clipboard.js library),
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/resources/AUTHORS),
MathQuill contributors [ctb] (The MathQuill library; authors listed in
inst/resources/AUTHORS),
FriendCode Inc [cph, ctb] (The gitbook style, with modifications)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between bookdown versions 0.14 dated 2019-10-01 and 0.15 dated 2019-11-12
DESCRIPTION | 6 ++-- MD5 | 12 ++++----- R/gitbook.R | 34 ++++++++++++++++++++++------ R/html.R | 6 ++-- inst/resources/gitbook/js/plugin-sharing.js | 14 ++--------- tests/rmd/parse-footnotes.Rmd | 9 ++++++- tests/test-rmd.R | 17 ++++++++++++++ 7 files changed, 67 insertions(+), 31 deletions(-)
Title: Miscellaneous Functions by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>),
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brüggemann [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.10 dated 2019-10-01 and 0.11 dated 2019-11-12
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 10 +++++++++- R/io.R | 3 +++ R/revcheck.R | 2 +- inst/doc/xfun.Rmd | 4 ++-- inst/doc/xfun.html | 12 ++++++------ vignettes/xfun.Rmd | 4 ++-- 8 files changed, 33 insertions(+), 22 deletions(-)
Title: Find, Download and Process Sentinel-2 Data
Description: Functions to download Sentinel-2 optical images
and perform preliminary processing operations.
'sen2r' provides the instruments required to easily perform
(and eventually automate) the steps necessary to build a complete
Sentinel-2 processing chain.
A Graphical User Interface to facilitate data processing is also provided.
Author: Luigi Ranghetti [aut, cre] (<https://orcid.org/0000-0001-6207-5188>),
Lorenzo Busetto [aut] (<https://orcid.org/0000-0001-9634-6038>)
Maintainer: Luigi Ranghetti <luigi@ranghetti.info>
Diff between sen2r versions 1.1.0 dated 2019-10-21 and 1.2.1 dated 2019-11-12
sen2r-1.1.0/sen2r/R/ask_permission.R |only sen2r-1.1.0/sen2r/man/ask_permission.Rd |only sen2r-1.1.0/sen2r/tests/testthat/test-t11_s2_download.R |only sen2r-1.1.0/sen2r/tests/testthat/test-t12_install_sen2cor.R |only sen2r-1.1.0/sen2r/tests/testthat/test-t13_sen2cor.R |only sen2r-1.2.1/sen2r/DESCRIPTION | 14 sen2r-1.2.1/sen2r/MD5 | 113 - sen2r-1.2.1/sen2r/NAMESPACE | 8 sen2r-1.2.1/sen2r/NEWS.md | 62 sen2r-1.2.1/sen2r/R/build_example_param_file.R | 8 sen2r-1.2.1/sen2r/R/check_param_list.R | 5 sen2r-1.2.1/sen2r/R/check_sen2r_deps.R | 7 sen2r-1.2.1/sen2r/R/compute_s2_paths.R | 24 sen2r-1.2.1/sen2r/R/give_write_permission.R |only sen2r-1.2.1/sen2r/R/init_python.R | 19 sen2r-1.2.1/sen2r/R/install_sen2cor.R | 58 sen2r-1.2.1/sen2r/R/mountpoint.R | 4 sen2r-1.2.1/sen2r/R/s2_download.R | 132 + sen2r-1.2.1/sen2r/R/s2_gui.R | 74 sen2r-1.2.1/sen2r/R/s2_list.R | 160 + sen2r-1.2.1/sen2r/R/s2_mask.R | 1 sen2r-1.2.1/sen2r/R/s2_order.R |only sen2r-1.2.1/sen2r/R/s2_translate.R | 11 sen2r-1.2.1/sen2r/R/safe_getMetadata.R | 959 ++++++---- sen2r-1.2.1/sen2r/R/safe_is_online.R |only sen2r-1.2.1/sen2r/R/safe_shortname.R | 213 -- sen2r-1.2.1/sen2r/R/safelist-class.R |only sen2r-1.2.1/sen2r/R/scihub_login.R | 7 sen2r-1.2.1/sen2r/R/sen2cor.R | 26 sen2r-1.2.1/sen2r/R/sen2r.R | 384 ++-- sen2r-1.2.1/sen2r/R/zzz.R | 8 sen2r-1.2.1/sen2r/inst/CITATION | 4 sen2r-1.2.1/sen2r/inst/WORDLIST | 7 sen2r-1.2.1/sen2r/inst/doc/docker.R | 4 sen2r-1.2.1/sen2r/inst/doc/docker.Rmd | 8 sen2r-1.2.1/sen2r/inst/doc/docker.html | 45 sen2r-1.2.1/sen2r/inst/doc/installation.R | 9 sen2r-1.2.1/sen2r/inst/doc/installation.Rmd | 21 sen2r-1.2.1/sen2r/inst/doc/installation.html | 21 sen2r-1.2.1/sen2r/inst/extdata/settings/indices.json | 4 sen2r-1.2.1/sen2r/man/build_example_param_file.Rd | 2 sen2r-1.2.1/sen2r/man/give_write_permission.Rd |only sen2r-1.2.1/sen2r/man/install_sen2cor.Rd | 12 sen2r-1.2.1/sen2r/man/s2_download.Rd | 35 sen2r-1.2.1/sen2r/man/s2_list.Rd | 36 sen2r-1.2.1/sen2r/man/s2_order.Rd |only sen2r-1.2.1/sen2r/man/safe_getMetadata.Rd | 110 - sen2r-1.2.1/sen2r/man/safe_is_online.Rd |only sen2r-1.2.1/sen2r/man/safe_shortname.Rd | 66 sen2r-1.2.1/sen2r/man/safelist-class.Rd |only sen2r-1.2.1/sen2r/man/sen2r.Rd | 58 sen2r-1.2.1/sen2r/tests/testthat/test-t05_load_binpaths.R |only sen2r-1.2.1/sen2r/tests/testthat/test-t08_build_example_param_file.R |only sen2r-1.2.1/sen2r/tests/testthat/test-t10_s2_list.R | 177 + sen2r-1.2.1/sen2r/tests/testthat/test-t11_s2_classes.R |only sen2r-1.2.1/sen2r/tests/testthat/test-t12_s2_download.R |only sen2r-1.2.1/sen2r/tests/testthat/test-t13_install_sen2cor.R |only sen2r-1.2.1/sen2r/tests/testthat/test-t14_sen2cor.R |only sen2r-1.2.1/sen2r/tests/testthat/test-t15_s2_order.R |only sen2r-1.2.1/sen2r/tests/testthat/test-t20_s2_merge.R | 15 sen2r-1.2.1/sen2r/tests/testthat/test-t21_s2_warp.R | 115 - sen2r-1.2.1/sen2r/tests/testthat/test-t22_s2_mask.R | 18 sen2r-1.2.1/sen2r/tests/testthat/test-t23_s2_indices.R | 20 sen2r-1.2.1/sen2r/tests/testthat/test-t24_s2_rgb.R | 9 sen2r-1.2.1/sen2r/tests/testthat/test-t32_list_indices.R | 9 sen2r-1.2.1/sen2r/tests/testthat/test-t36_mountpoint.R |only sen2r-1.2.1/sen2r/vignettes/docker.Rmd | 8 sen2r-1.2.1/sen2r/vignettes/installation.Rmd | 21 68 files changed, 1943 insertions(+), 1188 deletions(-)
Title: Article Formats for R Markdown
Description: A suite of custom R Markdown formats and templates for
authoring journal articles and conference submissions.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
R Foundation [aut, cph],
Hadley Wickham [aut],
Journal of Statistical Software [aut, cph],
RStudio [cph],
Ramnath Vaidyanathan [aut, cph],
Association for Computing Machinery [aut, cph],
Carl Boettiger [aut, cph],
Elsevier [aut, cph],
Karl Broman [aut, cph],
Kirill Mueller [aut, cph],
Bastiaan Quast [aut, cph],
Randall Pruim [aut, cph],
Ben Marwick [aut, cph],
Charlotte Wickham [aut, cph],
Oliver Keyes [aut, cph],
Miao Yu [aut, cph],
Daniel Emaasit [aut, cph],
Thierry Onkelinx [aut, cph],
Alessandro Gasparini [aut, cph]
(<https://orcid.org/0000-0002-8319-7624>),
Marc-Andre Desautels [aut, cph],
Dominik Leutnant [aut, cph] (<https://orcid.org/0000-0003-3293-2315>),
MDPI [aut, cph],
Taylor and Francis [aut, cph],
Oğuzhan Öğreden [aut] (<https://orcid.org/0000-0002-9949-3348>),
Dalton Hance [aut],
Daniel Nüst [aut, cph] (<https://orcid.org/0000-0002-0024-5046>),
Petter Uvesten [aut, cph],
Elio Campitelli [aut, cph] (<https://orcid.org/0000-0002-7742-9230>),
John Muschelli [aut, cph] (<https://orcid.org/0000-0001-6469-1750>),
Zhian N. Kamvar [aut, cph] (<https://orcid.org/0000-0003-1458-7108>),
Noam Ross [aut, cph] (<https://orcid.org/0000-0002-2136-0000>)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rticles versions 0.11 dated 2019-10-01 and 0.12 dated 2019-11-12
rticles-0.11/rticles/inst/rmarkdown/templates/pnas_article/resources/pnas-new.cls |only rticles-0.11/rticles/inst/rmarkdown/templates/pnas_article/resources/pnas.csl |only rticles-0.11/rticles/inst/rmarkdown/templates/pnas_article/skeleton/pnasinvited.sty |only rticles-0.11/rticles/inst/rmarkdown/templates/pnas_article/skeleton/pnasmathematics.sty |only rticles-0.12/rticles/DESCRIPTION | 6 rticles-0.12/rticles/MD5 | 18 rticles-0.12/rticles/NEWS.md | 5 rticles-0.12/rticles/R/article.R | 2 rticles-0.12/rticles/inst/rmarkdown/templates/pnas_article/skeleton/pnas-new.cls | 203 +++++----- rticles-0.12/rticles/inst/rmarkdown/templates/pnas_article/skeleton/pnasresearcharticle.sty | 12 rticles-0.12/rticles/man/article.Rd | 2 rticles-0.12/rticles/tests/testit/test-formats.R | 1 12 files changed, 139 insertions(+), 110 deletions(-)
Title: In-Line Documentation for R
Description: Generate your Rd documentation, 'NAMESPACE' file,
and collation field using specially formatted comments. Writing
documentation in-line with code makes it easier to keep your
documentation up-to-date as your requirements change. 'Roxygen2' is
inspired by the 'Doxygen' system for C++.
