Title: Formula-Driven Table Generation
Description: Computes and displays complex tables of summary statistics.
Output may be in LaTeX, HTML, plain text, or an R
matrix for further processing.
Author: Duncan Murdoch
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between tables versions 0.9.4 dated 2020-08-28 and 0.9.6 dated 2020-09-22
DESCRIPTION | 8 - MD5 | 20 ++-- inst/doc/HTML.R | 6 + inst/doc/HTML.Rmd | 6 + inst/doc/HTML.html | 224 +++++++++++++++++++++++----------------------- inst/doc/knitrTables.R | 6 + inst/doc/knitrTables.Rmd | 6 + inst/doc/knitrTables.pdf |binary inst/doc/tables.pdf |binary vignettes/HTML.Rmd | 6 + vignettes/knitrTables.Rmd | 6 + 11 files changed, 162 insertions(+), 126 deletions(-)
Title: Display User Feedback in Shiny Apps
Description: Easily display user feedback in Shiny apps.
Author: Andy Merlino [aut, cre],
Patrick Howard [aut]
Maintainer: Andy Merlino <andy.merlino@tychobra.com>
Diff between shinyFeedback versions 0.2.0 dated 2020-04-29 and 0.3.0 dated 2020-09-22
DESCRIPTION | 10 MD5 | 40 +- NAMESPACE | 2 NEWS.md | 11 R/hideToast.R |only R/showToast.R | 63 ++- README.md | 10 build/vignette.rds |binary inst/assets/js/shinyfeedback.js | 462 ++++++++++------------------ inst/assets/toastr/js/shinytoastr.js | 13 inst/assets/toastr/js/toastr.js.map |only inst/doc/loading-button-and-toast.html | 4 inst/doc/shinyFeedback-intro.R | 2 inst/doc/shinyFeedback-intro.Rmd | 15 inst/doc/shinyFeedback-intro.html | 19 - inst/doc/valueBoxModule.html | 4 inst/examples/supported_inputs_app/server.R | 21 + inst/examples/supported_inputs_app/ui.R | 29 + inst/img/feedback_screenshot.png |only inst/img/shinyfeedback_hex_sticker.png |only man/hideToast.Rd |only man/showToast.Rd | 12 vignettes/feedback_screenshot.png |only vignettes/shinyFeedback-intro.Rmd | 15 24 files changed, 369 insertions(+), 363 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>),
Alex Hayes [aut] (<https://orcid.org/0000-0002-4985-5160>),
Zhian N. Kamvar [aut, cph] (<https://orcid.org/0000-0003-1458-7108>),
Noam Ross [aut, cph] (<https://orcid.org/0000-0002-2136-0000>),
Robrecht Cannoodt [aut, cph] (<https://orcid.org/0000-0003-3641-729X>,
rcannood),
Duncan Luguern [aut],
David M. Kaplan [aut, ctb] (<https://orcid.org/0000-0001-6087-359X>,
dmkaplan2000),
Sebastian Kreutzer [aut] (<https://orcid.org/0000-0002-0734-2199>),
Shixiang Wang [aut, ctb] (<https://orcid.org/0000-0001-9855-7357>),
Jay Hesselberth [aut, ctb] (<https://orcid.org/0000-0002-6299-179X>),
Alfredo Hernández [ctb] (<https://orcid.org/0000-0002-2660-4545>),
Christophe Dervieux [aut] (<https://orcid.org/0000-0003-4474-2498>)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rticles versions 0.15 dated 2020-08-26 and 0.16 dated 2020-09-22
rticles-0.15/rticles/README.md |only rticles-0.16/rticles/DESCRIPTION | 10 +- rticles-0.16/rticles/MD5 | 19 ++-- rticles-0.16/rticles/NEWS.md | 7 + rticles-0.16/rticles/R/article.R | 10 +- rticles-0.16/rticles/R/jss_article.R | 40 ++++------ rticles-0.16/rticles/R/rjournal_article.R | 21 ----- rticles-0.16/rticles/inst/rmarkdown/templates/ctex/skeleton/skeleton.Rmd | 1 rticles-0.16/rticles/inst/rmarkdown/templates/jss/skeleton/skeleton.Rmd | 4 + rticles-0.16/rticles/man/article.Rd | 8 +- rticles-0.16/rticles/tests/testit/test-formats.R | 1 11 files changed, 53 insertions(+), 68 deletions(-)
Title: Include Tables, Images and Graphs in Leaflet Pop-Ups
Description: Creates 'HTML' strings to embed tables, images or graphs in pop-ups
of interactive maps created with packages like 'leaflet' or 'mapview'. Handles
local images located on the file system or via remote URL. Handles graphs created
with 'lattice' or 'ggplot2' as well as interactive plots created with 'htmlwidgets'.
Author: Tim Appelhans [cre, aut],
Florian Detsch [aut]
Maintainer: Tim Appelhans <tim.appelhans@gmail.com>
Diff between leafpop versions 0.0.5 dated 2019-12-09 and 0.0.6 dated 2020-09-22
DESCRIPTION | 12 +++-- MD5 | 18 +++---- NEWS | 6 ++ NEWS.md | 6 ++ R/addPopupImages.R | 4 - R/brewRy.R | 89 +++++++++++++++++++++----------------- R/table.R | 93 +++++++++++++++++++++++++++++++++++++--- inst/htmlwidgets/popup.js | 4 - inst/templates/popup-graph.brew | 42 ++++++++++-------- man/popup.Rd | 71 ++++++++++++++++++++++++++++++ 10 files changed, 265 insertions(+), 80 deletions(-)
Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Description: NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D
biological image data, especially traced neurons. Reads and writes 3D images
in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf
format. Traced neurons can be imported from and written to SWC and 'Amira'
LineSet and SkeletonGraph formats. These data can then be visualised in 3D
via 'rgl', manipulated including applying calculated registrations, e.g.
using the 'CMTK' registration suite, and analysed. There is also a simple
representation for neurons that have been subjected to 3D skeletonisation
but not formally traced; this allows morphological comparison between
neurons including searches and clustering (via the 'nat.nblast' extension
package).
Author: Gregory Jefferis [aut, cre] (<https://orcid.org/0000-0002-0587-9355>),
James Manton [aut] (<https://orcid.org/0000-0001-9260-3156>)
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between nat versions 1.8.14 dated 2020-02-07 and 1.8.16 dated 2020-09-22
DESCRIPTION | 10 - MD5 | 42 ++--- NEWS | 10 + R/amiralandmarks-io.R | 2 R/neuron-io-fiji.R | 4 R/neuron-io-neuroml.R | 4 R/neuron-io.R | 58 ++++---- README.md | 14 - build/vignette.rds |binary inst/doc/Installation.Rmd | 2 inst/doc/Installation.html | 60 +++++--- inst/doc/neurons-intro.Rmd | 12 - inst/doc/neurons-intro.html | 282 ++++++++++++++++++++------------------- man/read.landmarks.Rd | 2 man/read.morphml.Rd | 2 man/read.neuron.Rd | 52 +++---- man/read.neuron.fiji.Rd | 4 man/read.neuron.neuroml.Rd | 2 man/read.neuron.swc.Rd | 2 tests/testthat/test-neuronlist.R | 2 vignettes/Installation.Rmd | 2 vignettes/neurons-intro.Rmd | 12 - 22 files changed, 313 insertions(+), 267 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],
Ellis Hughes [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 1.29 dated 2020-06-23 and 1.30 dated 2020-09-22
DESCRIPTION | 8 +- MD5 | 98 +++++++++++++++--------------- NAMESPACE | 9 ++ R/block.R | 3 R/citation.R | 28 ++++++-- R/defaults.R | 2 R/hooks-asciidoc.R | 8 ++ R/hooks-extra.R | 11 --- R/hooks-html.R | 28 +++++--- R/hooks-latex.R | 125 +++++++++++++++++++++++++++------------ R/hooks-md.R | 41 +++++++++--- R/hooks-rst.R | 11 ++- R/hooks-textile.R | 19 +++-- R/output.R | 4 - R/pandoc.R | 2 R/plot.R | 14 +++- R/table.R | 4 - R/themes.R | 2 R/utils-vignettes.R | 8 +- R/utils.R | 17 ++--- README.md | 4 - build/vignette.rds |binary inst/doc/datatables.Rmd | 2 inst/doc/datatables.html | 2 inst/doc/docco-classic.html | 2 inst/doc/docco-linear.Rmd | 2 inst/doc/docco-linear.html | 2 inst/doc/knit_expand.Rmd | 2 inst/doc/knit_expand.html | 6 - inst/doc/knit_print.html | 12 +-- inst/doc/knitr-intro.html | 14 ++-- inst/doc/knitr-markdown.Rmd | 2 inst/doc/knitr-markdown.html | 4 - inst/doc/knitr-refcard.pdf |binary inst/examples/knitr-manual.bib | 2 inst/examples/knitr-packages.bib | 2 inst/misc/tweak_bib.csv | 24 +++---- man/chunk_hook.Rd | 11 --- man/image_uri.Rd | 2 man/knit.Rd | 4 - man/knit_theme.Rd | 2 man/opts_chunk.Rd | 2 man/output_hooks.Rd | 101 ++++++++++++++++++++++++------- man/pandoc.Rd | 2 man/plot_crop.Rd | 13 +++- man/write_bib.Rd | 5 + vignettes/datatables.Rmd | 2 vignettes/docco-linear.Rmd | 2 vignettes/knit_expand.Rmd | 2 vignettes/knitr-markdown.Rmd | 2 50 files changed, 427 insertions(+), 247 deletions(-)
Title: Unified Parallel and Distributed Processing in R for Everyone
Description: The purpose of this package is to provide a lightweight and
unified Future API for sequential and parallel processing of R
expression via futures. The simplest way to evaluate an expression
in parallel is to use `x %<-% { expression }` with `plan(multiprocess)`.
This package implements sequential, multicore, multisession, and
cluster futures. With these, R expressions can be evaluated on the
local machine, in parallel a set of local machines, or distributed
on a mix of local and remote machines.
Extensions to this package implement additional backends for
processing futures via compute cluster schedulers etc.
