Title: Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source
or Commercial Software
Description: An interface to the 'mclust' package to easily carry out latent profile
analysis ("LPA"). Provides functionality to estimate commonly-specified models.
Follows a tidy approach, in that output is in the form of a data frame that can
subsequently be computed on. Also has functions to interface to the commercial
'MPlus' software via the 'MplusAutomation' package.
Author: Joshua M Rosenberg [aut, cre],
Jennifer A Schmidt [ctb],
Patrick N Beymer [ctb],
Daniel Anderson [ctb],
Caspar van Lissa [aut],
Matthew J. Schell [ctb]
Maintainer: Joshua M Rosenberg <jmichaelrosenberg@gmail.com>
Diff between tidyLPA versions 0.2.1 dated 2018-10-11 and 0.2.3 dated 2018-11-20
DESCRIPTION | 12 MD5 | 42 - NEWS.md | 11 R/compare-solutions-mplus.R | 20 R/compare-solutions.R | 4 R/estimate-profiles-mplus.R | 766 ++++++++++++++-------------- R/helpers.R | 28 - R/plot-profiles-mplus.R | 99 +++ README.md | 2 build/vignette.rds |binary inst/CITATION |only inst/doc/Introduction_to_tidyLPA.Rmd | 4 inst/doc/Introduction_to_tidyLPA.html | 6 inst/doc/brief-overview.Rmd |only inst/doc/brief-overview.html |only inst/doc/introduction-to-major-changes.R |only inst/doc/introduction-to-major-changes.Rmd |only inst/doc/introduction-to-major-changes.html |only man/compare_solutions_mplus.Rd | 4 man/estimate_profiles_mplus.Rd | 6 man/extract_LL_mplus.Rd | 2 man/figures/README-unnamed-chunk-5-1.png |binary man/plot_profiles_mplus.Rd | 21 vignettes/Introduction_to_tidyLPA.Rmd | 4 vignettes/brief-overview.Rmd |only vignettes/introduction-to-major-changes.Rmd |only 26 files changed, 614 insertions(+), 417 deletions(-)
Title: A Tidy API for Graph Manipulation
Description: A graph, while not "tidy" in itself, can be thought of as two tidy
data frames describing node and edge data respectively. 'tidygraph'
provides an approach to manipulate these two virtual data frames using the
API defined in the 'dplyr' package, as well as provides tidy interfaces to
a lot of common graph algorithms.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between tidygraph versions 1.1.0 dated 2018-02-10 and 1.1.1 dated 2018-11-20
DESCRIPTION | 12 ++++----- MD5 | 53 +++++++++++++++++++++++--------------------- NAMESPACE | 6 ++++ R/dplyr.R |only R/list.R | 22 +++++++++++------- R/morphers.R | 39 +++++++++++++++++++++++--------- R/network.R | 2 - R/node.R | 14 +++++++++++ R/phylo.R | 6 ++++ R/plot.R |only R/tbl_graph.R | 26 ++++++++++++++------- R/tibble.R | 2 - man/activate.Rd | 4 +-- man/centrality.Rd | 8 +++--- man/create_graphs.Rd | 3 +- man/fortify.tbl_graph.Rd |only man/graph_join.Rd | 6 +++- man/local_graph.Rd | 2 - man/map_dfs.Rd | 2 - man/map_dfs_back.Rd | 2 - man/morphers.Rd | 10 ++++++-- man/mutate_as_tbl.Rd | 4 +-- man/node_rank.Rd | 11 ++++----- man/node_types.Rd | 12 +++++++++ man/sampling_games.Rd | 3 +- man/tbl_graph.Rd | 14 +++++++++-- man/tidygraph-package.Rd | 8 +++--- man/type_games.Rd | 8 ++++-- tests/testthat/test-group.R | 6 ++-- 29 files changed, 188 insertions(+), 97 deletions(-)
Title: UK National River Flow Archive Data from R
Description: Utility functions to retrieve data from the UK National River Flow Archive (<http://nrfa.ceh.ac.uk/>). The package contains R wrappers to the UK NRFA data temporary-API. There are functions to retrieve stations falling in a bounding box, to generate a map and extracting time series and general information.