Author: Hadley Wickham [aut, cre, cph]
(<https://orcid.org/0000-0003-4757-117X>),
Peter Danenberg [aut, cph],
Gábor Csárdi [aut],
Manuel Eugster [aut, cph],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between roxygen2 versions 6.1.1 dated 2018-11-07 and 7.0.0 dated 2019-11-12
roxygen2-6.1.1/roxygen2/R/object-name.R |only roxygen2-6.1.1/roxygen2/R/object-usage.R |only roxygen2-6.1.1/roxygen2/R/object.R |only roxygen2-6.1.1/roxygen2/R/source.R |only roxygen2-6.1.1/roxygen2/inst/doc/collate.R |only roxygen2-6.1.1/roxygen2/inst/doc/collate.Rmd |only roxygen2-6.1.1/roxygen2/inst/doc/collate.html |only roxygen2-6.1.1/roxygen2/inst/doc/formatting.R |only roxygen2-6.1.1/roxygen2/inst/doc/formatting.Rmd |only roxygen2-6.1.1/roxygen2/inst/doc/formatting.html |only roxygen2-6.1.1/roxygen2/inst/doc/markdown.R |only roxygen2-6.1.1/roxygen2/inst/doc/markdown.Rmd |only roxygen2-6.1.1/roxygen2/inst/doc/markdown.html |only roxygen2-6.1.1/roxygen2/inst/doc/rdkeywords.R |only roxygen2-6.1.1/roxygen2/inst/doc/rdkeywords.Rmd |only roxygen2-6.1.1/roxygen2/inst/doc/rdkeywords.html |only roxygen2-6.1.1/roxygen2/src/wrapString.cpp |only roxygen2-6.1.1/roxygen2/tests/testthat/Rd-example-4.R |only roxygen2-6.1.1/roxygen2/tests/testthat/Rd-example-5.txt |only roxygen2-6.1.1/roxygen2/tests/testthat/helper-env.R |only roxygen2-6.1.1/roxygen2/tests/testthat/man-roxygen/UCase.R |only roxygen2-6.1.1/roxygen2/tests/testthat/man-roxygen/lcase.r |only roxygen2-6.1.1/roxygen2/tests/testthat/man-roxygen/reg.ex.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-Rbuildignore.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-Rd-inherit.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-eval.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-nice-name.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-object-s4.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-object.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-parse-block.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-rd-alias.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-rd-data.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-rd-describein.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-rd-doctype.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-rd-field.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-rd-introduction.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-rd-keyword.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-rd-markdown-links.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-rd-markdown-on-off.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-rd-name.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-rd-package.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-rd-param.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-rd-slot.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-rdComplete.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-reexport.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-select_args.R |only roxygen2-6.1.1/roxygen2/tests/testthat/test-utf8.R |only roxygen2-6.1.1/roxygen2/vignettes/collate.Rmd |only roxygen2-6.1.1/roxygen2/vignettes/formatting.Rmd |only roxygen2-6.1.1/roxygen2/vignettes/markdown.Rmd |only roxygen2-6.1.1/roxygen2/vignettes/rdkeywords.Rmd |only roxygen2-6.1.1/roxygen2/vignettes/releases |only roxygen2-7.0.0/roxygen2/DESCRIPTION | 60 roxygen2-7.0.0/roxygen2/MD5 | 312 ++--- roxygen2-7.0.0/roxygen2/NAMESPACE | 234 ++- roxygen2-7.0.0/roxygen2/NEWS.md | 283 ++++ roxygen2-7.0.0/roxygen2/R/RcppExports.R | 8 roxygen2-7.0.0/roxygen2/R/block.R | 270 ++-- roxygen2-7.0.0/roxygen2/R/collate.R | 44 roxygen2-7.0.0/roxygen2/R/field.R | 355 ----- roxygen2-7.0.0/roxygen2/R/load.R |only roxygen2-7.0.0/roxygen2/R/markdown-escaping.R | 48 roxygen2-7.0.0/roxygen2/R/markdown-link.R |only roxygen2-7.0.0/roxygen2/R/markdown-state.R |only roxygen2-7.0.0/roxygen2/R/markdown.R | 606 +++------- roxygen2-7.0.0/roxygen2/R/namespace.R | 334 +++-- roxygen2-7.0.0/roxygen2/R/object-defaults.R | 77 - roxygen2-7.0.0/roxygen2/R/object-format.R | 10 roxygen2-7.0.0/roxygen2/R/object-from-call.R | 293 +++- roxygen2-7.0.0/roxygen2/R/object-import.R |only roxygen2-7.0.0/roxygen2/R/object-package.R | 13 roxygen2-7.0.0/roxygen2/R/object-r6.R |only roxygen2-7.0.0/roxygen2/R/object-rc.R | 20 roxygen2-7.0.0/roxygen2/R/object-s3.R | 23 roxygen2-7.0.0/roxygen2/R/options.R |only roxygen2-7.0.0/roxygen2/R/package_files.R |only roxygen2-7.0.0/roxygen2/R/parse.R | 81 - roxygen2-7.0.0/roxygen2/R/rd-backref.R |only roxygen2-7.0.0/roxygen2/R/rd-describe-in.R | 92 + roxygen2-7.0.0/roxygen2/R/rd-examples.R |only roxygen2-7.0.0/roxygen2/R/rd-family.R | 60 roxygen2-7.0.0/roxygen2/R/rd-include-rmd.R |only roxygen2-7.0.0/roxygen2/R/rd-inherit.R | 281 +++- roxygen2-7.0.0/roxygen2/R/rd-markdown.R |only roxygen2-7.0.0/roxygen2/R/rd-name-alias.R |only roxygen2-7.0.0/roxygen2/R/rd-params.R | 42 roxygen2-7.0.0/roxygen2/R/rd-r6.R |only roxygen2-7.0.0/roxygen2/R/rd-raw.R |only roxygen2-7.0.0/roxygen2/R/rd-s4.R |only roxygen2-7.0.0/roxygen2/R/rd-section.R |only roxygen2-7.0.0/roxygen2/R/rd-simple.R |only roxygen2-7.0.0/roxygen2/R/rd-template.R | 66 - roxygen2-7.0.0/roxygen2/R/rd-usage.R |only roxygen2-7.0.0/roxygen2/R/rd.R | 439 +------ roxygen2-7.0.0/roxygen2/R/roclet.R | 56 roxygen2-7.0.0/roxygen2/R/roxygen.R | 3 roxygen2-7.0.0/roxygen2/R/roxygenize.R | 81 - roxygen2-7.0.0/roxygen2/R/safety.R | 28 roxygen2-7.0.0/roxygen2/R/tag-parser.R |only roxygen2-7.0.0/roxygen2/R/tag.R | 250 ---- roxygen2-7.0.0/roxygen2/R/tokenize.R | 11 roxygen2-7.0.0/roxygen2/R/topic.R | 146 +- roxygen2-7.0.0/roxygen2/R/topics.R | 6 roxygen2-7.0.0/roxygen2/R/topo-sort.R | 2 roxygen2-7.0.0/roxygen2/R/utils-io.R | 17 roxygen2-7.0.0/roxygen2/R/utils-rd.R | 73 - roxygen2-7.0.0/roxygen2/R/utils.R | 96 - roxygen2-7.0.0/roxygen2/R/vignette.R | 10 roxygen2-7.0.0/roxygen2/R/zzz.R |only roxygen2-7.0.0/roxygen2/README.md | 129 -- roxygen2-7.0.0/roxygen2/build/vignette.rds |binary roxygen2-7.0.0/roxygen2/inst/doc/extending.R |only roxygen2-7.0.0/roxygen2/inst/doc/extending.Rmd |only roxygen2-7.0.0/roxygen2/inst/doc/extending.html |only roxygen2-7.0.0/roxygen2/inst/doc/namespace.Rmd | 29 roxygen2-7.0.0/roxygen2/inst/doc/namespace.html | 41 roxygen2-7.0.0/roxygen2/inst/doc/rd-formatting.R |only roxygen2-7.0.0/roxygen2/inst/doc/rd-formatting.Rmd |only roxygen2-7.0.0/roxygen2/inst/doc/rd-formatting.html |only roxygen2-7.0.0/roxygen2/inst/doc/rd.R | 155 ++ roxygen2-7.0.0/roxygen2/inst/doc/rd.Rmd | 459 +++++-- roxygen2-7.0.0/roxygen2/inst/doc/rd.html | 602 ++++++--- roxygen2-7.0.0/roxygen2/inst/doc/roxygen2.R | 31 roxygen2-7.0.0/roxygen2/inst/doc/roxygen2.Rmd | 124 +- roxygen2-7.0.0/roxygen2/inst/doc/roxygen2.html | 196 +++ roxygen2-7.0.0/roxygen2/man/RoxyTopic.Rd |only roxygen2-7.0.0/roxygen2/man/double_escape_md.Rd | 23 roxygen2-7.0.0/roxygen2/man/load.Rd |only roxygen2-7.0.0/roxygen2/man/load_options.Rd | 15 roxygen2-7.0.0/roxygen2/man/markdown-internals.Rd | 4 roxygen2-7.0.0/roxygen2/man/markdown-test.Rd | 8 roxygen2-7.0.0/roxygen2/man/namespace_roclet.Rd | 45 roxygen2-7.0.0/roxygen2/man/object.Rd | 4 roxygen2-7.0.0/roxygen2/man/object_format.Rd | 2 roxygen2-7.0.0/roxygen2/man/parse_package.Rd | 21 roxygen2-7.0.0/roxygen2/man/rd_roclet.Rd | 28 roxygen2-7.0.0/roxygen2/man/rd_section.Rd |only roxygen2-7.0.0/roxygen2/man/roc_proc_text.Rd | 7 roxygen2-7.0.0/roxygen2/man/roclet.Rd | 30 roxygen2-7.0.0/roxygen2/man/roxy_block.Rd |only roxygen2-7.0.0/roxygen2/man/roxy_tag.Rd | 75 - roxygen2-7.0.0/roxygen2/man/roxy_tag_rd.Rd |only roxygen2-7.0.0/roxygen2/man/roxygen |only roxygen2-7.0.0/roxygen2/man/roxygen2-package.Rd | 19 roxygen2-7.0.0/roxygen2/man/roxygenize.Rd | 21 roxygen2-7.0.0/roxygen2/man/tag_parsers.Rd |only roxygen2-7.0.0/roxygen2/man/update_collate.Rd | 44 roxygen2-7.0.0/roxygen2/man/vignette_roclet.Rd | 7 roxygen2-7.0.0/roxygen2/src/RcppExports.cpp | 22 roxygen2-7.0.0/roxygen2/src/parser2.cpp | 9 roxygen2-7.0.0/roxygen2/src/wrapUsage.cpp |only roxygen2-7.0.0/roxygen2/tests/testthat.R | 6 roxygen2-7.0.0/roxygen2/tests/testthat/helper-test.R | 12 roxygen2-7.0.0/roxygen2/tests/testthat/roxygen-block-3-A.Rd |only roxygen2-7.0.0/roxygen2/tests/testthat/roxygen-block-3-B.Rd |only roxygen2-7.0.0/roxygen2/tests/testthat/roxygen-block-3-C.Rd |only roxygen2-7.0.0/roxygen2/tests/testthat/roxygen-block-3-warnings.txt |only roxygen2-7.0.0/roxygen2/tests/testthat/roxygen-block-3.R |only roxygen2-7.0.0/roxygen2/tests/testthat/templates |only roxygen2-7.0.0/roxygen2/tests/testthat/test-block-print.txt |only roxygen2-7.0.0/roxygen2/tests/testthat/test-block.