Because of its unified API, there is no need to modify any code in order
switch from sequential on the local machine to, say, distributed
processing on a remote compute cluster.
Another strength of this package is that global variables and functions
are automatically identified and exported as needed, making it
straightforward to tweak existing code to make use of futures.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 1.18.0 dated 2020-07-09 and 1.19.1 dated 2020-09-22
future-1.18.0/future/man/values.Rd |only future-1.19.1/future/DESCRIPTION | 8 future-1.19.1/future/MD5 | 100 +-- future-1.19.1/future/NAMESPACE | 1 future-1.19.1/future/NEWS | 96 +++ future-1.19.1/future/R/Future-class.R | 120 ---- future-1.19.1/future/R/FutureGlobals-class.R | 4 future-1.19.1/future/R/MulticoreFuture-class.R | 26 future-1.19.1/future/R/UniprocessFuture-class.R | 3 future-1.19.1/future/R/availableCores.R | 61 ++ future-1.19.1/future/R/availableWorkers.R | 20 future-1.19.1/future/R/future.R | 4 future-1.19.1/future/R/globals.R | 33 + future-1.19.1/future/R/makeClusterPSOCK.R | 272 ++++++---- future-1.19.1/future/R/options.R | 6 future-1.19.1/future/R/resolved.R | 5 future-1.19.1/future/R/tweakExpression.R | 8 future-1.19.1/future/R/utils.R | 2 future-1.19.1/future/R/value.R |only future-1.19.1/future/R/values.R | 92 --- future-1.19.1/future/inst/CITATION |only future-1.19.1/future/inst/WORDLIST | 127 ---- future-1.19.1/future/inst/doc/future-4-issues.html | 4 future-1.19.1/future/inst/doc/future-4-issues.md.rsp | 4 future-1.19.1/future/inst/doc/future-4-non-exportable-objects.html | 191 +++++-- future-1.19.1/future/inst/doc/future-4-non-exportable-objects.md.rsp | 181 ++++-- future-1.19.1/future/man/Future-class.Rd | 8 future-1.19.1/future/man/FutureGlobals.Rd | 4 future-1.19.1/future/man/availableCores.Rd | 10 future-1.19.1/future/man/availableWorkers.Rd | 5 future-1.19.1/future/man/cluster.Rd | 8 future-1.19.1/future/man/figures |only future-1.19.1/future/man/future.Rd | 12 future-1.19.1/future/man/future.options.Rd | 6 future-1.19.1/future/man/getGlobalsAndPackages.Rd | 2 future-1.19.1/future/man/grapes-seed-grapes.Rd | 8 future-1.19.1/future/man/makeClusterMPI.Rd | 4 future-1.19.1/future/man/makeClusterPSOCK.Rd | 39 + future-1.19.1/future/man/multicore.Rd | 8 future-1.19.1/future/man/multiprocess.Rd | 8 future-1.19.1/future/man/multisession.Rd | 8 future-1.19.1/future/man/pid_exists.Rd | 2 future-1.19.1/future/man/remote.Rd | 8 future-1.19.1/future/man/resolved.Rd | 5 future-1.19.1/future/man/sequential.Rd | 8 future-1.19.1/future/man/value.Rd | 54 + future-1.19.1/future/tests/availableCores.R | 11 future-1.19.1/future/tests/availableWorkers.R | 14 future-1.19.1/future/tests/dotdotdot.R | 17 future-1.19.1/future/tests/multicore,multithreading.R | 8 future-1.19.1/future/tests/tweak.R | 17 future-1.19.1/future/vignettes/future-4-issues.md.rsp | 4 future-1.19.1/future/vignettes/future-4-non-exportable-objects.md.rsp | 181 ++++-- 53 files changed, 1101 insertions(+), 726 deletions(-)
Title: Run Code 'With' Temporarily Modified Global State
Description: A set of functions to run code 'with' safely and
temporarily modified global state. Many of these functions were
originally a part of the 'devtools' package, this provides a simple
package with limited dependencies to provide access to these
functions.
Author: Jim Hester [aut, cre],
Kirill Müller [aut],
Kevin Ushey [aut],
Hadley Wickham [aut],
Winston Chang [aut],
Jennifer Bryan [ctb],
Richard Cotton [ctb],
RStudio [cph]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between withr versions 2.2.0 dated 2020-04-20 and 2.3.0 dated 2020-09-22
withr-2.2.0/withr/inst/doc/withr.R |only withr-2.2.0/withr/inst/doc/withr.Rmd |only withr-2.2.0/withr/inst/doc/withr.html |only withr-2.2.0/withr/vignettes/releases |only withr-2.2.0/withr/vignettes/withr.Rmd |only withr-2.3.0/withr/DESCRIPTION | 27 +-- withr-2.3.0/withr/MD5 | 94 +++++------ withr-2.3.0/withr/NAMESPACE | 3 withr-2.3.0/withr/NEWS.md | 23 ++ withr-2.3.0/withr/R/compat-defer.R |only withr-2.3.0/withr/R/defer.R | 70 +------- withr-2.3.0/withr/R/dir.R | 20 -- withr-2.3.0/withr/R/env.R | 5 withr-2.3.0/withr/R/file.R | 18 +- withr-2.3.0/withr/R/libpaths.R | 1 withr-2.3.0/withr/R/local_.R | 39 +++- withr-2.3.0/withr/R/locale.R | 8 withr-2.3.0/withr/R/makevars.R | 19 +- withr-2.3.0/withr/R/options.R | 5 withr-2.3.0/withr/R/par.R | 5 withr-2.3.0/withr/R/path.R | 1 withr-2.3.0/withr/R/seed.R | 33 +++ withr-2.3.0/withr/R/tempfile.R | 56 ++++++ withr-2.3.0/withr/R/utils.R | 7 withr-2.3.0/withr/R/with_.R | 6 withr-2.3.0/withr/README.md | 6 withr-2.3.0/withr/build/vignette.rds |binary withr-2.3.0/withr/inst/doc/changing-and-restoring-state.R |only withr-2.3.0/withr/inst/doc/changing-and-restoring-state.Rmd |only withr-2.3.0/withr/inst/doc/changing-and-restoring-state.html |only withr-2.3.0/withr/man/devices.Rd | 29 +-- withr-2.3.0/withr/man/with_.Rd | 2 withr-2.3.0/withr/man/with_collate.Rd | 2 withr-2.3.0/withr/man/with_dir.Rd | 8 withr-2.3.0/withr/man/with_envvar.Rd | 11 + withr-2.3.0/withr/man/with_file.Rd | 6 withr-2.3.0/withr/man/with_libpaths.Rd | 2 withr-2.3.0/withr/man/with_locale.Rd | 6 withr-2.3.0/withr/man/with_makevars.Rd | 19 +- withr-2.3.0/withr/man/with_options.Rd | 6 withr-2.3.0/withr/man/with_par.Rd | 11 + withr-2.3.0/withr/man/with_path.Rd | 2 withr-2.3.0/withr/man/with_seed.Rd | 8 withr-2.3.0/withr/man/with_sink.Rd | 4 withr-2.3.0/withr/man/with_tempfile.Rd | 31 +++ withr-2.3.0/withr/man/withr.Rd | 7 withr-2.3.0/withr/tests/testthat/test-defer.R | 19 ++ withr-2.3.0/withr/tests/testthat/test-file.R | 12 + withr-2.3.0/withr/tests/testthat/test-local.R | 6 withr-2.3.0/withr/tests/testthat/test-seed.R | 63 +++++++ withr-2.3.0/withr/tests/testthat/test-tempdir.R | 20 ++ withr-2.3.0/withr/tests/testthat/test-tempfile.R | 35 +++- withr-2.3.0/withr/vignettes/changing-and-restoring-state.Rmd |only 53 files changed, 527 insertions(+), 228 deletions(-)
Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of node support;
calculation of ancestor-descendant relationships;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <http://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>),
Emmanuel Paradis [cph] (<https://orcid.org/0000-0003-3092-2199>)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeTools versions 1.2.0 dated 2020-08-03 and 1.3.0 dated 2020-09-22
TreeTools-1.2.0/TreeTools/src/phangorn_bip.cpp |only TreeTools-1.2.0/TreeTools/src/renumber_tree.cpp |only TreeTools-1.2.0/TreeTools/src/types.h |only TreeTools-1.3.0/TreeTools/DESCRIPTION | 24 TreeTools-1.3.0/TreeTools/MD5 | 142 +++-- TreeTools-1.3.0/TreeTools/NAMESPACE | 16 TreeTools-1.3.0/TreeTools/NEWS.md | 22 TreeTools-1.3.0/TreeTools/R/Combinatorics.R | 2 TreeTools-1.3.0/TreeTools/R/RcppExports-manual.R |only TreeTools-1.3.0/TreeTools/R/RcppExports.R | 16 TreeTools-1.3.0/TreeTools/R/Splits.R | 34 - TreeTools-1.3.0/TreeTools/R/Stemwardness.R |only TreeTools-1.3.0/TreeTools/R/TreeNumber.R | 51 +- TreeTools-1.3.0/TreeTools/R/TreeTools-package.R | 6 TreeTools-1.3.0/TreeTools/R/data.R | 2 TreeTools-1.3.0/TreeTools/R/helper_functions.R | 1 TreeTools-1.3.0/TreeTools/R/mst.R |only TreeTools-1.3.0/TreeTools/R/parse_files.R | 2 TreeTools-1.3.0/TreeTools/R/split_analysis.R |only TreeTools-1.3.0/TreeTools/R/sysdata.rda |binary TreeTools-1.3.0/TreeTools/R/tree_generation.R | 26 - TreeTools-1.3.0/TreeTools/R/tree_rearrangement.R | 23 TreeTools-1.3.0/TreeTools/build/partial.rdb |binary TreeTools-1.3.0/TreeTools/inst/REFERENCES.bib | 20 TreeTools-1.3.0/TreeTools/inst/WORDLIST | 9 TreeTools-1.3.0/TreeTools/inst/doc/filesystem-navigation.html | 4 TreeTools-1.3.0/TreeTools/inst/doc/load-data.html | 4 TreeTools-1.3.0/TreeTools/inst/doc/load-trees.R | 2 TreeTools-1.3.0/TreeTools/inst/doc/load-trees.Rmd | 4 TreeTools-1.3.0/TreeTools/inst/doc/load-trees.html | 8 TreeTools-1.3.0/TreeTools/inst/extdata/tests/tnt-namedtree.tre | 4 TreeTools-1.3.0/TreeTools/inst/include |only TreeTools-1.3.0/TreeTools/man/ApeTime.Rd | 52 +- TreeTools-1.3.0/TreeTools/man/CladisticInfo.Rd | 1 TreeTools-1.3.0/TreeTools/man/Lobo.data.Rd | 50 +- TreeTools-1.3.0/TreeTools/man/MSTEdges.Rd |only TreeTools-1.3.0/TreeTools/man/MatrixToPhyDat.Rd | 76 +-- TreeTools-1.3.0/TreeTools/man/NJTree.Rd | 72 +- TreeTools-1.3.0/TreeTools/man/NPartitionPairs.Rd | 100 ++-- TreeTools-1.3.0/TreeTools/man/Neworder.Rd | 124 ++--- TreeTools-1.3.0/TreeTools/man/ReadTntTree.Rd | 242 +++++----- TreeTools-1.3.0/TreeTools/man/RightmostCharacter.Rd | 56 +- TreeTools-1.3.0/TreeTools/man/RootTree.Rd | 3 TreeTools-1.3.0/TreeTools/man/SampleOne.Rd | 56 +- TreeTools-1.3.0/TreeTools/man/Stemwardness.Rd |only TreeTools-1.3.0/TreeTools/man/Subsplit.Rd | 86 +-- TreeTools-1.3.0/TreeTools/man/TipsInSplits.Rd | 33 + TreeTools-1.3.0/TreeTools/man/TotalCopheneticIndex.Rd | 3 TreeTools-1.3.0/TreeTools/man/TreeTools-package.Rd | 4 TreeTools-1.3.0/TreeTools/man/TrivialSplits.Rd | 90 +-- TreeTools-1.3.0/TreeTools/man/UnshiftTree.Rd | 80 +-- TreeTools-1.3.0/TreeTools/man/as.Newick.Rd | 94 +-- TreeTools-1.3.0/TreeTools/man/brewer.Rd | 66 +- TreeTools-1.3.0/TreeTools/man/doubleFactorials.Rd | 52 +- TreeTools-1.3.0/TreeTools/man/figures |only TreeTools-1.3.0/TreeTools/man/logDoubleFactorials.Rd | 46 - TreeTools-1.3.0/TreeTools/man/nRootedShapes.Rd | 56 +- TreeTools-1.3.0/TreeTools/man/sapply64.Rd | 4 TreeTools-1.3.0/TreeTools/src/RcppExports-manual.cpp |only TreeTools-1.3.0/TreeTools/src/RcppExports.cpp | 45 - TreeTools-1.3.0/TreeTools/src/TreeTools-init.c | 8 TreeTools-1.3.0/TreeTools/src/ape_reorder.h | 8 TreeTools-1.3.0/TreeTools/src/int_to_tree.cpp | 2 TreeTools-1.3.0/TreeTools/src/splits.cpp | 4 TreeTools-1.3.0/TreeTools/src/tips_in_splits.cpp |only TreeTools-1.3.0/TreeTools/src/tree_shape.cpp | 2 TreeTools-1.3.0/TreeTools/tests/figs |only TreeTools-1.3.0/TreeTools/tests/testthat/test-Splits.R | 11 TreeTools-1.3.0/TreeTools/tests/testthat/test-Stemwardness.R |only TreeTools-1.3.0/TreeTools/tests/testthat/test-TreeNumber.R | 6 TreeTools-1.3.0/TreeTools/tests/testthat/test-combinatorics.R | 9 TreeTools-1.3.0/TreeTools/tests/testthat/test-int_to_tree.cpp.R | 8 TreeTools-1.3.0/TreeTools/tests/testthat/test-mst.R |only TreeTools-1.3.0/TreeTools/tests/testthat/test-parsers.R | 2 TreeTools-1.3.0/TreeTools/tests/testthat/test-root_tree.h.R |only TreeTools-1.3.0/TreeTools/tests/testthat/test-split_analysis.R |only TreeTools-1.3.0/TreeTools/tests/testthat/test-tree_generation.R | 6 TreeTools-1.3.0/TreeTools/tests/testthat/test-tree_properties.R | 6 TreeTools-1.3.0/TreeTools/vignettes/load-trees.Rmd | 4 79 files changed, 1057 insertions(+), 932 deletions(-)
Title: Conduct Simulation Studies with a Minimal Amount of Source Code
Description: Tool for statistical simulations that have two components.
One component generates the data and the other one
analyzes the data. The main aims of the package are the reduction
of the administrative source code (mainly loops and management code for the
results) and a simple applicability of the package that allows the user to
quickly learn how to work with it. Parallel computing is
also supported. Finally, convenient functions are provided to summarize the
simulation results.
Author: Marsel Scheer [aut, cre]
Maintainer: Marsel Scheer <scheer@freescience.de>
Diff between simTool versions 1.1.6 dated 2020-05-17 and 1.1.7 dated 2020-09-22
simTool-1.1.6/simTool/tests/testthat |only simTool-1.1.6/simTool/tests/testthat.R |only simTool-1.1.7/simTool/DESCRIPTION | 13 - simTool-1.1.7/simTool/MD5 | 32 +-- simTool-1.1.7/simTool/NAMESPACE | 1 simTool-1.1.7/simTool/R/bind_or_combine.R | 2 simTool-1.1.7/simTool/R/define_simulation.R | 3 simTool-1.1.7/simTool/R/eval_tibbles.R | 27 +- simTool-1.1.7/simTool/R/unnest_simulation.R | 3 simTool-1.1.7/simTool/build/vignette.rds |binary simTool-1.1.7/simTool/inst/doc/simTool.R | 298 ++++++++++++++-------------- simTool-1.1.7/simTool/inst/doc/simTool.html | 232 ++++++--------------- simTool-1.1.7/simTool/inst/tinytest |only simTool-1.1.7/simTool/tests/tinytest.R |only 14 files changed, 258 insertions(+), 353 deletions(-)
Title: Simulation of Diffusion Processes
Description: It provides users with a wide range of tools to simulate, estimate, analyze, and visualize the dynamics of stochastic differential systems in both forms Ito and Stratonovich. Statistical analysis with parallel Monte Carlo and moment equations methods of SDE's. Enabled many searchers in different domains to use these equations to modeling practical problems in financial and actuarial modeling and other areas of application, e.g., modeling and simulate of first passage time problem in shallow water using the attractive center (Boukhetala K, 1996) ISBN:1-56252-342-2.
Author: Arsalane Chouaib Guidoum [cre, aut],
Kamal Boukhetala [aut]
Maintainer: Arsalane Chouaib Guidoum <acguidoum@usthb.dz>
Diff between Sim.DiffProc versions 4.6 dated 2020-05-04 and 4.7 dated 2020-09-22
DESCRIPTION | 8 MD5 | 80 ++-- R/utils.R | 24 - R/zzz.r | 4 README.md | 8 build/vignette.rds |binary inst/NEWS.Rd | 7 inst/doc/bridgesde.Rmd | 2 inst/doc/bridgesde.html | 504 +++++++++++++++++++-------- inst/doc/fitsde.Rmd | 4 inst/doc/fitsde.html | 713 +++++++++++++++++++++++++------------- inst/doc/fptsde.Rmd | 2 inst/doc/fptsde.html | 744 ++++++++++++++++++++++++++------------- inst/doc/mcmsde.Rmd | 2 inst/doc/mcmsde.html | 556 +++++++++++++++++++++-------- inst/doc/sdetotex.Rmd | 4 inst/doc/sdetotex.html | 494 ++++++++++++++++++++------ inst/doc/snssde.Rmd | 2 inst/doc/snssde.html | 820 +++++++++++++++++++++++++++----------------- man/HWV.Rd | 2 man/Sim.DiffProc-package.Rd | 4 man/TEX.sde.Rd | 2 man/bridgesde1d.Rd | 2 man/bridgesde2d.Rd | 2 man/bridgesde3d.Rd | 2 man/fitsde.Rd | 4 man/fptsde1d.Rd | 4 man/fptsde2d.Rd | 4 man/fptsde3d.Rd | 6 man/plot2d.Rd | 4 man/rsde1d.Rd | 8 man/rsde2d.Rd | 8 man/rsde3d.Rd | 8 man/snssde1d.Rd | 2 man/snssde3d.Rd | 2 vignettes/bridgesde.Rmd | 2 vignettes/fitsde.Rmd | 4 vignettes/fptsde.Rmd | 2 vignettes/mcmsde.Rmd | 2 vignettes/sdetotex.Rmd | 4 vignettes/snssde.Rmd | 2 41 files changed, 2759 insertions(+), 1299 deletions(-)
Title: Portable Address Space Mapping
Description: Portable '/proc/self/maps' as a data frame.
Determine which library or other region is mapped to a specific
address of a process. --
R packages can contain native code, compiled to shared libraries at build or
installation time.
When loaded, each shared library occupies a portion of the address space of
the main process.
When only a machine instruction pointer is available (e.g. from a backtrace
during error inspection or profiling), the address space map determines
which library this instruction pointer corresponds to.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
R Consortium [fnd],
Kostya Serebryany [ctb] (Bundled gperftools library),
Sanjay Ghemawat [ctb] (Bundled gperftools library),
Craig Silverstein [ctb] (Bundled gperftools library),
Google Inc. [cph] (Bundled gperftools library)
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between procmaps versions 0.0.2 dated 2020-09-20 and 0.0.3 dated 2020-09-22
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 5 +++++ src/vendor/gperftools/src/base/sysinfo.cc | 14 +++++++++----- 4 files changed, 21 insertions(+), 12 deletions(-)
Title: Methods for Graphical Models and Causal Inference
Description: Functions for causal structure
learning and causal inference using graphical models. The main algorithms
for causal structure learning are PC (for observational data without hidden
variables), FCI and RFCI (for observational data with hidden variables),
and GIES (for a mix of data from observational studies
(i.e. observational data) and data from experiments
involving interventions (i.e. interventional data) without hidden
variables). For causal inference the IDA algorithm, the Generalized
Backdoor Criterion (GBC), the Generalized Adjustment Criterion (GAC)
and some related functions are implemented. Functions for incorporating
background knowledge are provided.