Author: Claudia Vitolo [aut, cre],
Matthew Fry [ctb] (Matthew supervised the unofficial API integration.),
Wouter Buytaert [ctb] (This package is part of Claudia Vitolo's PhD
work and Wouter is the supervisor.),
Michael Spencer [ctb] (Michael updated the function osg_parse to work
with grid references of different lengths.),
Tobias Gauster [ctb] (Tobias improved the function osg_parse
introducing vectorisation)
Maintainer: Claudia Vitolo <cvitolodev@gmail.com>
Diff between rnrfa versions 1.4.0 dated 2018-04-13 and 1.5.0 dated 2018-11-20
DESCRIPTION | 8 ++--- MD5 | 20 +++++++------ R/catalogue.R | 49 ++++++++++++++++++-------------- R/osg_parse.R | 2 - R/plot_rain_flow.R | 47 +++++++++++++++--------------- R/plot_trend.R | 39 +++++++++++++------------ R/seasonal_averages.R | 20 +++++++------ README.md | 4 -- inst |only tests/testthat.R | 16 ++++++++-- tests/testthat/test-get_ts.R | 32 +++++++++++--------- tests/testthat/test-seasonal_averages.R |only 12 files changed, 133 insertions(+), 104 deletions(-)
Title: Vectorised Colour Conversion and Comparison
Description: The encoding of colour can be handled in many different ways, using
different colour spaces. As different colour spaces have different uses,
efficient conversion between these representations are important. The
'farver' package provides a set of functions that gives access to very fast
colour space conversion and comparisons implemented in C++, and offers
100-fold speed improvements over the 'convertColor' function in the
'grDevices' package.
Author: Thomas Lin Pedersen [cre, aut],
Berendea Nicolae [aut] (Author of the ColorSpace C++ library),
Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>)
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between farver versions 1.0 dated 2018-09-17 and 1.1.0 dated 2018-11-20
DESCRIPTION | 10 +- MD5 | 31 +++---- NAMESPACE | 1 R/RcppExports.R | 8 - R/aaa.R | 105 +++++++++++++++++++++++++ R/compare_colour.R | 8 + R/convert_colour.R | 26 ++++-- README.md | 129 +++++++++++++++++-------------- man/as_white_ref.Rd |only man/compare_colour.Rd | 6 + man/convert_colour.Rd | 23 ++++- man/figures/README-unnamed-chunk-5-1.png |binary src/Conversion.cpp | 17 ++-- src/Conversion.h | 2 src/RcppExports.cpp | 20 ++-- src/rcpp_colorspace.cpp | 120 ++++++++++++++-------------- tests/testthat/test-conversion.R | 2 17 files changed, 335 insertions(+), 173 deletions(-)
Title: Make Static HTML Documentation for a Package
Description: Generate an attractive and useful website from a source package.
'pkgdown' converts your documentation, vignettes, 'README', and more to
'HTML' making it easy to share information about your package online.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>),
Jay Hesselberth [aut] (<https://orcid.org/0000-0002-6299-179X>),
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between pkgdown versions 1.1.0 dated 2018-06-02 and 1.2.0 dated 2018-11-20