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-collate.R | 9 roxygen2-7.0.0/roxygen2/tests/testthat/test-load.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-markdown-link.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-markdown-state.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-markdown-table.txt |only roxygen2-7.0.0/roxygen2/tests/testthat/test-markdown.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-namespace.R | 97 + roxygen2-7.0.0/roxygen2/tests/testthat/test-object-defaults.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-object-format.R | 91 - roxygen2-7.0.0/roxygen2/tests/testthat/test-object-from-call.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-object-import.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-object-import.txt |only roxygen2-7.0.0/roxygen2/tests/testthat/test-object-package.R | 2 roxygen2-7.0.0/roxygen2/tests/testthat/test-object-rc.R | 4 roxygen2-7.0.0/roxygen2/tests/testthat/test-object-s3.R | 6 roxygen2-7.0.0/roxygen2/tests/testthat/test-object-usage-wrap-new.txt |only roxygen2-7.0.0/roxygen2/tests/testthat/test-object-usage-wrap-old.txt |only roxygen2-7.0.0/roxygen2/tests/testthat/test-options |only roxygen2-7.0.0/roxygen2/tests/testthat/test-options.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-package_files.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-parse.R | 133 -- roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-backref.R | 11 roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-describe-in.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-examples-dotrun-escape.txt |only roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-examples-interleave.txt |only roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-examples.R | 103 - roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-family.R | 49 roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-includermd.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-inherit-dots-inherit.txt |only roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-inherit-dots-multi.txt |only roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-inherit-dots.txt |only roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-inherit-link.txt |only roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-inherit.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-markdown-escaping.R | 2 roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-markdown.R | 439 ------- roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-name-alias.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-params.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-r6.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-raw.R | 7 roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-s4.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-section.R | 11 roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-simple.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-template.R | 51 roxygen2-7.0.0/roxygen2/tests/testthat/test-rd-usage.R | 456 +++---- roxygen2-7.0.0/roxygen2/tests/testthat/test-rd.R | 87 - roxygen2-7.0.0/roxygen2/tests/testthat/test-safety.R | 15 roxygen2-7.0.0/roxygen2/tests/testthat/test-select-args.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-tag.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-tokenize.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-topic.R | 20 roxygen2-7.0.0/roxygen2/tests/testthat/test-utils-io.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-utils-rd.R |only roxygen2-7.0.0/roxygen2/tests/testthat/test-utils.R | 18 roxygen2-7.0.0/roxygen2/vignettes/extending.Rmd |only roxygen2-7.0.0/roxygen2/vignettes/namespace.Rmd | 29 roxygen2-7.0.0/roxygen2/vignettes/rd-formatting.Rmd |only roxygen2-7.0.0/roxygen2/vignettes/rd.Rmd | 459 +++++-- roxygen2-7.0.0/roxygen2/vignettes/roxygen2.Rmd | 124 +- 219 files changed, 4989 insertions(+), 4232 deletions(-)
Title: Space-Time Estimation of Forest Variables using the FIA Database
Description: The goal of 'rFIA' is to increase the accessibility and use of the United States Forest Services (USFS) Forest Inventory and Analysis (FIA) Database by providing a user-friendly, open source toolkit to easily query and analyze FIA Data. Designed to accommodate a wide range of potential user objectives, 'rFIA' simplifies the estimation of forest variables from the FIA Database and allows all R users (experts and newcomers alike) to unlock the flexibility inherent to the Enhanced FIA design. Specifically, 'rFIA' improves accessibility to the spatio-temporal estimation capacity of the FIA Database by producing space-time indexed summaries of forest variables within user-defined population boundaries. Direct integration with other popular R packages (e.g., 'dplyr', 'tidyr', and 'sf') facilitates efficient space-time query and data summary, and supports common data representations and API design. The package implements design-based estimation procedures outlined by Bechtold & Patterson (2005) <doi:10.2737/SRS-GTR-80>, and has been validated against estimates and sampling errors produced by FIA 'EVALIDator'. Current development is focused on the implementation of spatially-enabled model-assisted estimators to improve population, change, and ratio estimates.
Author: Hunter Stanke [aut, cre],
Andrew Finley [aut]
Maintainer: Hunter Stanke <stankehu@msu.edu>
Diff between rFIA versions 0.1.0 dated 2019-10-28 and 0.1.1 dated 2019-11-12
DESCRIPTION | 6 +- MD5 | 12 ++-- R/dwmHelper.R | 4 - R/functionsFIA.R | 147 ++++++++++++++++++++++++++++++++++++++++--------------- R/plotFIA.R | 15 +++-- README.md | 14 ++++- man/plotFIA.Rd | 16 +++-- 7 files changed, 148 insertions(+), 66 deletions(-)
Title: Interface to OGC Web-Services (OWS)
Description: Provides an Interface to Web-Services defined as standards by the Open Geospatial Consortium (OGC), including Web Feature Service
(WFS) for vector data, Catalogue Service (CSW) for ISO/OGC metadata and associated standards such as the common web-service specification (OWS) and
OGC Filter Encoding. The long-term purpose is to add support for additional OGC service standards such as Web Coverage Service (WCS) and
Web Processing Service (WPS).
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>),
Norbert Billet [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between ows4R versions 0.1-3 dated 2019-11-05 and 0.1-4 dated 2019-11-12
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 14 +++++++++----- R/WFSGetFeature.R | 3 +-- R/ows4R.R | 4 ++-- README.md | 2 +- 6 files changed, 22 insertions(+), 19 deletions(-)
Title: A Simple Package for Testing R Packages
Description: Provides two convenience functions assert() and test_pkg() to
facilitate testing R packages.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Steven Mortimer [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between testit versions 0.10 dated 2019-10-01 and 0.11 dated 2019-11-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 6 ++++++ README.md | 2 +- 4 files changed, 14 insertions(+), 8 deletions(-)
Title: MAGIC - Markov Affinity-Based Graph Imputation of Cells
Description: MAGIC (Markov affinity-based graph imputation of cells) is a method for addressing technical noise in single-cell data, including under-sampling of mRNA molecules, often termed "dropout" which can severely obscure important gene-gene relationships. MAGIC shares information across similar cells, via data diffusion, to denoise the cell count matrix and fill in missing transcripts. Read more: van Dijk et al. (2018) <DOI:10.1016/j.cell.2018.05.061>.