Author: Markus Kalisch [aut, cre],
Alain Hauser [aut],
Martin Maechler [aut],
Diego Colombo [ctb],
Doris Entner [ctb],
Patrik Hoyer [ctb],
Antti Hyttinen [ctb],
Jonas Peters [ctb],
Nicoletta Andri [ctb],
Emilija Perkovic [ctb],
Preetam Nandy [ctb],
Philipp Ruetimann [ctb],
Daniel Stekhoven [ctb],
Manuel Schuerch [ctb],
Marco Eigenmann [ctb]
Maintainer: Markus Kalisch <kalisch@stat.math.ethz.ch>
Diff between pcalg versions 2.6-11 dated 2020-08-16 and 2.6-12 dated 2020-09-22
DESCRIPTION | 8 +- MD5 | 10 +-- R/pcalg.R | 151 +++++++++++++++++++++++++++++----------------- inst/CITATION | 2 inst/doc/pcalgDoc.pdf |binary inst/doc/vignette2018.pdf |binary 6 files changed, 106 insertions(+), 65 deletions(-)
Title: Feature Selection for 'mlr3'
Description: Implements methods for feature selection with
'mlr3', e.g. random search and sequential selection. Various
termination criteria can be set and combined. The class 'AutoFSelect'
provides a convenient way to perform nested resampling in combination
with 'mlr3'.
Author: Marc Becker [aut, cre] (<https://orcid.org/0000-0002-8115-0400>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>),
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>),
Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>)
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3fselect versions 0.2.1 dated 2020-09-10 and 0.3.0 dated 2020-09-22
DESCRIPTION | 10 ++--- MD5 | 44 ++++++++++++------------ NAMESPACE | 1 NEWS.md | 6 +++ R/ArchiveFSelect.R |only R/AutoFSelect.R | 4 +- R/FSelectInstanceMultiCrit.R | 12 ++++-- R/FSelectInstanceSingleCrit.R | 12 ++++-- R/FSelector.R | 2 - R/FSelectorFromOptimizer.R | 2 - R/FSelectorRFE.R | 6 ++- R/ObjectiveFSelect.R | 25 +++++++++---- build/partial.rdb |binary man/ArchiveFSelect.Rd |only man/AutoFSelect.Rd | 4 +- man/FSelectInstanceMultiCrit.Rd | 9 ++-- man/FSelectInstanceSingleCrit.Rd | 9 ++-- man/FSelector.Rd | 2 - man/FSelectorFromOptimizer.Rd | 2 - man/ObjectiveFSelect.Rd | 17 +++++---- tests/testthat/helper.R | 8 ++-- tests/testthat/test_FSelectInstanceMultiCrit.R | 20 +++++++--- tests/testthat/test_FSelectInstanceSingleCrit.R | 27 +++++++++----- tests/testthat/test_ObjectiveFSelect.R | 10 +++-- 24 files changed, 140 insertions(+), 92 deletions(-)
Title: Dose Response for Omics
Description: Several functions are provided for dose-response (or concentration-response) characterization from omics data. 'DRomics' is especially dedicated to omics data obtained using a typical dose-response design, favoring a great number of tested doses (or concentrations) rather than a great number of replicates (no need of three replicates). 'DRomics' provides functions 1) to check, normalize and or transform data, 2) to select monotonic or biphasic significantly responding items (e.g. probes, metabolites), 3) to choose the best-fit model among a predefined family of monotonic and biphasic models to describe each selected item, 4) to derive a benchmark dose or concentration and a typology of response from each fitted curve. In the available version data are supposed to be single-channel microarray data in log2, RNAseq data in raw counts, or already pretreated metabolomic data in log scale. In order to link responses across biological levels based on a common method, 'DRomics' also handles apical data as long as they are continuous and follow a Gaussian distribution for each dose or concentration, with a common standard error. For further details see Larras et al (2018) <DOI:10.1021/acs.est.8b04752> at <https://hal.archives-ouvertes.fr/hal-02309919>.
Author: Marie-Laure Delignette-Muller [aut],
Elise Billoir [aut],
Floriane Larras [ctb],
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between DRomics versions 2.0-1 dated 2019-09-16 and 2.1-2 dated 2020-09-22
DRomics-2.0-1/DRomics/inst/extdata/Zhou_kidney_pce.txt |only DRomics-2.1-2/DRomics/DESCRIPTION | 14 DRomics-2.1-2/DRomics/MD5 | 96 +-- DRomics-2.1-2/DRomics/NAMESPACE | 12 DRomics-2.1-2/DRomics/R/RNAseqdata.R | 116 ++- DRomics-2.1-2/DRomics/R/bmdboot.R | 10 DRomics-2.1-2/DRomics/R/bmdcalc.R | 19 DRomics-2.1-2/DRomics/R/bmdplotwithgradient.R |only DRomics-2.1-2/DRomics/R/continuousanchoringdata.R |only DRomics-2.1-2/DRomics/R/curvesplot.R | 41 + DRomics-2.1-2/DRomics/R/drcfit.R | 46 + DRomics-2.1-2/DRomics/R/ecdfplotwithCI.R | 14 DRomics-2.1-2/DRomics/R/ecdfquantileplot.R |only DRomics-2.1-2/DRomics/R/itemselect.R | 59 + DRomics-2.1-2/DRomics/R/metabolomicdata.R | 46 - DRomics-2.1-2/DRomics/R/microarraydata.R | 39 - DRomics-2.1-2/DRomics/R/targetplot.R |only DRomics-2.1-2/DRomics/R/util-plotfunc.R | 243 ++++--- DRomics-2.1-2/DRomics/data |only DRomics-2.1-2/DRomics/inst/CITATION | 2 DRomics-2.1-2/DRomics/inst/DRomics-shiny/global.R | 12 DRomics-2.1-2/DRomics/inst/DRomics-shiny/rinstall.txt | 23 DRomics-2.1-2/DRomics/inst/DRomics-shiny/server.R | 128 +++- DRomics-2.1-2/DRomics/inst/DRomics-shiny/ui.R | 221 ++++--- DRomics-2.1-2/DRomics/inst/DRomics-shiny/www/Dromics_tutorial.pdf |binary DRomics-2.1-2/DRomics/inst/DRomics-shiny/www/informations_datafile_input.txt | 6 DRomics-2.1-2/DRomics/inst/DRomics-shiny/www/logodromics-dr.png |only DRomics-2.1-2/DRomics/inst/DRomics-shiny/www/logodromics.png |only DRomics-2.1-2/DRomics/inst/NEWS | 28 DRomics-2.1-2/DRomics/inst/extdata/apical_anchoring.txt |only DRomics-2.1-2/DRomics/inst/extdata/triclosanSVcontigannot.txt |only DRomics-2.1-2/DRomics/inst/extdata/triclosanSVcontigres.txt |only DRomics-2.1-2/DRomics/inst/extdata/triclosanSVmetabannot.txt |only DRomics-2.1-2/DRomics/inst/extdata/triclosanSVmetabres.txt |only DRomics-2.1-2/DRomics/man/DRomics.Rd | 306 ++++++++-- DRomics-2.1-2/DRomics/man/RNAseqdata.Rd | 71 +- DRomics-2.1-2/DRomics/man/Scenedesmus.Rd |only DRomics-2.1-2/DRomics/man/Zhou.Rd |only DRomics-2.1-2/DRomics/man/bmdboot.Rd | 2 DRomics-2.1-2/DRomics/man/bmdcalc.Rd | 2 DRomics-2.1-2/DRomics/man/bmdplotwithgradient.Rd |only DRomics-2.1-2/DRomics/man/continuousanchoringdata.Rd |only DRomics-2.1-2/DRomics/man/curvesplot.Rd | 67 +- DRomics-2.1-2/DRomics/man/drcfit.Rd | 56 + DRomics-2.1-2/DRomics/man/ecdfplotwithCI.Rd | 72 +- DRomics-2.1-2/DRomics/man/ecdfquantileplot.Rd |only DRomics-2.1-2/DRomics/man/itemselect.Rd | 24 DRomics-2.1-2/DRomics/man/metabolomicdata.Rd | 45 + DRomics-2.1-2/DRomics/man/microarraydata.Rd | 28 DRomics-2.1-2/DRomics/man/targetplot.Rd |only DRomics-2.1-2/DRomics/tests/examplewithLprobit.R | 23 DRomics-2.1-2/DRomics/tests/examplewithRNAseq.R | 146 +++- DRomics-2.1-2/DRomics/tests/examplewithanchoringdata.R |only DRomics-2.1-2/DRomics/tests/examplewithmetabolomic.R | 60 + DRomics-2.1-2/DRomics/tests/examplewithmicroarray.R | 75 +- DRomics-2.1-2/DRomics/tests/testthat/test_drcfit.R | 9 56 files changed, 1609 insertions(+), 552 deletions(-)
Title: Interface to the 'Azure Machine Learning' 'SDK'
Description: Interface to the 'Azure Machine Learning' Software Development Kit
('SDK'). Data scientists can use the 'SDK' to train, deploy, automate, and
manage machine learning models on the 'Azure Machine Learning' service. To
learn more about 'Azure Machine Learning' visit the website:
<https://docs.microsoft.com/en-us/azure/machine-learning/service/overview-what-is-azure-ml>.