pkgdown-1.1.0/pkgdown/tests/testthat/assets/autolink-out.html |only pkgdown-1.1.0/pkgdown/tests/testthat/assets/news-multi-page/docs |only pkgdown-1.2.0/pkgdown/DESCRIPTION | 28 - pkgdown-1.2.0/pkgdown/MD5 | 205 ++++--- pkgdown-1.2.0/pkgdown/NAMESPACE | 3 pkgdown-1.2.0/pkgdown/NEWS.md | 98 +++ pkgdown-1.2.0/pkgdown/R/autolink_html.R | 2 pkgdown-1.2.0/pkgdown/R/build-articles.R | 98 ++- pkgdown-1.2.0/pkgdown/R/build-cname.R |only pkgdown-1.2.0/pkgdown/R/build-home-authors.R | 12 pkgdown-1.2.0/pkgdown/R/build-home-citation.R | 5 pkgdown-1.2.0/pkgdown/R/build-home-index.R | 14 pkgdown-1.2.0/pkgdown/R/build-home.R | 68 +- pkgdown-1.2.0/pkgdown/R/build-logo.R | 99 +++ pkgdown-1.2.0/pkgdown/R/build-news.R | 38 - pkgdown-1.2.0/pkgdown/R/build-reference-index.R | 2 pkgdown-1.2.0/pkgdown/R/build-reference.R | 113 +--- pkgdown-1.2.0/pkgdown/R/build-tutorials.R | 2 pkgdown-1.2.0/pkgdown/R/build.r | 63 +- pkgdown-1.2.0/pkgdown/R/clean.R | 2 pkgdown-1.2.0/pkgdown/R/context.R | 8 pkgdown-1.2.0/pkgdown/R/deploy-site.R |only pkgdown-1.2.0/pkgdown/R/development.R | 6 pkgdown-1.2.0/pkgdown/R/github.R | 51 + pkgdown-1.2.0/pkgdown/R/html-tweak.R | 27 pkgdown-1.2.0/pkgdown/R/init.R | 40 + pkgdown-1.2.0/pkgdown/R/link-href.R | 38 + pkgdown-1.2.0/pkgdown/R/link-packages.R | 6 pkgdown-1.2.0/pkgdown/R/pkgdown.R | 5 pkgdown-1.2.0/pkgdown/R/rd-data.R | 8 pkgdown-1.2.0/pkgdown/R/rd-html.R | 81 +- pkgdown-1.2.0/pkgdown/R/rd.r | 14 pkgdown-1.2.0/pkgdown/R/render.r | 6 pkgdown-1.2.0/pkgdown/R/replay-html.r | 6 pkgdown-1.2.0/pkgdown/R/template.R | 21 pkgdown-1.2.0/pkgdown/R/test.R | 62 ++ pkgdown-1.2.0/pkgdown/R/topics.R | 17 pkgdown-1.2.0/pkgdown/R/usage.R | 16 pkgdown-1.2.0/pkgdown/R/utils-fs.R | 12 pkgdown-1.2.0/pkgdown/R/utils.r | 11 pkgdown-1.2.0/pkgdown/README.md | 57 +- pkgdown-1.2.0/pkgdown/build/vignette.rds |binary pkgdown-1.2.0/pkgdown/inst/assets/pkgdown.css | 10 pkgdown-1.2.0/pkgdown/inst/assets/pkgdown.js | 10 pkgdown-1.2.0/pkgdown/inst/doc/pkgdown.Rmd | 202 +++++-- pkgdown-1.2.0/pkgdown/inst/doc/pkgdown.html | 272 ++++++---- pkgdown-1.2.0/pkgdown/inst/templates/content-citation-authors.html | 1 pkgdown-1.2.0/pkgdown/inst/templates/content-home.html | 2 pkgdown-1.2.0/pkgdown/inst/templates/content-reference-index.html | 4 pkgdown-1.2.0/pkgdown/inst/templates/docsearch.html | 2 pkgdown-1.2.0/pkgdown/inst/templates/footer.html | 3 pkgdown-1.2.0/pkgdown/inst/templates/head.html | 28 - pkgdown-1.2.0/pkgdown/inst/templates/layout.html | 2 pkgdown-1.2.0/pkgdown/inst/templates/navbar.html | 5 pkgdown-1.2.0/pkgdown/man/autolink_html.Rd | 2 pkgdown-1.2.0/pkgdown/man/build_articles.Rd | 83 +-- pkgdown-1.2.0/pkgdown/man/build_favicon.Rd |only pkgdown-1.2.0/pkgdown/man/build_home.Rd | 66 +- pkgdown-1.2.0/pkgdown/man/build_news.Rd | 27 pkgdown-1.2.0/pkgdown/man/build_reference.Rd | 90 +-- pkgdown-1.2.0/pkgdown/man/build_site.Rd | 38 - pkgdown-1.2.0/pkgdown/man/build_tutorials.Rd | 2 pkgdown-1.2.0/pkgdown/man/clean_site.Rd | 2 pkgdown-1.2.0/pkgdown/man/deploy_site_github.Rd |only pkgdown-1.2.0/pkgdown/man/figures/logo.png |only pkgdown-1.2.0/pkgdown/man/in_pkgdown.Rd | 2 pkgdown-1.2.0/pkgdown/man/init_site.Rd | 24 pkgdown-1.2.0/pkgdown/man/pkgdown-package.Rd |only pkgdown-1.2.0/pkgdown/man/rd2html.Rd |only pkgdown-1.2.0/pkgdown/man/render_page.Rd | 2 pkgdown-1.2.0/pkgdown/man/templates.Rd | 14 pkgdown-1.2.0/pkgdown/man/test-crayon.Rd |only pkgdown-1.2.0/pkgdown/man/test-dont.Rd | 7 pkgdown-1.2.0/pkgdown/man/test-figures.Rd | 7 pkgdown-1.2.0/pkgdown/man/test-links.Rd | 7 pkgdown-1.2.0/pkgdown/man/test-lists.Rd | 20 pkgdown-1.2.0/pkgdown/man/test-output-styles.Rd |only pkgdown-1.2.0/pkgdown/man/test-params.Rd | 8 pkgdown-1.2.0/pkgdown/tests/testthat/assets/cname |only pkgdown-1.2.0/pkgdown/tests/testthat/assets/home-index-template-md |only pkgdown-1.2.0/pkgdown/tests/testthat/assets/home-index-template-rmd |only pkgdown-1.2.0/pkgdown/tests/testthat/assets/home-old-skool |only pkgdown-1.2.0/pkgdown/tests/testthat/assets/home-readme-rmd/DESCRIPTION | 3 pkgdown-1.2.0/pkgdown/tests/testthat/assets/news-github-links/NEWS.md | 2 pkgdown-1.2.0/pkgdown/tests/testthat/assets/open-graph/DESCRIPTION | 3 pkgdown-1.2.0/pkgdown/tests/testthat/assets/search-site/docs |only pkgdown-1.2.0/pkgdown/tests/testthat/assets/site-empty/DESCRIPTION | 2 pkgdown-1.2.0/pkgdown/tests/testthat/test-autolink_html.R | 1 pkgdown-1.2.0/pkgdown/tests/testthat/test-build-citation-authors.R | 18 pkgdown-1.2.0/pkgdown/tests/testthat/test-build-cname.R |only pkgdown-1.2.0/pkgdown/tests/testthat/test-build-home-authors.R |only pkgdown-1.2.0/pkgdown/tests/testthat/test-build-home-index.R |only pkgdown-1.2.0/pkgdown/tests/testthat/test-build-home-license.R |only pkgdown-1.2.0/pkgdown/tests/testthat/test-build-news.R | 5 pkgdown-1.2.0/pkgdown/tests/testthat/test-build_home.R | 139 ----- pkgdown-1.2.0/pkgdown/tests/testthat/test-github.R |only pkgdown-1.2.0/pkgdown/tests/testthat/test-highlight.R | 19 pkgdown-1.2.0/pkgdown/tests/testthat/test-html-build.R |only pkgdown-1.2.0/pkgdown/tests/testthat/test-html-tweak.R | 84 +++ pkgdown-1.2.0/pkgdown/tests/testthat/test-link-href.R | 44 + pkgdown-1.2.0/pkgdown/tests/testthat/test-metadata.R | 3 pkgdown-1.2.0/pkgdown/tests/testthat/test-rd-html.R | 103 +++ pkgdown-1.2.0/pkgdown/tests/testthat/test-topics.R | 18 pkgdown-1.2.0/pkgdown/tests/testthat/test-usage.R | 9 pkgdown-1.2.0/pkgdown/tests/testthat/test-utils.R | 6 pkgdown-1.2.0/pkgdown/vignettes/pkgdown.Rmd | 202 +++++-- pkgdown-1.2.0/pkgdown/vignettes/test/crayon.Rmd |only pkgdown-1.2.0/pkgdown/vignettes/test/highlight.Rmd | 9 pkgdown-1.2.0/pkgdown/vignettes/test/mathjax.Rmd |only 109 files changed, 2030 insertions(+), 926 deletions(-)
Title: Covariate Assisted Ranking and Screening for Large-Scale
Two-Sample Inference
Description: It implements the CARS procedure, which is a two-sample multiple testing procedure that utilizes an additional auxiliary variable to capture the sparsity information, hence improving power. The CARS procedure is shown to be asymptotically valid and optimal for FDR control. For more information, please see the website <http://www-bcf.usc.edu/~wenguans/Papers/CARS.html> and the accompanying paper.