Author: David van Dijk [aut],
Scott Gigante [cre] (<https://orcid.org/0000-0002-4544-2764>)
Maintainer: Scott Gigante <scott.gigante@yale.edu>
Diff between Rmagic versions 1.4.0 dated 2018-11-24 and 2.0.0 dated 2019-11-12
DESCRIPTION | 10 LICENSE | 680 +-- MD5 | 67 NAMESPACE | 28 R/magic.R | 777 ++- R/magic_testdata.R | 14 R/preprocessing.R | 52 R/utils.R | 219 - README.md | 545 +- inst/CITATION | 50 inst/examples/BMMSC_data_R_after_magic.png |binary inst/examples/BMMSC_data_R_before_magic.png |binary inst/examples/BMMSC_data_R_pca_colored_by_magic.png |binary inst/examples/BMMSC_data_R_phate_colored_by_magic.png |binary inst/examples/EMT_data_R_after_magic.png |binary inst/examples/EMT_data_R_pca_colored_by_magic.png |binary inst/examples/bonemarrow_tutorial.Rmd | 367 - inst/examples/bonemarrow_tutorial.html | 3562 ++++++++--------- inst/examples/emt_tutorial.Rmd | 327 - inst/examples/emt_tutorial.html | 3585 +++++++++--------- man/as.data.frame.Rd | 32 man/as.matrix.Rd | 32 man/figures/README-plot_magic-1.png |binary man/figures/README-plot_raw-1.png |binary man/figures/README-plot_reduced_t-1.png |binary man/figures/README-run_pca-1.png |binary man/figures/README-run_phate-1.png |binary man/ggplot.Rd | 52 man/install.magic.Rd | 66 man/library.size.normalize.Rd | 54 man/magic.Rd | 236 - man/magic_testdata.Rd | 34 man/print.Rd | 58 man/pymagic_is_available.Rd |only man/summary.Rd | 64 35 files changed, 5629 insertions(+), 5282 deletions(-)
Title: Paginate the HTML Output of R Markdown with CSS for Print
Description: Use the paged media properties in CSS and the JavaScript
library 'paged.js' to split the content of an HTML document into discrete
pages. Each page can have its page size, page numbers, margin boxes, and
running headers, etc. Applications of this package include books, letters,
reports, papers, business cards, resumes, and posters.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Romain Lesur [aut, cph] (<https://orcid.org/0000-0002-0721-5595>),
Brent Thorne [aut] (<https://orcid.org/0000-0002-1099-3857>),
Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>),
Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>),
RStudio, Inc. [cph],
Adam Hyde [ctb] (paged.js in resources/js/),
Min-Zhong Lu [ctb] (resume.css in resources/css/),
Zulko [ctb] (poster-relaxed.css in resources/css/)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between pagedown versions 0.5 dated 2019-10-01 and 0.6 dated 2019-11-12
DESCRIPTION | 9 +- MD5 | 12 +- NEWS.md | 8 + R/chrome.R | 171 ++++++++++++++++++++++------------------ R/utils.R | 5 + README.md | 2 inst/resources/html/resume.html | 32 +++++++ 7 files changed, 153 insertions(+), 86 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation (ODE) models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
VODE and LSODA are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut] (<https://orcid.org/0000-0001-8538-6691>),
Melissa Hallow [aut],
Wenping Wang [aut, cre],
Zufar Mulyukov [ctb],
Justin Wilkins [ctb] (<https://orcid.org/0000-0002-7099-9396>),
Simon Frost [ctb],
Goro Fuji [ctb],
Morwenn [ctb],
Heng Li [ctb],
Yu Feng [ctb],
Alan Hindmarsh [ctb],
Linda Petzold [ctb],
Ernst Hairer [ctb],
Gerhard Wanner [ctb],
J Colinge [ctb],
Hadley Wickham [ctb],
G Grothendieck [ctb],
Robert Gentleman [ctb],
Daniel C. Dillon [ctb],
Ross Ihaka [ctb],
Cleve Moler [ctb],
Jack Dongarra [ctb],
R core team [cph]
Maintainer: Wenping Wang <wwang8198@gmail.com>
Diff between RxODE versions 0.9.1-7 dated 2019-10-27 and 0.9.1-8 dated 2019-11-12
DESCRIPTION | 27 MD5 | 62 - NAMESPACE | 3 R/RcppExports.R | 33 R/RxODE.R | 7 R/etTran.R | 25 R/rxode-options.R | 7 R/rxsolve.R | 23 R/utils.R | 27 configure.win | 2 inst/WORDLIST | 7 inst/doc/RxODE-intro.html | 4 inst/doc/RxODE-syntax.html | 4 inst/include/RxODE.h | 3 inst/include/RxODE_model.h | 4 man/forderForceBase.Rd |only man/rxClean.Rd | 10 man/rxSetProgressBar.Rd |only man/rxSolve.Rd | 23 man/rxStack.Rd | 4 man/rxUseRadixSort.Rd |only src/RcppExports.cpp | 22 src/et.cpp | 221 +++-- src/etTran.cpp | 281 +++++- src/init.c | 6 src/par_solve.c | 316 ++++--- src/rxData.cpp | 27 src/rxStack.cpp | 4 src/tran.c | 182 +++- tests/testthat/test-data-table.R |only tests/testthat/test-et.R | 943 +++++++++++------------ tests/testthat/test-etTrans.R | 1505 ++++++++++++++++++------------------- tests/testthat/test-gc.R | 2 tests/testthat/test-lhs-param.R |only tests/testthat/test-missing-evid.R |only 35 files changed, 2156 insertions(+), 1628 deletions(-)
Title: Paired Lasso Regression
Description: Implements sparse regression with paired covariates (Rauschenberger et al. 2019). For the optional shrinkage, install ashr (<https://github.com/stephens999/ashr>) and CorShrink (<https://github.com/kkdey/CorShrink>) from GitHub (see README).
Author: Armin Rauschenberger [aut, cre]
Maintainer: Armin Rauschenberger <armin.rauschenberger@uni.lu>
Diff between palasso versions 0.0.5 dated 2019-04-19 and 0.0.6 dated 2019-11-12
palasso-0.0.5/palasso/NEWS |only palasso-0.0.6/palasso/DESCRIPTION | 10 palasso-0.0.6/palasso/MD5 | 23 palasso-0.0.6/palasso/NEWS.md | 8 palasso-0.0.6/palasso/R/function.R | 4 palasso-0.0.6/palasso/R/hidden.R | 2 palasso-0.0.6/palasso/R/methods.R | 18 palasso-0.0.6/palasso/README.md | 51 palasso-0.0.6/palasso/build/vignette.rds |binary palasso-0.0.6/palasso/inst/CITATION | 3 palasso-0.0.6/palasso/inst/doc/article.html | 187 ++ palasso-0.0.6/palasso/inst/doc/script.html | 2197 ++++++++++++++------------- palasso-0.0.6/palasso/inst/doc/vignette.html | 337 +++- 13 files changed, 1759 insertions(+), 1081 deletions(-)
Title: Fuzzy Logic Toolkit for R
Description: Design and simulate fuzzy logic systems using Type-1 and Interval Type-2 Fuzzy Logic.
This toolkit includes with graphical user interface (GUI) and an adaptive neuro-
fuzzy inference system (ANFIS). This toolkit is a continuation from the previous
package ('FuzzyToolkitUoN'). Produced by the Intelligent Modelling & Analysis Group (IMA)
and Lab for UnCertainty In Data and decision making (LUCID), University of Nottingham.
Author: Chao Chen, Jon Garibaldi, Tajul Razak
Maintainer: Chao Chen <fuzzyr@cs.nott.ac.uk>
Diff between FuzzyR versions 2.1 dated 2017-03-24 and 2.2 dated 2019-11-12
DESCRIPTION | 26 MD5 | 137 NAMESPACE | 133 NEWS.md |only R/ANFIS.R | 2569 ++++++++-------- R/FuzzyInferenceSystem.R | 6476 +++++++++++++++++++++-------------------- R/FuzzyMF.R | 788 +++- R/FuzzyOperation.R | 873 ++--- R/Utilities.R | 448 +- man/addmf.Rd | 65 man/addrule.Rd | 65 man/addvar.Rd | 65 man/anfis.L1.eval.Rd | 57 man/anfis.L2.eval.Rd | 53 man/anfis.L2.which.Rd | 57 man/anfis.L3.eval.Rd | 57 man/anfis.L4.eval.Rd | 53 man/anfis.L4.mf.eval.Rd | 53 man/anfis.L5.eval.Rd | 49 man/anfis.LI.eval.Rd | 53 man/anfis.builder.Rd | 59 man/anfis.dE.dO1.Rd | 59 man/anfis.dE.dO2.Rd | 51 man/anfis.dE.dO3.Rd | 55 man/anfis.dE.dO4.Rd | 55 man/anfis.dE.dO5.Rd | 53 man/anfis.dE.dP1.Rd | 55 man/anfis.dE.dP1.gbellmf.Rd | 51 man/anfis.dE.dP1.it2gbellmf.Rd | 51 man/anfis.dE.dP4.Rd | 59 man/anfis.dMF.dP.gbellmf.Rd | 45 man/anfis.dO2.dO1.Rd | 55 man/anfis.dO3.dO2.Rd | 55 man/anfis.dO4.dO3.Rd | 51 man/anfis.dO5.dO4.Rd | 49 man/anfis.eval.Rd | 65 man/anfis.optimise.Rd | 126 man/anfis.plotmf.Rd | 93 man/anfis.tipper.Rd | 35 man/defuzz.Rd | 49 man/evalfis.Rd | 55 man/evalmf.Rd | 81 man/evalmftype.Rd | 57 man/fis.builder.Rd | 71 man/fuzzy.firing.Rd | 69 man/fuzzy.optimise.Rd | 61 man/fuzzy.t.Rd | 65 man/fuzzy.tconorm.Rd | 65 man/fuzzy.tnorm.Rd | 65 man/fuzzyr.accuracy.Rd | 70 man/fuzzyr.match.fun.Rd | 39 man/gbell.fuzzification.Rd | 59 man/gbellmf.Rd | 63 man/genmf.Rd | 85 man/gensurf.Rd | 55 man/it2tipper.Rd |only man/km.da.Rd | 93 man/linearmf.Rd | 41 man/newfis.Rd | 70 man/plotmf.Rd | 73 man/readfis.Rd | 35 man/showGUI.Rd | 59 man/showfis.Rd | 43 man/showrule.Rd | 47 man/singleton.fuzzification.Rd | 53 man/singletonmf.Rd | 63 man/tipper.Rd | 35 man/tipperGUI.Rd | 41 man/tipperGUI2.Rd | 41 man/writefis.Rd |only man/x.fuzzification.Rd | 65 71 files changed, 7757 insertions(+), 7210 deletions(-)
More information about AzureCognitive at CRAN
Permanent link
Title: Analysis of Simulation Studies Including Monte Carlo Error
Description: Summarise results from simulation studies and compute Monte Carlo
standard errors of commonly used summary statistics. This package is modelled
on the 'simsum' user-written command in 'Stata' (White I.R., 2010
<http://www.stata-journal.com/article.html?article=st0200>), further extending
it with additional functionality.