Author: Diondra Peck [cre, aut],
Minna Xiao [aut],
AzureML R SDK Team [ctb],
Microsoft [cph, fnd],
Google Inc. [cph] (Examples and Tutorials),
The TensorFlow Authors [cph] (Examples and Tutorials),
RStudio Inc. [cph] (Examples and Tutorials)
Maintainer: Diondra Peck <Diondra.Peck@microsoft.com>
Diff between azuremlsdk versions 0.6.85 dated 2020-02-05 and 1.10.0 dated 2020-09-22
azuremlsdk-0.6.85/azuremlsdk/man/dot-create_run_details_plot.Rd |only azuremlsdk-0.6.85/azuremlsdk/man/generate_docker_file.Rd |only azuremlsdk-0.6.85/azuremlsdk/vignettes/deploy-to-aks/deploy-to-aks.Rmd |only azuremlsdk-0.6.85/azuremlsdk/vignettes/experiments-with-R |only azuremlsdk-0.6.85/azuremlsdk/vignettes/hyperparameter-tune-with-keras/hyperparameter-tune-with-keras.Rmd |only azuremlsdk-0.6.85/azuremlsdk/vignettes/train-and-deploy-to-aci |only azuremlsdk-0.6.85/azuremlsdk/vignettes/train-with-tensorflow/train-with-tensorflow.Rmd |only azuremlsdk-1.10.0/azuremlsdk/DESCRIPTION | 27 azuremlsdk-1.10.0/azuremlsdk/MD5 | 486 +- azuremlsdk-1.10.0/azuremlsdk/NAMESPACE | 325 - azuremlsdk-1.10.0/azuremlsdk/R/compute.R | 763 ++-- azuremlsdk-1.10.0/azuremlsdk/R/datasets.R | 1407 ++++--- azuremlsdk-1.10.0/azuremlsdk/R/datastore.R | 770 ++-- azuremlsdk-1.10.0/azuremlsdk/R/do_azureml_parallel.R |only azuremlsdk-1.10.0/azuremlsdk/R/environment.R | 579 +-- azuremlsdk-1.10.0/azuremlsdk/R/estimator.R | 266 - azuremlsdk-1.10.0/azuremlsdk/R/experiment.R | 248 - azuremlsdk-1.10.0/azuremlsdk/R/hyperdrive.R | 1387 +++---- azuremlsdk-1.10.0/azuremlsdk/R/install.R | 139 azuremlsdk-1.10.0/azuremlsdk/R/keyvault.R | 144 azuremlsdk-1.10.0/azuremlsdk/R/model.R | 1148 +++--- azuremlsdk-1.10.0/azuremlsdk/R/modules.R | 16 azuremlsdk-1.10.0/azuremlsdk/R/package.R | 90 azuremlsdk-1.10.0/azuremlsdk/R/run.R | 1850 +++++----- azuremlsdk-1.10.0/azuremlsdk/R/webservice-aci.R | 256 - azuremlsdk-1.10.0/azuremlsdk/R/webservice-aks.R | 558 +-- azuremlsdk-1.10.0/azuremlsdk/R/webservice-local.R | 176 azuremlsdk-1.10.0/azuremlsdk/R/webservice.R | 387 +- azuremlsdk-1.10.0/azuremlsdk/R/workspace.R | 761 ++-- azuremlsdk-1.10.0/azuremlsdk/README.md | 4 azuremlsdk-1.10.0/azuremlsdk/build/vignette.rds |binary azuremlsdk-1.10.0/azuremlsdk/inst/doc/configuration.R | 35 azuremlsdk-1.10.0/azuremlsdk/inst/doc/configuration.Rmd | 262 - azuremlsdk-1.10.0/azuremlsdk/inst/doc/configuration.html | 117 azuremlsdk-1.10.0/azuremlsdk/inst/doc/deploy-to-aks.R |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/deploy-to-aks.Rmd |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/deploy-to-aks.html |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/deploying-models.R |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/deploying-models.Rmd |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/deploying-models.html |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/experiments-deep-dive.R |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/experiments-deep-dive.Rmd |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/experiments-deep-dive.html |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/hyperparameter-tune-with-keras.R |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/hyperparameter-tune-with-keras.Rmd |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/hyperparameter-tune-with-keras.html |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/installation.R | 17 azuremlsdk-1.10.0/azuremlsdk/inst/doc/installation.Rmd | 226 - 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Title: Succinct and Correct Statistical Summaries for Reports
Description: Succinctly and correctly format statistical summaries of
various models and tests (F-test, Chi-Sq-test, Fisher-test, T-test, and rank-significance). The main purpose is unified reporting
of experimental results, working around issue such as the difficulty of
extracting model summary facts (such as with 'lm'/'glm'). This package also
includes empirical tests, such as bootstrap estimates.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between sigr versions 1.1.0 dated 2020-09-15 and 1.1.1 dated 2020-09-22
DESCRIPTION | 10 MD5 | 20 + NAMESPACE | 9 NEWS.md | 6 R/ROC.R | 317 +++++++++++++++++++++++++---- inst/doc/lmExample.html | 4 inst/doc/sigrFormatting.html | 4 man/find_AUC_q.Rd | 5 man/find_ROC_matching_ab.Rd |only man/find_ROC_matching_ab1.Rd |only man/find_area_q.Rd |only man/fit_beta_shapes.Rd |only man/sensitivity_and_specificity_s12p12n.Rd |only man/sensitivity_from_specificity_q.Rd |only 14 files changed, 323 insertions(+), 52 deletions(-)
Title: NEON Data Store
Description: The National Ecological Observatory Network (NEON) provides access
to its numerous data products through its REST API,
<https://data.neonscience.org/data-api/>. This package provides a
high-level user interface for downloading and storing NEON data products.
While each of NEON data products consist of hundreds or thousands of individual
files. Unlike 'neonUtilities', this package will avoid repeated downloading,
provides persistent storage, and improves performance. This package does not
provide expose interactions with the individual low-level NEON API endpoints.
Author: Carl Boettiger [aut, cre] (<https://orcid.org/0000-0002-1642-628X>),
Quinn Thomas [aut] (<https://orcid.org/0000-0003-1282-7825>),
Christine Laney [aut] (<https://orcid.org/0000-0002-4944-2083>),
Claire Lunch [aut] (<https://orcid.org/0000-0001-8753-6593>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between neonstore versions 0.2.2 dated 2020-09-08 and 0.2.3 dated 2020-09-22
DESCRIPTION | 18 +++++++++++------- MD5 | 26 +++++++++++++------------- NEWS.md | 8 ++++++++ R/neon_download.R | 35 +++++++++++++++++++++++++++++------ R/neon_download_s3.R | 4 ++-- R/neon_export.R | 5 ++++- R/neon_filename_parser.R | 37 ++++++++++++++++++++++--------------- R/neon_index.R | 21 +++++++++++++++------ R/neon_read.R | 31 +++++++++++++++++-------------- inst/WORDLIST | 4 ++++ man/neon_download_s3.Rd | 2 +- man/neon_read.Rd | 5 +++++ tests/testthat/test-additional.R | 4 ++-- tests/testthat/test-store.R | 24 +++++++++++++++++++++--- 14 files changed, 154 insertions(+), 70 deletions(-)
Title: A Wrapper of the JavaScript Library 'jsTree'
Description: Creates interactive trees that can be included in 'Shiny' apps and R markdown documents. A tree allows to represent hierarchical data (e.g. the contents of a directory). Similar to the 'shinyTree' package but offers more features and options, such as the grid extension, restricting the drag-and-drop behavior, and settings for the search functionality. It is possible to attach some data to the nodes of a tree and then to get these data in 'Shiny' when a node is selected. Also provides a 'Shiny' gadget allowing to manipulate one or more folders.
Author: Stéphane Laurent [aut, cre],
jQuery contributors [ctb, cph] (jQuery),
Ivan Bozhanov [ctb, cph] (jsTree),
Vedran Opacic [ctb, cph] (jsTree bootstrap theme),
Avi Deitcher [ctb, cph] (jsTreeGrid),
Terence Eden [ctb, cph] (SuperTinyIcons)
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Diff between jsTreeR versions 0.1.0 dated 2020-08-31 and 1.0.0 dated 2020-09-22
DESCRIPTION | 12 LICENSE.note | 20 MD5 | 38 NAMESPACE | 14 NEWS.md | 17 R/folderGadget.R |only R/jstree.R | 45 R/zzz.R | 23 README.md | 29 inst/htmlwidgets/OtherIcons |only inst/htmlwidgets/SuperTinyIcons/SuperTinyIcons.json | 1225 ++++++++++++++++---- inst/htmlwidgets/jstree.js | 129 +- inst/htmlwidgets/jstree.yaml | 4 inst/htmlwidgets/lib/bootstrap-theme/style.min.css | 2 inst/rstudio |only man/folderGadget.Rd |only man/jstree-shiny.Rd | 33 man/jstree.Rd | 12 18 files changed, 1282 insertions(+), 321 deletions(-)
Title: Model for Semisupervised Text Analysis Based on Word Embeddings
Description: A word embeddings-based semisupervised models for document scaling Watanabe (2017) <doi:10.1177/0267323117695735>.
LSS allows users to analyze large and complex corpora on arbitrary dimensions with seed words exploiting efficiency of word embeddings (SVD, Glove).
Author: Kohei Watanabe [aut, cre, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between LSX versions 0.9.1 dated 2020-09-14 and 0.9.2 dated 2020-09-22
DESCRIPTION | 12 +++---- MD5 | 10 ++--- NEWS.md | 8 ++++ tests/testthat/test-textmodel.R | 68 +++++++++++++++++++--------------------- tests/testthat/test-textplot.R | 4 -- tests/testthat/test-utils.R | 6 ++- 6 files changed, 58 insertions(+), 50 deletions(-)
Title: Scenario Weights for Importance Measurement
Description: An efficient sensitivity analysis for stochastic models based on
Monte Carlo samples. Provides weights on simulated scenarios from a
stochastic model, such that stressed random variables fulfil given
probabilistic constraints (e.g. specified values for risk measures),
under the new scenario weights. Scenario weights are selected by
constrained minimisation of the relative entropy to the baseline model.
The 'SWIM' package is based on Pesenti S.M, Millossovich P., Tsanakas A.
(2019) "Reverse Sensitivity Testing: What does it take to break the model",
<openaccess.city.ac.uk/id/eprint/18896/>.