Author: Weinan Wang [cre, aut]
Maintainer: Weinan Wang <weinanw@usc.edu>
Diff between CARS versions 0.2 dated 2017-09-09 and 0.2.1 dated 2018-11-20
DESCRIPTION | 6 MD5 | 10 - R/CARS.R | 4 build/vignette.rds |binary inst/doc/Vignette.html | 395 +++++++++++++++++++++++++++++++++++++------------ man/CARS.Rd | 4 6 files changed, 314 insertions(+), 105 deletions(-)
Title: Assertions to Check Properties of Matrices
Description: A set of predicates and assertions for checking the properties of
matrices. This is mainly for use by other package developers who want to
include run-time testing features in their own packages. End-users will
usually want to use assertive directly.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive.matrices versions 0.0-1 dated 2015-10-06 and 0.0-2 dated 2018-11-20
DESCRIPTION | 11 MD5 | 28 +- NAMESPACE | 3 NEWS | 3 R/imports.R | 12 R/is-matrix.R | 511 +++++++++++++++++++------------------- README.md | 5 man/is_diagonal_matrix.Rd | 77 ++--- man/is_identity_matrix.Rd | 79 ++--- man/is_lower_triangular_matrix.Rd | 107 ++++--- man/is_square_matrix.Rd | 62 ++-- man/is_symmetric_matrix.Rd | 77 ++--- man/is_zero_matrix.Rd | 77 ++--- tests/testthat.R | 12 tests/testthat/test-is-matrix.R | 48 +-- 15 files changed, 556 insertions(+), 556 deletions(-)
More information about assertive.matrices at CRAN
Permanent link
Title: General Resampling Infrastructure
Description: Classes and functions to create and summarize different types of resampling objects (e.g. bootstrap, cross-validation).
Author: Max Kuhn [aut, cre],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between rsample versions 0.0.2 dated 2017-11-11 and 0.0.3 dated 2018-11-20
rsample-0.0.2/rsample/R/recipes.R |only rsample-0.0.2/rsample/inst/doc/Recipes_and_rsample.R |only rsample-0.0.2/rsample/inst/doc/Recipes_and_rsample.Rmd |only rsample-0.0.2/rsample/inst/doc/Recipes_and_rsample.html |only rsample-0.0.2/rsample/man/prepper.Rd |only rsample-0.0.2/rsample/vignettes/Recipes_and_rsample.Rmd |only rsample-0.0.3/rsample/DESCRIPTION | 19 rsample-0.0.3/rsample/MD5 | 135 +-- rsample-0.0.3/rsample/NAMESPACE | 13 rsample-0.0.3/rsample/NEWS.md | 19 rsample-0.0.3/rsample/R/complement.R | 78 + rsample-0.0.3/rsample/R/data.R | 36 rsample-0.0.3/rsample/R/initial_split.R | 47 - rsample-0.0.3/rsample/R/loo.R | 16 rsample-0.0.3/rsample/R/reexports.R |only rsample-0.0.3/rsample/R/rolling_origin.R | 50 - rsample-0.0.3/rsample/R/rsplit.R | 81 + rsample-0.0.3/rsample/R/tidy.R | 1 rsample-0.0.3/rsample/R/vfold.R | 2 rsample-0.0.3/rsample/build/vignette.rds |binary rsample-0.0.3/rsample/data/datalist | 4 rsample-0.0.3/rsample/data/drinks.rda |only rsample-0.0.3/rsample/data/two_class_dat.RData |only rsample-0.0.3/rsample/inst/doc/Basics.html | 390 +++++++-- rsample-0.0.3/rsample/inst/doc/Working_with_rsets.R | 3 rsample-0.0.3/rsample/inst/doc/Working_with_rsets.Rmd | 3 