Author: Alessandro Gasparini [aut, cre]
(<https://orcid.org/0000-0002-8319-7624>),
Ian R. White [aut]
Maintainer: Alessandro Gasparini <alessandro.gasparini@ki.se>
Diff between rsimsum versions 0.6.1 dated 2019-09-12 and 0.7.0 dated 2019-11-12
DESCRIPTION | 10 - MD5 | 66 ++++---- NEWS.md | 14 + R/dropbig.R | 4 R/multisimsum.R | 20 +- R/performance.R | 115 +++++--------- R/print.multisimsum.R | 6 R/print.simsum.R | 5 R/rsimsum-package.R | 2 R/simsum.R | 27 ++- R/summary.simsum.R | 1 R/utils.R | 32 ++- README.md | 15 - build/partial.rdb |binary inst/doc/A-introduction.html | 303 ++++++++++++++++++++----------------- inst/doc/B-relhaz.html | 137 +++++++++------- inst/doc/C-plotting.Rmd | 2 inst/doc/C-plotting.html | 139 +++++++++------- inst/doc/D-nlp.html | 21 +- inst/doc/E-rsimsumtidyverse.html | 4 man/dropbig.Rd | 4 man/figures/README-ba-1.png |binary man/figures/README-lolly-1.png |binary man/figures/README-nlp-1.png |binary man/figures/README-ridgeline-1.png |binary man/figures/README-zipper-1.png |binary man/multisimsum.Rd | 28 ++- man/rsimsum.Rd | 2 man/simsum.Rd | 25 +-- man/summary.simsum.Rd | 5 tests/testthat/test-dropbig.R | 14 + tests/testthat/test-multisimsum.R | 66 ++++---- tests/testthat/test-simsum.R | 72 +++++--- vignettes/C-plotting.Rmd | 2 34 files changed, 650 insertions(+), 491 deletions(-)
Title: 'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest
Neighbors
Description: 'Annoy' is a small C++ library for Approximate Nearest Neighbors
written for efficient memory usage as well an ability to load from / save to
disk. This package provides an R interface by relying on the 'Rcpp' package,
exposing the same interface as the original Python wrapper to 'Annoy'. See
<https://github.com/spotify/annoy> for more on 'Annoy'. 'Annoy' is released
under Version 2.0 of the Apache License. Also included is a small Windows
port of 'mmap' which is released under the MIT license.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppAnnoy versions 0.0.13 dated 2019-09-23 and 0.0.14 dated 2019-11-12
ChangeLog | 12 +++++ DESCRIPTION | 8 +-- MD5 | 12 ++--- cleanup | 2 inst/NEWS.Rd | 8 +++ inst/doc/UsingAnnoyInCcppWrapper.pdf |binary inst/include/annoylib.h | 82 ++++++++++++++++++++--------------- 7 files changed, 80 insertions(+), 44 deletions(-)
Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data
sets, regression models, and more. The code to create the tables is
concise and highly customizable. Data frames can be summarized with
any function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers. The package is enhanced when the 'gt' package is installed.
Use this code to install: 'remotes::install_github("rstudio/gt")'.
Author: Daniel D. Sjoberg [aut, cre] (<https://orcid.org/0000-0003-0862-2018>),
Margie Hannum [aut] (<https://orcid.org/0000-0002-2953-0449>),
Karissa Whiting [aut] (<https://orcid.org/0000-0002-4683-1868>),
Emily C. Zabor [aut] (<https://orcid.org/0000-0002-1402-4498>),
Michael Curry [ctb] (<https://orcid.org/0000-0002-0261-4044>),
Esther Drill [ctb] (<https://orcid.org/0000-0002-3315-4538>),
Jessica Flynn [ctb] (<https://orcid.org/0000-0001-8310-6684>)
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between gtsummary versions 1.2.2 dated 2019-11-10 and 1.2.3 dated 2019-11-12
gtsummary-1.2.2/gtsummary/man/figures/README-tbl_regression.png |only gtsummary-1.2.2/gtsummary/man/figures/README-tbl_summary.png |only gtsummary-1.2.2/gtsummary/man/figures/add_comp_ex1.png |only gtsummary-1.2.2/gtsummary/man/figures/tbl_merge_ex.png |only gtsummary-1.2.2/gtsummary/man/figures/tbl_nostrata_ex.png |only gtsummary-1.2.2/gtsummary/man/figures/tbl_strata_ex.png |only gtsummary-1.2.2/gtsummary/man/figures/tbl_summary_ex3.png |only gtsummary-1.2.3/gtsummary/DESCRIPTION | 15 gtsummary-1.2.3/gtsummary/MD5 | 165 gtsummary-1.2.3/gtsummary/NEWS.md | 8 gtsummary-1.2.3/gtsummary/R/tbl_regression.R | 36 gtsummary-1.2.3/gtsummary/R/tbl_stack.R | 14 gtsummary-1.2.3/gtsummary/R/tbl_uvregression.R | 211 gtsummary-1.2.3/gtsummary/README.md | 2 gtsummary-1.2.3/gtsummary/build/gtsummary.pdf |10507 +++++----- gtsummary-1.2.3/gtsummary/build/vignette.rds |binary gtsummary-1.2.3/gtsummary/inst/WORDLIST | 1 gtsummary-1.2.3/gtsummary/inst/doc/gallery.R | 56 gtsummary-1.2.3/gtsummary/inst/doc/gallery.Rmd | 67 gtsummary-1.2.3/gtsummary/inst/doc/gallery.html | 633 gtsummary-1.2.3/gtsummary/inst/doc/global_options.R | 3 gtsummary-1.2.3/gtsummary/inst/doc/global_options.Rmd | 10 gtsummary-1.2.3/gtsummary/inst/doc/global_options.html | 2 gtsummary-1.2.3/gtsummary/inst/doc/tbl_regression.R | 15 gtsummary-1.2.3/gtsummary/inst/doc/tbl_regression.Rmd | 22 gtsummary-1.2.3/gtsummary/inst/doc/tbl_regression.html | 355 gtsummary-1.2.3/gtsummary/inst/doc/tbl_summary.R | 15 gtsummary-1.2.3/gtsummary/inst/doc/tbl_summary.Rmd | 22 gtsummary-1.2.3/gtsummary/inst/doc/tbl_summary.html | 423 gtsummary-1.2.3/gtsummary/man/add_n.Rd | 3 gtsummary-1.2.3/gtsummary/man/add_overall.Rd | 3 gtsummary-1.2.3/gtsummary/man/add_p.Rd | 3 gtsummary-1.2.3/gtsummary/man/add_q.tbl_summary.Rd | 3 gtsummary-1.2.3/gtsummary/man/add_stat_label.Rd | 3 gtsummary-1.2.3/gtsummary/man/bold_italicize_labels_levels.Rd | 3 gtsummary-1.2.3/gtsummary/man/bold_p.tbl_summary.Rd | 3 gtsummary-1.2.3/gtsummary/man/figures/README-tbl_regression_print-1.png |binary gtsummary-1.2.3/gtsummary/man/figures/README-tbl_summary_print-1.png |binary gtsummary-1.2.3/gtsummary/man/figures/add_p_ex1.png |binary gtsummary-1.2.3/gtsummary/man/figures/add_p_ex2.png |binary gtsummary-1.2.3/gtsummary/man/figures/as_gt_ex.png |binary gtsummary-1.2.3/gtsummary/man/figures/bold_p_stack_ex.png |binary gtsummary-1.2.3/gtsummary/man/figures/inline_text_ex1.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_bold_ital_ex.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_col_ex1.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_col_ex2.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_lm_bold_p_ex.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_lm_global_ex1.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_lm_sort_p_ex.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_merge_ex1.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_merge_ex2.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_n_ex.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_nostrata_ex2.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_overall_ex.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_reg_nevent_ex.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_regression_ex1.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_regression_ex2.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_regression_ex3.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_stack_ex1.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_stack_ex2.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_stat_ex.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_strata_ex1.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_sum_bold_p_ex.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_sum_q_ex.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_sum_sort_p_ex.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_summary_ex1.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_summary_ex2.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_uv_ex1.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_uv_ex2.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_uv_global_ex2.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_uv_nevent_ex.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_uvglm_bold_p_ex.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_uvglm_sort_p_ex.png |binary gtsummary-1.2.3/gtsummary/man/figures/tbl_uvr_q_ex.png |binary gtsummary-1.2.3/gtsummary/man/inline_text.tbl_summary.Rd | 3 gtsummary-1.2.3/gtsummary/man/modify_header.Rd | 3 gtsummary-1.2.3/gtsummary/man/sort_p.tbl_summary.Rd | 2 gtsummary-1.2.3/gtsummary/man/tbl_merge.Rd | 2 gtsummary-1.2.3/gtsummary/man/tbl_stack.Rd | 21 gtsummary-1.2.3/gtsummary/man/tbl_summary.Rd | 3 gtsummary-1.2.3/gtsummary/man/tbl_uvregression.Rd | 31 gtsummary-1.2.3/gtsummary/tests/testthat/test-tbl_stack.R | 10 gtsummary-1.2.3/gtsummary/tests/testthat/test-tbl_uvregression.R | 59 gtsummary-1.2.3/gtsummary/vignettes/gallery.Rmd | 67 gtsummary-1.2.3/gtsummary/vignettes/global_options.Rmd | 10 gtsummary-1.2.3/gtsummary/vignettes/tbl_regression.Rmd | 22 gtsummary-1.2.3/gtsummary/vignettes/tbl_summary.Rmd | 22 87 files changed, 6606 insertions(+), 6252 deletions(-)
Title: Data Table Back-End for 'dplyr'
Description: Provides a data.table backend for 'dplyr'. The goal of 'dtplyr'
is to allow you to write 'dplyr' code that is automatically translated to
the equivalent, but usually much faster, data.table code.