Author: Silvana M. Pesenti [aut, cre],
Alberto Bettini [aut],
Pietro Millossovich [aut],
Andreas Tsanakas [aut]
Maintainer: Silvana M. Pesenti <swimpackage@gmail.com>
Diff between SWIM versions 0.2.1 dated 2020-05-22 and 0.2.2 dated 2020-09-22
DESCRIPTION | 8 - MD5 | 66 +++++++------ NAMESPACE | 2 NEWS.md | 29 +++++ R/cdf.R | 1 R/class.R | 27 +++-- R/plot_cdf.R | 3 R/plot_hist.R | 3 R/plot_quantile.R |only R/plot_weights.R |only R/quantile.R | 2 R/stress_VaR_ES.R | 26 ++++- R/stress_moment.R | 52 ++++++++-- README.md | 23 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/REFERENCES.bib | 2 inst/WORDLIST | 5 + inst/doc/SWIM-vignette.R | 33 ++---- inst/doc/SWIM-vignette.Rmd | 42 +++----- inst/doc/SWIM-vignette.html | 165 ++++++++++++++++----------------- man/get_data.Rd | 181 +++++++++++++++++++------------------ man/plot_quantile.Rd |only man/plot_weights.Rd |only man/stress_VaR_ES.Rd | 8 + man/stress_mean.Rd | 8 + man/stress_mean_sd.Rd | 8 + man/stress_moment.Rd | 13 ++ man/summary.SWIM.Rd | 126 ++++++++++++------------- tests/testthat/testget_data.R | 5 - tests/testthat/testplot_cdf.R | 2 tests/testthat/testplot_quantile.R |only tests/testthat/testplot_weights.R |only tests/testthat/testsensitivity.R | 8 - vignettes/SWIM-vignette.Rmd | 42 +++----- vignettes/bibliography.bib | 2 37 files changed, 494 insertions(+), 400 deletions(-)
Title: Tools for Assessment the Association Between Two Spatial
Processes
Description: Tools to assess the association between two spatial processes. Currently,
several methodologies are implemented: A modified t-test to perform hypothesis testing
about the independence between the processes, a suitable nonparametric correlation
coefficient, the codispersion coefficient, and an F test for assessing the multiple
correlation between one spatial process and several others. Functions for image
processing and computing the spatial association between images are also provided.
Author: Felipe Osorio [aut, cre] (<https://orcid.org/0000-0002-4675-5201>),
Ronny Vallejos [aut] (<https://orcid.org/0000-0001-5519-0946>),
Francisco Cuevas [ctb],
Diego Mancilla [ctb]
Maintainer: Felipe Osorio <felipe.osorios@usm.cl>
Diff between SpatialPack versions 0.3-819 dated 2020-06-21 and 0.3-8196 dated 2020-09-22
SpatialPack-0.3-819/SpatialPack/src/image.h |only SpatialPack-0.3-819/SpatialPack/src/similarity.h |only SpatialPack-0.3-819/SpatialPack/src/utils.c |only SpatialPack-0.3-819/SpatialPack/src/utils.h |only SpatialPack-0.3-8196/SpatialPack/ChangeLog | 5 + SpatialPack-0.3-8196/SpatialPack/DESCRIPTION | 22 +++--- SpatialPack-0.3-8196/SpatialPack/MD5 | 43 ++++++------- SpatialPack-0.3-8196/SpatialPack/NAMESPACE | 3 SpatialPack-0.3-8196/SpatialPack/R/codisp.R | 2 SpatialPack-0.3-8196/SpatialPack/R/image.R | 24 +++++-- SpatialPack-0.3-8196/SpatialPack/R/similarity.R | 4 - SpatialPack-0.3-8196/SpatialPack/data/wheat.rda |only SpatialPack-0.3-8196/SpatialPack/inst/CITATION | 20 +++--- SpatialPack-0.3-8196/SpatialPack/man/wheat.Rd |only SpatialPack-0.3-8196/SpatialPack/src/base.c | 1 SpatialPack-0.3-8196/SpatialPack/src/base.h | 17 +---- SpatialPack-0.3-8196/SpatialPack/src/codisp.c | 9 +- SpatialPack-0.3-8196/SpatialPack/src/denoise.f | 48 ++++++++++++--- SpatialPack-0.3-8196/SpatialPack/src/distn.c |only SpatialPack-0.3-8196/SpatialPack/src/image.c | 24 ++++++- SpatialPack-0.3-8196/SpatialPack/src/init.c | 67 ++++++++++++++------- SpatialPack-0.3-8196/SpatialPack/src/mod_ttest.c | 1 SpatialPack-0.3-8196/SpatialPack/src/similarity.c | 6 - SpatialPack-0.3-8196/SpatialPack/src/spatialpack.h | 19 ++++- SpatialPack-0.3-8196/SpatialPack/src/stats.c | 51 ++++----------- SpatialPack-0.3-8196/SpatialPack/src/stats.h | 12 +-- 26 files changed, 226 insertions(+), 152 deletions(-)
Title: Modelling Spatial Extremes
Description: Tools for the statistical modelling of spatial extremes using max-stable processes, copula or Bayesian hierarchical models. More precisely, this package allows (conditional) simulations from various parametric max-stable models, analysis of the extremal spatial dependence, the fitting of such processes using composite likelihoods or least square (simple max-stable processes only), model checking and selection and prediction. Other approaches (although not completely in agreement with the extreme value theory) are available such as the use of (spatial) copula and Bayesian hierarchical models assuming the so-called conditional assumptions. The latter approaches is handled through an (efficient) Gibbs sampler. Some key references: Davison et al. (2012) <doi:10.1214/11-STS376>, Padoan et al. (2010) <doi:10.1198/jasa.2009.tm08577>, Dombry et al. (2013) <doi:10.1093/biomet/ass067>.
Author: Mathieu Ribatet [aut, cre],
Richard Singleton [ctb],
R Core team [ctb]
Maintainer: Mathieu Ribatet <mathieu.ribatet@ec-nantes.fr>
Diff between SpatialExtremes versions 2.0-8 dated 2020-03-09 and 2.0-9 dated 2020-09-22
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/smith.R | 1 - build/vignette.rds |binary inst/doc/SpatialExtremesGuide.R | 1 - inst/doc/SpatialExtremesGuide.pdf |binary 6 files changed, 9 insertions(+), 11 deletions(-)
More information about SpatialExtremes at CRAN
Permanent link
Title: A Framework to Smooth L1 Penalized Regression Operators using
Nesterov Smoothing
Description: We provide full functionality to smooth L1 penalized regression operators and to compute regression estimates thereof. For this, the objective function of a user-specified regression operator is first smoothed using Nesterov smoothing (see Y. Nesterov (2005) <doi:10.1007/s10107-004-0552-5>), resulting in a modified objective function with explicit gradients everywhere. The smoothed objective function and its gradient are minimized via BFGS, and the obtained minimizer is returned. Using Nesterov smoothing, the smoothed objective function can be made arbitrarily close to the original (unsmoothed) one. In particular, the Nesterov approach has the advantage that it comes with explicit accuracy bounds, both on the L1/L2 difference of the unsmoothed to the smoothed objective functions as well as on their respective minimizers (see G. Hahn, S.M. Lutz, N. Laha, C. Lange (2020) <doi:10.1101/2020.09.17.301788>). A progressive smoothing approach is provided which iteratively smoothes the objective function, resulting in more stable regression estimates.
Author: Georg Hahn [aut,cre], Sharon M. Lutz [ctb], Nilanjana Laha [ctb], Christoph Lange [ctb]
Maintainer: Georg Hahn <ghahn@hsph.harvard.edu>
Diff between smoothedLasso versions 1.3 dated 2020-06-14 and 1.4 dated 2020-09-22
smoothedLasso-1.3/smoothedLasso/man/solveSmoothedLASSO.Rd |only smoothedLasso-1.3/smoothedLasso/man/solveSmoothedLASSOSequence.Rd |only smoothedLasso-1.3/smoothedLasso/man/solveUnsmoothedLASSO.Rd |only smoothedLasso-1.4/smoothedLasso/DESCRIPTION | 15 smoothedLasso-1.4/smoothedLasso/MD5 | 24 smoothedLasso-1.4/smoothedLasso/NAMESPACE | 10 smoothedLasso-1.4/smoothedLasso/R/smoothedLasso.r | 456 ++++++---- smoothedLasso-1.4/smoothedLasso/man/elasticNet.Rd |only smoothedLasso-1.4/smoothedLasso/man/fusedLasso.Rd |only smoothedLasso-1.4/smoothedLasso/man/graphicalLasso.Rd |only smoothedLasso-1.4/smoothedLasso/man/minimizeFunction.Rd |only smoothedLasso-1.4/smoothedLasso/man/minimizeSmoothedSequence.Rd |only smoothedLasso-1.4/smoothedLasso/man/objFunction.Rd | 26 smoothedLasso-1.4/smoothedLasso/man/objFunctionGradient.Rd | 28 smoothedLasso-1.4/smoothedLasso/man/objFunctionSmooth.Rd | 26 smoothedLasso-1.4/smoothedLasso/man/objFunctionSmoothGradient.Rd | 28 smoothedLasso-1.4/smoothedLasso/man/prsLasso.Rd |only smoothedLasso-1.4/smoothedLasso/man/standardLasso.Rd |only 18 files changed, 403 insertions(+), 210 deletions(-)
Title: Create Reports Using R and 'asciidoc'
Description: Inspired by Karl Broman`s reader on using 'knitr'
with 'asciidoc'
(<http://kbroman.org/knitr_knutshell/pages/asciidoc.html>), this is
merely a wrapper to 'knitr' and 'asciidoc'.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between rasciidoc versions 2.1.3 dated 2020-08-16 and 2.2.0 dated 2020-09-22
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NEWS.md | 5 +++++ R/render.R | 41 ++++++++++++++++++++++++++++++++++++----- 4 files changed, 49 insertions(+), 13 deletions(-)
Title: Segment Images in Text Lines and Words
Description: Find text lines in scanned images and segment the lines into words.
Includes implementations of the paper 'Novel A* Path Planning Algorithm for Line Segmentation of Handwritten Documents' by Surinta O. et al (2014) <doi:10.1109/ICFHR.2014.37> available at <https://github.com/smeucci/LineSegm>,
an implementation of 'A Statistical approach to line segmentation in handwritten documents' by Arivazhagan M. et al (2007) <doi:10.1117/12.704538>,
and a wrapper for an image segmentation technique to detect words in text lines as described in the paper 'Scale Space Technique for Word Segmentation in Handwritten Documents' by Manmatha R. and Srimal N. (1999) paper at <doi:10.1007/3-540-48236-9_3>, wrapper for code available at <https://github.com/arthurflor23/text-segmentation>.
Author: Jan Wijffels [aut, cre, cph] (R wrapper),
Vrije Universiteit Brussel - DIGI: Brussels Platform for Digital
Humanities [cph] (R wrapper),
Jeroen Ooms [ctb, cph] (More details in LICENSE.note file),
Arthur Flôr [ctb, cph] (More details in LICENSE.note file),
Saverio Meucci [ctb, cph] (More details in LICENSE.note file),
Yeara Kozlov [ctb, cph] (More details in LICENSE.note file),
Tino Weinkauf [ctb, cph] (More details in LICENSE.note file)
Maintainer: Jan Wijffels <jan.wijffels@vub.be>
Diff between image.textlinedetector versions 0.1.1 dated 2020-09-21 and 0.1.2 dated 2020-09-22
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ src/Makevars.win | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
More information about image.textlinedetector at CRAN
Permanent link
Title: Ensemble Boolean Model Biomarker Analysis
Description: Analysis and visualization of an ensemble of boolean models for
biomarker discovery in cancer cell networks. The package allows to easily
load the simulation data results of the DrugLogics software pipeline which predicts synergistic drug
combinations in cancer cell lines (developed by the DrugLogics research group
in NTNU). It has generic functions that can be used to split a boolean model
dataset to model groups with regards to the models predictive performance (number of true
positive predictions/Matthews correlation coefficient score) or synergy prediction based on a given set
of gold standard synergies and find the average activity difference per network
node between all model group pairs. Thus, given user-specific thresholds,
important nodes (biomarkers) can be accessed in the sense that they make the
models predict specific synergies (synergy biomarkers) or have better
performance in general (performance biomarkers). Lastly, if the
boolean models have a specific equation form and differ only in their link operator,
link operator biomarkers can also be found.
Author: John Zobolas [aut, cph, cre] (<https://orcid.org/0000-0002-3609-8674>)
Maintainer: John Zobolas <bblodfon@gmail.com>
Diff between emba versions 0.1.6 dated 2020-07-08 and 0.1.7 dated 2020-09-22
DESCRIPTION | 10 ++++++---- MD5 | 20 ++++++++++---------- NEWS.md | 6 ++++++ R/input.R | 28 +++++++++++++++------------- README.md | 2 +- inst/doc/emba.html | 22 +++++++++++----------- man/get_fitness_from_models_dir.Rd | 3 ++- man/get_link_operators_from_models_dir.Rd | 5 ++--- man/get_model_names.Rd | 3 ++- man/get_node_names.Rd | 4 ++-- man/get_stable_state_from_models_dir.Rd | 5 +++-- 11 files changed, 60 insertions(+), 48 deletions(-)
More information about LifeInsuranceContracts at CRAN
Permanent link
Title: Compute, Handle and Plot Incidence of Dated Events
Description: Provides functions and classes to compute, handle and visualise
incidence from dated events for a defined time interval. Dates can be
provided in various standard formats. The class 'incidence2' is used to store
computed incidence and can be easily manipulated, subsetted, and plotted.
This package is part of the RECON (<https://www.repidemicsconsortium.org/>)
toolkit for outbreak analysis.
Author: Tim Taylor [aut, cre] (<https://orcid.org/0000-0002-8587-7113>),
Thibaut Jombart [aut],
Zhian N. Kamvar [aut] (<https://orcid.org/0000-0003-1458-7108>),
Rich FitzJohn [aut],
Jun Cai [ctb] (<https://orcid.org/0000-0001-9495-1226>),
Sangeeta Bhatia [ctb],
Jakob Schumacher [ctb],
Juliet R.C. Pulliam [ctb] (<https://orcid.org/0000-0003-3314-8223>)
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between incidence2 versions 0.1.0 dated 2020-09-07 and 0.2.0 dated 2020-09-22
DESCRIPTION | 8 ++--- MD5 | 40 +++++++++++++-------------- NAMESPACE | 1 NEWS.md | 11 +++++++ R/dplyr.R | 18 +++++++++++- R/incidence.R | 43 +++++++++++++----------------- R/make_incidence.R | 2 - R/plot.R | 41 ++++++++++++++++------------ R/scale_x_incidence.R | 12 ++++++-- build/vignette.rds |binary inst/doc/Introduction.html | 14 ++++----- inst/doc/customizing_incidence_plots.R | 8 ++--- inst/doc/customizing_incidence_plots.Rmd | 8 ++--- inst/doc/customizing_incidence_plots.html | 34 +++++++++++------------ inst/doc/handling_incidence_objects.R | 2 - inst/doc/handling_incidence_objects.Rmd | 2 - inst/doc/handling_incidence_objects.html | 28 +++++++++---------- man/plot.incidence2.Rd | 8 ++--- tests/testthat/test-incidence.R | 9 ++++++ vignettes/customizing_incidence_plots.Rmd | 8 ++--- vignettes/handling_incidence_objects.Rmd | 2 - 21 files changed, 171 insertions(+), 128 deletions(-)
More information about BayesianLaterality at CRAN
Permanent link
More information about testComplexity at CRAN
Permanent link
Title: L1 Constrained Estimation aka `lasso'
Description: Routines and documentation for solving regression problems
while imposing an L1 constraint on the estimates, based on
the algorithm of Osborne et al. (1998).
Author: Justin Lokhorst, Bill Venables and Berwin Turlach;
port to R, tests etc: Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Berwin Turlach <Berwin.Turlach@gmail.com>
Diff between lasso2 versions 1.2-20 dated 2018-11-27 and 1.2-21.1 dated 2020-09-22
DESCRIPTION | 11 +++++------ MD5 | 16 ++++++++-------- R/gl1ce.q | 2 +- R/l1ce.q | 2 +- build/vignette.rds |binary data/Prostate.rda |binary inst/doc/Manual-vignette.pdf |binary man/gl1ce.Rd | 6 ++---- man/l1ce.Rd | 2 +- 9 files changed, 18 insertions(+), 21 deletions(-)
Title: In-depth Characterization and Analysis of Mutational Signatures
('ICAMS')
Description: Analysis and visualization of experimentally elucidated mutational
signatures -- the kind of analysis and visualization in Boot et al.,
"In-depth characterization of the cisplatin mutational signature in
human cell lines and in esophageal and liver tumors", Genome Research 2018,
<doi:10.1101/gr.230219.117> and
"Characterization of colibactin-associated mutational signature in an
Asian oral squamous cell carcinoma and in other mucosal tumor types",
Genome Research 2020 <doi:10.1101/gr.255620.119>.
'ICAMS' stands for In-depth Characterization
and Analysis of Mutational Signatures. 'ICAMS' has functions to read in
variant call files (VCFs) and to collate the corresponding catalogs of
mutational spectra and to analyze and plot catalogs of mutational spectra
and signatures. Handles both "counts-based" and "density-based" catalogs
of mutational spectra or signatures.
Author: Steve Rozen, Nanhai Jiang, Arnoud Boot, Mo Liu
Maintainer: Steve Rozen <steverozen@gmail.com>
Diff between ICAMS versions 2.2.3 dated 2020-09-18 and 2.2.4 dated 2020-09-22
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS.md |only README.md | 6 +++--- tests/testthat/test_1TransformCatalog.R | 4 ++++ tests/testthat/test_discarded_variants.R | 8 ++++++++ 6 files changed, 23 insertions(+), 10 deletions(-)
Title: Sequence Manipulation Utilities
Description: Supports reading and writing sequences for different formats (currently interleaved and sequential formats for 'FASTA' and 'PHYLIP'), file conversion, and manipulation (e.g. filter sequences that contain specify pattern, export consensus sequence from an alignment).
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between seqmagick versions 0.1.3 dated 2019-12-19 and 0.1.4 dated 2020-09-22
DESCRIPTION | 10 +-- MD5 | 18 +++-- R/NCBI.R | 2 build/vignette.rds |binary inst/doc/seqmagick.R | 14 ++-- inst/doc/seqmagick.Rmd | 6 - inst/doc/seqmagick.html | 145 +++++++++++++++++++++++++---------------------- inst/extdata/AB115403.fa |only inst/extdata/AB115403.gb |only man/download_genbank.Rd | 2 vignettes/seqmagick.Rmd | 6 - 11 files changed, 111 insertions(+), 92 deletions(-)
Title: Verbs and Nouns for Corpus Analysis
Description: Package for corpus analysis using the Corpus Workbench
('CWB', <http://cwb.sourceforge.net/>) as an efficient back end for indexing
and querying large corpora. The package offers functionality to flexibly create
subcorpora and to carry out basic statistical operations (count, co-occurrences
etc.). The original full text of documents can be reconstructed and inspected at
any time. Beyond that, the package is intended to serve as an interface to
packages implementing advanced statistical procedures. Respective data structures
(document-term matrices, term-co-occurrence matrices etc.) can be created based
on the indexed corpora.