Author: Lionel Henry [aut],
Hadley Wickham [cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between dtplyr versions 0.0.3 dated 2019-02-25 and 1.0.0 dated 2019-11-12
dtplyr-0.0.3/dtplyr/R/compat-dplyr-0.6.0.R |only dtplyr-0.0.3/dtplyr/R/do.R |only dtplyr-0.0.3/dtplyr/R/grouped-dt.r |only dtplyr-0.0.3/dtplyr/R/joins.R |only dtplyr-0.0.3/dtplyr/R/sample.R |only dtplyr-0.0.3/dtplyr/R/sets.R |only dtplyr-0.0.3/dtplyr/R/src.R |only dtplyr-0.0.3/dtplyr/R/tbl-dt.r |only dtplyr-0.0.3/dtplyr/man/grouped_dt.Rd |only dtplyr-0.0.3/dtplyr/man/join.tbl_dt.Rd |only dtplyr-0.0.3/dtplyr/man/src_local.Rd |only dtplyr-0.0.3/dtplyr/man/tbl_dt.Rd |only dtplyr-0.0.3/dtplyr/tests/testthat/helper-data.R |only dtplyr-0.0.3/dtplyr/tests/testthat/test-arrange.R |only dtplyr-0.0.3/dtplyr/tests/testthat/test-distinct.R |only dtplyr-0.0.3/dtplyr/tests/testthat/test-do.R |only dtplyr-0.0.3/dtplyr/tests/testthat/test-filter.R |only dtplyr-0.0.3/dtplyr/tests/testthat/test-group-by.R |only dtplyr-0.0.3/dtplyr/tests/testthat/test-joins.R |only dtplyr-0.0.3/dtplyr/tests/testthat/test-mutate.R |only dtplyr-0.0.3/dtplyr/tests/testthat/test-pronouns.R |only dtplyr-0.0.3/dtplyr/tests/testthat/test-sample.R |only dtplyr-0.0.3/dtplyr/tests/testthat/test-select.R |only dtplyr-0.0.3/dtplyr/tests/testthat/test-slice.R |only dtplyr-1.0.0/dtplyr/DESCRIPTION | 47 +++-- dtplyr-1.0.0/dtplyr/MD5 | 69 ++++---- dtplyr-1.0.0/dtplyr/NAMESPACE | 130 ++++++++++++---- dtplyr-1.0.0/dtplyr/NEWS.md | 25 +++ dtplyr-1.0.0/dtplyr/R/dtplyr-package.R | 7 dtplyr-1.0.0/dtplyr/R/eager.R |only dtplyr-1.0.0/dtplyr/R/step-call.R |only dtplyr-1.0.0/dtplyr/R/step-first.R |only dtplyr-1.0.0/dtplyr/R/step-group.R |only dtplyr-1.0.0/dtplyr/R/step-join.R |only dtplyr-1.0.0/dtplyr/R/step-modify.R |only dtplyr-1.0.0/dtplyr/R/step-mutate.R |only dtplyr-1.0.0/dtplyr/R/step-set.R |only dtplyr-1.0.0/dtplyr/R/step-subset.R |only dtplyr-1.0.0/dtplyr/R/step.R |only dtplyr-1.0.0/dtplyr/R/tidyeval.R |only dtplyr-1.0.0/dtplyr/R/utils.R | 58 ------- dtplyr-1.0.0/dtplyr/R/zzz.R |only dtplyr-1.0.0/dtplyr/README.md | 135 +++++++++++++++-- dtplyr-1.0.0/dtplyr/build |only dtplyr-1.0.0/dtplyr/inst |only dtplyr-1.0.0/dtplyr/man/collect.Rd |only dtplyr-1.0.0/dtplyr/man/dtplyr-package.Rd | 13 - dtplyr-1.0.0/dtplyr/man/group_modify.dtplyr_step.Rd |only dtplyr-1.0.0/dtplyr/man/lazy_dt.Rd |only dtplyr-1.0.0/dtplyr/tests/testthat/test-step-call.R |only dtplyr-1.0.0/dtplyr/tests/testthat/test-step-first.R |only dtplyr-1.0.0/dtplyr/tests/testthat/test-step-group.R |only dtplyr-1.0.0/dtplyr/tests/testthat/test-step-join.R |only dtplyr-1.0.0/dtplyr/tests/testthat/test-step-modify.R |only dtplyr-1.0.0/dtplyr/tests/testthat/test-step-mutate.R |only dtplyr-1.0.0/dtplyr/tests/testthat/test-step-print.txt |only dtplyr-1.0.0/dtplyr/tests/testthat/test-step-set.R |only dtplyr-1.0.0/dtplyr/tests/testthat/test-step-subset.R |only dtplyr-1.0.0/dtplyr/tests/testthat/test-step.R |only dtplyr-1.0.0/dtplyr/tests/testthat/test-tidyeval.R |only dtplyr-1.0.0/dtplyr/vignettes |only 61 files changed, 327 insertions(+), 157 deletions(-)
Title: Creates Co-Occurrence Matrices of Spatial Data
Description: Builds co-occurrence matrices based on spatial raster data.
It includes creation of weighted co-occurrence matrices (wecoma) and
integrated co-occurrence matrices
(incoma; Vadivel et al. (2007) <doi:10.1016/j.patrec.2007.01.004>).
Author: Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>),
Maximillian H.K. Hesselbarth [ctb] (Co-author of underlying C++ code
for get_class_index_map(), get_unique_values(), and rcpp_get_coma()
functions),
Marco Sciaini [ctb] (Co-author of underlying C++ code for
get_class_index_map(), get_unique_values(), and rcpp_get_coma()
functions),
Sebastian Hanss [ctb] (Co-author of underlying C++ code for
get_class_index_map(), get_unique_values(), and rcpp_get_coma()
functions)
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between comat versions 0.7.0 dated 2019-10-10 and 0.7.2 dated 2019-11-12
DESCRIPTION | 6 ++-- MD5 | 21 +++++++-------- NEWS.md | 4 ++ R/get_incove.R | 3 ++ inst/testdata |only inst/tinytest/test_get_coma.R | 3 ++ inst/tinytest/test_get_incoma.R | 6 +--- inst/tinytest/test_rcpp_get_incoma.R | 7 ++--- man/get_incove.Rd | 3 ++ src/rcpp_get_coma.cpp | 9 ++++++ src/rcpp_get_incoma.cpp | 4 +- src/rcpp_get_vec.cpp | 49 ++++++++++++++++++++++------------- 12 files changed, 75 insertions(+), 40 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 0.5.0 dated 2019-06-24 and 0.5.1 dated 2019-11-12
DESCRIPTION | 9 - MD5 | 12 - NAMESPACE | 1 NEWS.md | 4 R/lime.R | 8 - inst/doc/Understanding_lime.html | 248 +++++++++++++++++++++++++-------------- man/lime-package.Rd | 1 7 files changed, 177 insertions(+), 106 deletions(-)
Title: Toolkit for Credit Modeling
Description: Provides a highly efficient R tool suite for Credit Modeling, Analysis and Visualization. Contains infrastructure functionalities such as data exploration and preparation, missing values treatment, outliers treatment, variable derivation, variable selection, dimensionality reduction, grid search for hyper parameters, data mining and visualization, model evaluation, strategy analysis etc. This package is designed to make the development of binary classification models (machine learning based models as well as credit scorecard) simpler and faster.
Author: Dongping Fan [aut, cre]
Maintainer: Dongping Fan <fdp@pku.edu.cn>
Diff between creditmodel versions 1.1.5 dated 2019-10-23 and 1.1.6 dated 2019-11-12
DESCRIPTION | 14 MD5 | 42 - NAMESPACE | 8 NEWS.md | 7 R/data_cleansing.R | 9 R/data_process_tools.R | 243 +++--- R/data_transformation.R | 184 +++-- R/data_visualization.R | 17 R/essential_algorithms.R | 69 + R/model_training.R | 184 ++--- R/outliers_missing_treatment.R | 11 R/variable_binning.R | 11 R/variable_selection.R | 14 R/zzz.R | 2 build/vignette.rds |binary inst/doc/introduction.R | 131 +-- inst/doc/introduction.Rmd | 154 ++-- inst/doc/introduction.html | 1430 ++++++++++++++--------------------------- man/cos_sim.Rd | 9 man/gbm_filter.Rd | 2 man/process_outliers.Rd | 7 vignettes/introduction.Rmd | 154 ++-- 22 files changed, 1154 insertions(+), 1548 deletions(-)
Title: Best Subset GLM and Regression Utilities
Description: Best subset glm using information criteria or cross-validation. Implements PCR and PLS using AIC/BIC. Implements one-standard deviation rule for use with the `caret` package.
Author: A.I. McLeod and Changjiang Xu
Maintainer: A.I. McLeod <aimcleod@uwo.ca>
Diff between bestglm versions 0.37 dated 2018-05-27 and 0.37.1 dated 2019-11-12
DESCRIPTION | 7 +++---- MD5 | 4 ++-- NAMESPACE | 2 +- 3 files changed, 6 insertions(+), 7 deletions(-)
Title: Kernel-Based Machine Learning Lab
Description: Kernel-based machine learning methods for classification,
regression, clustering, novelty detection, quantile regression
and dimensionality reduction. Among other methods 'kernlab'
includes Support Vector Machines, Spectral Clustering, Kernel
PCA, Gaussian Processes and a QP solver.
Author: Alexandros Karatzoglou [aut, cre],
Alex Smola [aut],
Kurt Hornik [aut],
National ICT Australia (NICTA) [cph],
Michael A. Maniscalco [ctb, cph],
Choon Hui Teo [ctb]
Maintainer: Alexandros Karatzoglou <alexandros.karatzoglou@gmail.com>
Diff between kernlab versions 0.9-28 dated 2019-11-09 and 0.9-29 dated 2019-11-12
DESCRIPTION | 7 ++++--- MD5 | 4 ++-- inst/doc/kernlab.pdf |binary 3 files changed, 6 insertions(+), 5 deletions(-)
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Description: Statistical methods for the modeling and monitoring of time series
of counts, proportions and categorical data, as well as for the modeling
of continuous-time point processes of epidemic phenomena.
The monitoring methods focus on aberration detection in count data time
series from public health surveillance of communicable diseases, but
applications could just as well originate from environmetrics,
reliability engineering, econometrics, or social sciences. The package
implements many typical outbreak detection procedures such as the
(improved) Farrington algorithm, or the negative binomial GLR-CUSUM
method of H<f6>hle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>.
A novel CUSUM approach combining logistic and multinomial logistic
modeling is also included. The package contains several real-world data
sets, the ability to simulate outbreak data, and to visualize the
results of the monitoring in a temporal, spatial or spatio-temporal
fashion. A recent overview of the available monitoring procedures is
given by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>.
For the retrospective analysis of epidemic spread, the package provides
three endemic-epidemic modeling frameworks with tools for visualization,
likelihood inference, and simulation. hhh4() estimates models for
(multivariate) count time series following Paul and Held (2011)
<doi:10.1002/sim.4177> and Meyer and Held (2014) <doi:10.1214/14-AOAS743>.
twinSIR() models the susceptible-infectious-recovered (SIR) event
history of a fixed population, e.g, epidemics across farms or networks,
as a multivariate point process as proposed by H<f6>hle (2009)
<doi:10.1002/bimj.200900050>. twinstim() estimates self-exciting point
process models for a spatio-temporal point pattern of infective events,
e.g., time-stamped geo-referenced surveillance data, as proposed by
Meyer et al. (2012) <doi:10.1111/j.1541-0420.2011.01684.x>.
A recent overview of the implemented space-time modeling frameworks
for epidemic phenomena is given by Meyer et al. (2017)
<doi:10.18637/jss.v077.i11>.
Author: Michael H<f6>hle [aut, ths] (<https://orcid.org/0000-0002-0423-6702>),
Sebastian Meyer [aut, cre] (<https://orcid.org/0000-0002-1791-9449>),
Michaela Paul [aut],
Leonhard Held [ctb, ths],
Howard Burkom [ctb],
Thais Correa [ctb],
Mathias Hofmann [ctb],
Christian Lang [ctb],
Juliane Manitz [ctb],
Andrea Riebler [ctb],
Daniel Saban<e9>s Bov<e9> [ctb],
Ma<eb>lle Salmon [ctb],
Dirk Schumacher [ctb],
Stefan Steiner [ctb],
Mikko Virtanen [ctb],
Wei Wei [ctb],
Valentin Wimmer [ctb],
R Core Team [ctb] (A few code segments are modified versions of code
from base R)
Maintainer: Sebastian Meyer <seb.meyer@fau.de>
Diff between surveillance versions 1.17.1 dated 2019-09-13 and 1.17.2 dated 2019-11-12
surveillance-1.17.1/surveillance/data/foofit.RData |only surveillance-1.17.2/surveillance/DESCRIPTION | 8 surveillance-1.17.2/surveillance/MD5 | 43 ++--- surveillance-1.17.2/surveillance/R/AllClass.R | 10 + surveillance-1.17.2/surveillance/R/sts.R | 3 surveillance-1.17.2/surveillance/R/twinSIR_simulation.R | 86 +++++----- surveillance-1.17.2/surveillance/build/partial.rdb |binary surveillance-1.17.2/surveillance/data/salmHospitalized.RData |binary surveillance-1.17.2/surveillance/inst/NEWS.Rd | 25 ++ surveillance-1.17.2/surveillance/inst/doc/glrnb.pdf |binary surveillance-1.17.2/surveillance/inst/doc/hhh4.pdf |binary surveillance-1.17.2/surveillance/inst/doc/hhh4_spacetime.pdf |binary surveillance-1.17.2/surveillance/inst/doc/monitoringCounts.R | 8 surveillance-1.17.2/surveillance/inst/doc/monitoringCounts.Rnw | 8 surveillance-1.17.2/surveillance/inst/doc/monitoringCounts.pdf |binary surveillance-1.17.2/surveillance/inst/doc/surveillance.pdf |binary surveillance-1.17.2/surveillance/inst/doc/twinSIR.pdf |binary surveillance-1.17.2/surveillance/inst/doc/twinstim.pdf |binary surveillance-1.17.2/surveillance/man/twinSIR_exData.Rd | 10 - surveillance-1.17.2/surveillance/man/twinSIR_simulation.Rd | 2 surveillance-1.17.2/surveillance/tests/testthat/test-sts.R | 18 ++ surveillance-1.17.2/surveillance/vignettes/monitoringCounts.Rnw | 8 surveillance-1.17.2/surveillance/vignettes/surveillance-hmm.pdf |binary 23 files changed, 140 insertions(+), 89 deletions(-)
Title: Create and Visualize Hillshaded Maps from Elevation Matrices
Description: Uses a combination of raytracing and multiple hill shading methods to produce 2D and 3D data visualizations and maps. Includes water detection and layering functions, programmable color palette generation, several built-in textures for hill shading, 2D and 3D plotting options, a built-in path tracer, 'Wavefront' OBJ file export, and the ability to save 3D visualizations to a 3D printable format.
Author: Tyler Morgan-Wall
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between rayshader versions 0.11.5 dated 2019-07-11 and 0.13.1 dated 2019-11-12
DESCRIPTION | 13 - MD5 | 106 +++++++------ NAMESPACE | 6 R/RcppExports.R | 4 R/add_overlay.R | 2 R/ambient_shade.R | 10 - R/detect_water.R | 10 + R/get_ids_with_labels.R | 90 +++++------ R/height_shade.R |only R/lamb_shade.R | 10 - R/make_base.R | 17 +- R/make_lines.R | 20 +- R/make_shadow.R | 4 R/make_vignette_overlay.R |only R/make_water.R | 48 ++++-- R/make_waterlines.R | 4 R/plot_3d.R | 40 ++++- R/plot_gg.R | 55 +++++-- R/plot_map.R | 10 + R/raster_to_matrix.R |only R/ray_shade.R | 34 +++- R/reduce_matrix_size.R |only R/render_camera.R | 75 ++++++--- R/render_depth.R | 328 +++++++++++++++++++++++++++++++++++-------- R/render_highquality.R |only R/render_label.R | 303 +++++++++++++++++++++------------------ R/render_movie.R | 187 +++++++++++++++++++++++- R/render_snapshot.R | 142 +++++++++++++++++- R/render_water.R | 19 ++ R/rot_to_euler.R |only R/save_obj.R |only R/sphere_shade.R | 20 ++ man/add_overlay.Rd | 2 man/ambient_shade.Rd | 13 - man/detect_water.Rd | 6 man/get_ids_with_labels.Rd | 5 man/height_shade.Rd |only man/lamb_shade.Rd | 8 - man/make_vignette_overlay.Rd |only man/plot_3d.Rd | 6 man/plot_gg.Rd | 5 man/plot_map.Rd | 7 man/raster_to_matrix.Rd |only man/ray_shade.Rd | 23 +-- man/reduce_matrix_size.Rd |only man/render_camera.Rd | 59 ++++--- man/render_depth.Rd | 90 ++++++++++- man/render_highquality.Rd |only man/render_label.Rd | 32 ++-- man/render_movie.Rd | 48 +++++- man/render_snapshot.Rd | 60 +++++++ man/render_water.Rd | 8 + man/rot_to_euler.Rd |only man/save_obj.Rd |only man/sphere_shade.Rd | 14 + src/RcppExports.cpp | 14 + src/interpolate_color.cpp | 8 - src/make_base_cpp.cpp | 59 +++---- src/pointspread.cpp | 11 + src/rayshade.cpp | 2 src/rayshade_multicore.cpp | 2 61 files changed, 1521 insertions(+), 518 deletions(-)
Title: Quantile G-Computation
Description: G-computation for a set of time-fixed exposures
with quantile-based basis functions, possibly under linearity and
homogeneity assumptions. This approach estimates a regression line
corresponding to the expected change in the outcome (on the link
basis) given a simultaneous increase in the quantile-based category
for all exposures. Works with continuous, binary, and right-censored
time-to-event outcomes. Reference: Alexander P. Keil, Jessie P.
Buckley, Katie M. OBrien, Kelly K. Ferguson, Shanshan Zhao Alexandra
J. White (2019) A quantile-based g-computation approach to addressing
the effects of exposure mixtures; <arXiv:1902.04200> [stat.ME].