Author: Andreas Blaette [aut, cre] (<https://orcid.org/0000-0001-8970-8010>),
Christoph Leonhardt [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between polmineR versions 0.8.4 dated 2020-07-22 and 0.8.5 dated 2020-09-22
DESCRIPTION | 10 +- MD5 | 37 ++++--- NEWS.md | 16 +++ R/as.markdown.R | 5 - R/corpus.R | 1 R/decode.R | 46 +++++++++ R/registry.R | 12 ++ R/stats.R | 2 R/templates.R | 14 +- R/utils.R | 1 inst/CITATION | 4 inst/doc/OpenCPU.html | 4 inst/doc/vignette.Rmd | 2 inst/doc/vignette.html | 169 +++++++++++++++++------------------- man/decode.Rd | 17 +++ man/ll.Rd | 2 man/registry_eval.Rd | 11 ++ man/templates.Rd | 10 +- tests/testthat/test_registry_eval.R |only vignettes/vignette.Rmd | 2 20 files changed, 233 insertions(+), 132 deletions(-)
Title: Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>),
RStudio, PBC [cph],
Fernando Cagua [ctb],
Ethan Heinzen [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.25 dated 2020-07-24 and 0.26 dated 2020-09-22
DESCRIPTION | 6 MD5 | 16 +- R/install.R | 317 +++++++++++++++++++++++++------------------------ R/latex.R | 12 + R/tlmgr.R | 80 +++++++++--- README.md | 8 - man/install_tinytex.Rd | 39 +++--- man/tl_pkgs.Rd | 11 + man/tl_sizes.Rd | 21 ++- 9 files changed, 293 insertions(+), 217 deletions(-)
Title: Analysis Of The Interpopulation Difference In Degree of Sexual
Dimorphism Using Summary Statistics
Description: Provides two approaches of comparison; the univariate and the multivariate analysis in two or more populations. Since the main obstacle of performing systematic comparisons in anthropological studies is the absence of raw data, the current package offer a solution for this problem by allowing the use of published summary statistics of metric data (mean, standard deviation and sex specific sample size) as illustrated by the works of Greene, D. L. (1989) <doi:10.1002/ajpa.1330790113> and Konigsberg, L. W. (1991) <doi:10.1002/ajpa.1330840110>.
Author: Bassam A. Abulnoor [aut, cre] (<https://orcid.org/0000-0003-4351-2754>),
MennattAllah H. Attia [aut] (<https://orcid.org/0000-0002-2304-532X>),
Lyle W. Konigsberg [aut] (<https://orcid.org/0000-0003-4052-1575>)
Maintainer: Bassam A. Abulnoor <bas12@fayoum.edu.eg>
Diff between TestDimorph versions 0.3.3 dated 2020-09-20 and 0.3.4 dated 2020-09-22
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NAMESPACE | 1 - R/V_to_R.R | 1 + R/index_D.R | 1 + R/to_parms.R | 2 +- R/to_symm_diag.R | 1 + R/van_Vark.R | 1 + man/V_to_R.Rd | 1 + man/index_D.Rd | 1 + man/to_params.Rd | 1 + man/van_Vark.Rd | 1 + 12 files changed, 23 insertions(+), 16 deletions(-)
More information about rBiasCorrection at CRAN
Permanent link
Title: Fractional Hot Deck and Fully Efficient Fractional Imputation
Description: Impute general multivariate missing data with the fractional hot deck imputation based on Jaekwang Kim (2011) <doi:10.1093/biomet/asq073>.
Author: Inho Cho [aut, cre],
Jaekwang Kim [aut],
Jongho Im [aut],
Yicheng Yang [aut]
Maintainer: Inho Cho <icho@iastate.edu>
Diff between FHDI versions 1.4.0 dated 2020-04-23 and 1.4.1 dated 2020-09-22
DESCRIPTION | 8 MD5 | 18 R/FHDI_CellMake.R | 25 R/FHDI_CellProb.R | 6 R/FHDI_Driver.R | 48 man/FHDI-package.Rd | 7 man/FHDI_CellMake.Rd | 35 man/FHDI_CellProb.Rd | 15 man/FHDI_Driver.Rd | 34 src/FHDI.cc | 9435 +++++++++++++++++++++++++++++++++++++++++++++++++-- 10 files changed, 9190 insertions(+), 441 deletions(-)
Title: Discontinuous Regression and Image Processing
Description: This is a collection of functions for discontinuous regression
analysis and image processing (DRIP). This version removes the
dependence on the GNU Scientific Library.
Author: Yicheng Kang <kangx276@umn.edu>
Maintainer: Yicheng Kang <kangx276@umn.edu>
Diff between DRIP versions 1.5 dated 2020-09-10 and 1.6 dated 2020-09-22
DESCRIPTION | 15 ++++++-------- MD5 | 8 +++---- NAMESPACE | 2 - R/jpex.R | 4 +-- src/JPEX0.c | 64 ++++++++++++++++++++++++++++++++++++++++-------------------- 5 files changed, 57 insertions(+), 36 deletions(-)
Title: Test for Parallel Regression Assumption
Description: Tests the parallel regression assumption wit the brant test by Brant (1990) <doi: 10.2307/2532457> for ordinal logit models generated with the function polr() from the package 'MASS'.
Author: Benjamin Schlegel [aut,cre], Marco Steenbergen [aut]
Maintainer: Benjamin Schlegel <kontakt@benjaminschlegel.ch>
Diff between brant versions 0.2-0 dated 2018-01-10 and 0.3-0 dated 2020-09-22
DESCRIPTION | 10 +++---- MD5 | 10 +++---- NAMESPACE | 3 +- R/brant.R | 65 +++++++++++++++++++++++++------------------------- R/print.testresults.R | 2 - man/brant.Rd | 10 +++++-- 6 files changed, 53 insertions(+), 47 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-20 1.0.1
Title: Summarize Data for Scientific Publication
Description: Create and format tables and APA statistics for
scientific publication. This includes making a 'Table 1'
to summarize demographics across groups, correlation tables
with significance indicated by stars, and extracting formatted
statistical summarizes from simple tests for in-text notation.
The package also includes functions for Winsorizing data based
on a Z-statistic cutoff.
Author: David Pagliaccio [aut, cre] (<https://orcid.org/0000-0002-1214-1965>)
Maintainer: David Pagliaccio <david.pagliaccio@gmail.com>
Diff between scipub versions 1.1.0 dated 2020-06-04 and 1.2.0 dated 2020-09-22
DESCRIPTION | 14 ++--- MD5 | 14 +++-- NAMESPACE | 3 + NEWS.md | 4 + R/correltable.R | 69 +++----------------------- R/gg_groupplot.R |only build/vignette.rds |binary inst/doc/scipub_vignette.html | 108 +++++++++++++++++++++--------------------- man/gg_groupplot.Rd |only 9 files changed, 85 insertions(+), 127 deletions(-)
Title: Import and Handling for Plain and Formatted Text Files
Description: Functions for importing and handling text files and formatted text
files with additional meta-data, such including '.csv', '.tab', '.json', '.xml',
'.html', '.pdf', '.doc', '.docx', '.rtf', '.xls', '.xlsx', and others.
Author: Kenneth Benoit [aut, cre, cph],
Adam Obeng [aut],
Kohei Watanabe [ctb],
Akitaka Matsuo [ctb],
Paul Nulty [ctb],
Stefan Müller [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between readtext versions 0.76 dated 2020-03-04 and 0.80 dated 2020-09-22
DESCRIPTION | 14 - MD5 | 31 +- NEWS.md | 5 R/data.R | 2 R/encoding.R | 4 R/get-functions.R | 2 R/utils.R | 2 README.md | 19 - build/vignette.rds |binary data/data_char_encodedtexts.rda |only inst/doc/readtext_vignette.Rmd | 8 inst/doc/readtext_vignette.html | 560 +++++++++++++++++++++------------------- man/data_char_encodedtexts.Rd | 6 man/encoding.Rd | 4 tests/testthat/test-readtext.R | 35 -- tests/testthat/test-utils.R | 2 vignettes/readtext_vignette.Rmd | 8 17 files changed, 369 insertions(+), 333 deletions(-)
Title: Download DBnomics Data
Description: R access to hundreds of millions data series from DBnomics API
(<https://db.nomics.world/>).
Author: Sebastien Galais [cre, ctb],
Thomas Brand [aut]
Maintainer: Sebastien Galais <s915.stem@gmail.com>
Diff between rdbnomics versions 0.6.2 dated 2020-07-06 and 0.6.3 dated 2020-09-22
DESCRIPTION | 10 - MD5 | 46 ++-- NAMESPACE | 2 NEWS.md | 8 R/rdb.R | 12 - R/rdb_rename_xts.R |only R/rdb_to_xts.R |only R/sysdata.rda |binary R/utils.R | 6 R/zzz.R | 2 README.md | 393 +-------------------------------------- inst/doc/rdbnomics.R | 2 inst/doc/rdbnomics.Rmd | 2 inst/doc/rdbnomics.html | 65 ++---- man/dbnomics.Rd | 70 +++---- man/rdb.Rd | 474 ++++++++++++++++++++++++------------------------ man/rdb_by_api_link.Rd | 306 +++++++++++++++--------------- man/rdb_datasets.Rd | 162 ++++++++-------- man/rdb_dimensions.Rd | 186 +++++++++--------- man/rdb_last_updates.Rd | 122 ++++++------ man/rdb_providers.Rd | 124 ++++++------ man/rdb_rename_xts.Rd |only man/rdb_series.Rd | 228 +++++++++++------------ man/rdb_to_xts.Rd |only man/rdbnomics.Rd | 18 - vignettes/rdbnomics.Rmd | 2 26 files changed, 946 insertions(+), 1294 deletions(-)
Title: Geospatial Kriging with Metropolis Sampling
Description: Estimates kriging models for geographical point-referenced data. Method is described in Gill (2020) <doi:10.1177/1532440020930197>.
Author: Jason S. Byers [aut, cre], Le Bao [aut], Jamie Carson [aut], Jeff Gill [aut]
Maintainer: Jason S. Byers <jaybyers55@gmail.com>
Diff between krige versions 0.5.6 dated 2020-06-20 and 0.5.7 dated 2020-09-22
DESCRIPTION | 12 ++++++------ MD5 | 31 +++++++++++++++++-------------- NAMESPACE | 3 ++- R/krige.update.R |only man/NY_subset.Rd | 6 +++--- man/NYcity_subset.Rd | 6 +++--- man/WVwells.Rd | 7 +++---- man/congCombined.Rd | 4 ++-- man/geweke.Rd | 2 +- man/heidel.welch.Rd | 2 +- man/krige.posterior.Rd | 2 +- man/krige.pred.Rd | 2 +- man/krige.update.Rd |only man/lowerCombined.Rd | 2 +- man/metropolis.krige.Rd | 10 +++++----- man/stateCombined.Rd | 4 ++-- man/upperCombined.Rd | 4 ++-- src/Makevars |only 18 files changed, 50 insertions(+), 47 deletions(-)