Author: Alexander Keil [aut, cre]
Maintainer: Alexander Keil <akeil@unc.edu>
Diff between qgcomp versions 1.1.0 dated 2019-07-13 and 1.2.0 dated 2019-11-12
qgcomp-1.1.0/qgcomp/R/qgcomp_surv.R |only qgcomp-1.2.0/qgcomp/DESCRIPTION | 24 - qgcomp-1.2.0/qgcomp/MD5 | 53 +- qgcomp-1.2.0/qgcomp/NAMESPACE | 2 qgcomp-1.2.0/qgcomp/NEWS.md | 13 qgcomp-1.2.0/qgcomp/R/base.R | 286 ++++++++++-- qgcomp-1.2.0/qgcomp/R/base_surv.R |only qgcomp-1.2.0/qgcomp/R/data.R | 3 qgcomp-1.2.0/qgcomp/R/utility.R |only qgcomp-1.2.0/qgcomp/README.md | 133 +++-- qgcomp-1.2.0/qgcomp/build/vignette.rds |binary qgcomp-1.2.0/qgcomp/data/metals.RData |binary qgcomp-1.2.0/qgcomp/inst/doc/qgcomp-vignette.R | 97 ++++ qgcomp-1.2.0/qgcomp/inst/doc/qgcomp-vignette.Rmd | 110 ++++ qgcomp-1.2.0/qgcomp/inst/doc/qgcomp-vignette.html | 491 +++++++++++++++++----- qgcomp-1.2.0/qgcomp/inst/fig/res5.png |binary qgcomp-1.2.0/qgcomp/inst/fig/res7.png |only qgcomp-1.2.0/qgcomp/man/checknames.Rd |only qgcomp-1.2.0/qgcomp/man/coxmsm.fit.Rd | 32 + qgcomp-1.2.0/qgcomp/man/metals.Rd | 3 qgcomp-1.2.0/qgcomp/man/msm.fit.Rd | 9 qgcomp-1.2.0/qgcomp/man/plot.qgcompfit.Rd | 2 qgcomp-1.2.0/qgcomp/man/qgcomp.Rd | 24 - qgcomp-1.2.0/qgcomp/man/qgcomp.boot.Rd | 33 + qgcomp-1.2.0/qgcomp/man/qgcomp.cox.boot.Rd | 78 ++- qgcomp-1.2.0/qgcomp/man/qgcomp.cox.noboot.Rd | 2 qgcomp-1.2.0/qgcomp/man/qgcomp.noboot.Rd | 11 qgcomp-1.2.0/qgcomp/tests |only qgcomp-1.2.0/qgcomp/vignettes/qgcomp-vignette.Rmd | 110 ++++ 29 files changed, 1205 insertions(+), 311 deletions(-)
Title: Visualization of Spatial and Spatio-Temporal Objects in Google
Earth
Description: Writes sp-class, spacetime-class, raster-class and similar spatial and spatio-temporal objects to KML following some basic cartographic rules.
Author: Tomislav Hengl [cre, aut],
Pierre Roudier [ctb],
Dylan Beaudette [ctb],
Edzer Pebesma [ctb],
Michael Blaschek [ctb]
Maintainer: Tomislav Hengl <tom.hengl@opengeohub.org>
Diff between plotKML versions 0.5-9 dated 2019-01-09 and 0.6-0 dated 2019-11-12
DESCRIPTION | 14 MD5 | 46 - R/AAAA.R | 2 R/check_projection.R | 22 R/grid2poly.R | 121 ++-- R/kml.R | 52 +- R/kml_compress.R | 56 +- R/kml_open.R | 158 +++--- build/vignette.rds |binary data/datalist | 38 - demo/plotKML.R | 40 - inst/doc/jss1079.R | 295 ++++++------ inst/doc/jss1079.pdf |binary man/HRprec08.Rd | 2 man/HRtemp08.Rd | 274 +++++------ man/LST.Rd | 4 man/eberg.Rd | 2 man/geopath.rd | 77 +-- man/getCRS.Rd | 2 man/kml_compress.Rd | 87 +-- man/layer.SpatialLines.Rd | 80 +-- man/layer.SpatialPolygons.Rd | 100 ++-- man/plotKML.Rd | 1052 +++++++++++++++++++++---------------------- man/spMetadata.Rd | 2 24 files changed, 1269 insertions(+), 1257 deletions(-)
Title: Nonlinear Conditional Independence Tests
Description: Code for a variety of nonlinear conditional independence tests:
Kernel conditional independence test (Zhang et al., UAI 2011, <arXiv:1202.3775>),
Residual Prediction test (based on Shah and Buehlmann, <arXiv:1511.03334>),
Invariant environment prediction,
Invariant target prediction,
Invariant residual distribution test,
Invariant conditional quantile prediction (all from Heinze-Deml et al., <arXiv:1706.08576>).
Author: Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>,
Jonas Peters <jonas.peters@math.ku.dk>,
Asbjoern Marco Sinius Munk <fgp998@alumni.ku.dk>
Maintainer: Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>
Diff between CondIndTests versions 0.1.4 dated 2018-05-07 and 0.1.5 dated 2019-11-12
DESCRIPTION | 16 - MD5 | 26 +- NAMESPACE | 7 R/KCI.R | 323 ++++++++++++++++---------- R/covariance.R |only R/gpreg.R |only R/kernel.R | 5 man/CondIndTest.Rd | 4 man/InvariantConditionalQuantilePrediction.Rd | 6 man/InvariantEnvironmentPrediction.Rd | 3 man/InvariantResidualDistributionTest.Rd | 9 man/InvariantTargetPrediction.Rd | 3 man/KCI.Rd | 15 - man/ResidualPredictionTest.Rd | 15 - tests/testthat/test_output.R | 2 15 files changed, 266 insertions(+), 168 deletions(-)
Title: Authentication Services for Azure Active Directory
Description: Provides Azure Active Directory (AAD) authentication functionality for R users of Microsoft's 'Azure' cloud <https://azure.microsoft.com/>. Use this package to obtain 'OAuth' 2.0 tokens for services including Azure Resource Manager, Azure Storage and others. It supports both AAD v1.0 and v2.0, as well as multiple authentication methods, including device code and resource owner grant. Tokens are cached in a user-specific directory obtained using the 'rappdirs' package. The interface is based on the 'OAuth' framework in the 'httr' package, but customised and streamlined for Azure. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
httr development team [ctb] (Original OAuth listener code),
Scott Holden [ctb] (Advice on AAD authentication),
Chris Stone [ctb] (Advice on AAD authentication),
Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between AzureAuth versions 1.2.2 dated 2019-09-13 and 1.2.3 dated 2019-11-12
DESCRIPTION | 6 - MD5 | 34 +++--- NAMESPACE | 1 NEWS.md | 7 + R/AzureToken.R | 17 ++- R/format.R | 11 +- R/normalize.R | 37 ++++-- R/token.R | 12 +- R/utils.R | 5 README.md | 9 - inst/doc/shiny.html | 110 ++++++++++---------- inst/doc/token.Rmd | 60 ++++++++--- inst/doc/token.html | 207 +++++++++++++++++++++----------------- man/get_azure_token.Rd | 7 - man/guid.Rd | 16 ++ tests/testthat/test00_normalize.R | 7 + tests/testthat/test10_v1_token.R | 4 vignettes/token.Rmd | 60 ++++++++--- 18 files changed, 380 insertions(+), 230 deletions(-)
Title: Regions of Common Profiles Modelling with Mixtures-of-Experts
Description: Identifies regions of common (species) profiles (RCPs), possibly when sampling artefacts are present. Within a region the probability of sampling all species remains approximately constant. This is performed using mixtures-of-experts models. The package also contains associated methods, such as diagnostics.
Author: Scott D. Foster
Maintainer: Scott Foster <scott.foster@csiro.au>
Diff between RCPmod versions 2.186 dated 2017-09-29 and 2.190 dated 2019-11-12
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 10 +++++----- R/RCPmod.R | 8 ++++---- 4 files changed, 17 insertions(+), 17 deletions(-)
Title: Various Utilities for Microbial Genomics and Metagenomics
Description: A collection of functions for microbial ecology and other
applications of genomics and metagenomics. Companion package for the
Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016
<DOI:10.7287/peerj.preprints.1900v1>).
Author: Luis M. Rodriguez-R [aut, cre]
Maintainer: Luis M. Rodriguez-R <lmrodriguezr@gmail.com>
Diff between enveomics.R versions 1.5.0 dated 2019-10-27 and 1.6.0 dated 2019-11-12
DESCRIPTION | 6 MD5 | 22 - R/recplot2.R | 520 +++++++++++++++++---------------- README.md | 4 man/enve.recplot2.Rd | 4 man/enve.recplot2.__counts.Rd | 2 man/enve.recplot2.compareIdentities.Rd | 2 man/enve.recplot2.extractWindows.Rd | 8 man/enve.recplot2.findPeaks.Rd | 2 man/enve.recplot2.findPeaks.em.Rd | 4 man/enve.recplot2.findPeaks.mower.Rd | 8 man/plot.enve.RecPlot2.Rd | 4 12 files changed, 314 insertions(+), 272 deletions(-)
Title: Classification Based on Association Rules
Description: Provides a function to build an association rule-based classifier for data frames, and to classify incoming data frames using such a classifier.
Author: Ian Johnson [aut, cre, cph],
Michael Hahsler [aut, cph],
Tyler Giallanza [ctb]
Maintainer: Ian Johnson <ianjjohnson@icloud.com>
Diff between arulesCBA versions 1.1.4 dated 2018-12-16 and 1.1.5 dated 2019-11-12
arulesCBA-1.1.4/arulesCBA/tests/testthat/tests.R |only arulesCBA-1.1.5/arulesCBA/DESCRIPTION | 19 arulesCBA-1.1.5/arulesCBA/MD5 | 28 arulesCBA-1.1.5/arulesCBA/NAMESPACE | 7 arulesCBA-1.1.5/arulesCBA/NEWS.md | 7 arulesCBA-1.1.5/arulesCBA/R/CBA.R | 382 +++++++----- arulesCBA-1.1.5/arulesCBA/R/CBA.internal.R |only arulesCBA-1.1.5/arulesCBA/R/CBA.object.R | 86 +- arulesCBA-1.1.5/arulesCBA/R/RCAR.R |only arulesCBA-1.1.5/arulesCBA/R/mineCARs.R | 43 - arulesCBA-1.1.5/arulesCBA/inst/doc/arulesCBA.pdf |binary arulesCBA-1.1.5/arulesCBA/man/CBA.Rd | 36 - arulesCBA-1.1.5/arulesCBA/man/CBA.object.Rd | 10 arulesCBA-1.1.5/arulesCBA/man/RCAR.Rd |only arulesCBA-1.1.5/arulesCBA/man/mineCARs.Rd | 9 arulesCBA-1.1.5/arulesCBA/tests/testthat/test-CBA.R |only arulesCBA-1.1.5/arulesCBA/tests/testthat/test-CBA_ruleset.R |only arulesCBA-1.1.5/arulesCBA/tests/testthat/test-RCAR.R |only arulesCBA-1.1.5/arulesCBA/tests/testthat/test-discretize.R |only 19 files changed, 376 insertions(+), 251 deletions(-)