rsample-0.0.3/rsample/inst/doc/Working_with_rsets.html | 685 ++++++++++------ rsample-0.0.3/rsample/man/apparent.Rd | 20 rsample-0.0.3/rsample/man/as.data.frame.rsplit.Rd | 20 rsample-0.0.3/rsample/man/attrition.Rd | 14 rsample-0.0.3/rsample/man/bootstraps.Rd | 10 rsample-0.0.3/rsample/man/complement.Rd | 12 rsample-0.0.3/rsample/man/drinks.Rd |only rsample-0.0.3/rsample/man/fill.Rd | 22 rsample-0.0.3/rsample/man/form_pred.Rd | 12 rsample-0.0.3/rsample/man/gather.rset.Rd | 32 rsample-0.0.3/rsample/man/group_vfold_cv.Rd | 20 rsample-0.0.3/rsample/man/initial_split.Rd | 25 rsample-0.0.3/rsample/man/labels.rset.Rd | 6 rsample-0.0.3/rsample/man/labels.rsplit.Rd | 6 rsample-0.0.3/rsample/man/loo_cv.Rd | 4 rsample-0.0.3/rsample/man/make_strata.Rd | 40 rsample-0.0.3/rsample/man/mc_cv.Rd | 4 rsample-0.0.3/rsample/man/nested_cv.Rd | 20 rsample-0.0.3/rsample/man/populate.Rd |only rsample-0.0.3/rsample/man/pretty.vfold_cv.Rd | 2 rsample-0.0.3/rsample/man/reexports.Rd |only rsample-0.0.3/rsample/man/rolling_origin.Rd | 24 rsample-0.0.3/rsample/man/rsample.Rd | 44 - rsample-0.0.3/rsample/man/rsample2caret.Rd | 22 rsample-0.0.3/rsample/man/tidy.rsplit.Rd | 14 rsample-0.0.3/rsample/man/two_class_dat.Rd |only rsample-0.0.3/rsample/man/vfold_cv.Rd | 6 rsample-0.0.3/rsample/tests/testthat/test_boot.R | 22 rsample-0.0.3/rsample/tests/testthat/test_caret.R | 56 - rsample-0.0.3/rsample/tests/testthat/test_dplyr.R | 112 +- rsample-0.0.3/rsample/tests/testthat/test_for_pred.R | 2 rsample-0.0.3/rsample/tests/testthat/test_gather.R | 2 rsample-0.0.3/rsample/tests/testthat/test_group.R | 34 rsample-0.0.3/rsample/tests/testthat/test_initial.R | 11 rsample-0.0.3/rsample/tests/testthat/test_labels.R | 10 rsample-0.0.3/rsample/tests/testthat/test_loo.R | 14 rsample-0.0.3/rsample/tests/testthat/test_mc.R | 26 rsample-0.0.3/rsample/tests/testthat/test_names.R | 4 rsample-0.0.3/rsample/tests/testthat/test_nesting.R | 18 rsample-0.0.3/rsample/tests/testthat/test_rolling.R | 20 rsample-0.0.3/rsample/tests/testthat/test_rset.R | 44 - rsample-0.0.3/rsample/tests/testthat/test_rsplit.R | 8 rsample-0.0.3/rsample/tests/testthat/test_strata.R | 6 rsample-0.0.3/rsample/tests/testthat/test_tidy.R | 6 rsample-0.0.3/rsample/tests/testthat/test_vfold.R | 26 rsample-0.0.3/rsample/vignettes/Applications |only rsample-0.0.3/rsample/vignettes/Working_with_rsets.Rmd | 3 73 files changed, 1556 insertions(+), 829 deletions(-)
Title: 'Neuroconductor' Base Package with Helper Functions for 'nifti'
Objects
Description: Base package for 'Neuroconductor', which includes many helper
functions that interact with objects of class 'nifti', implemented by
package 'oro.nifti', for reading/writing and also other manipulation
functions.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between neurobase versions 1.26.1 dated 2018-02-01 and 1.27.6 dated 2018-11-20
DESCRIPTION | 8 MD5 | 78 ++--- NEWS.md |only R/applyEmptyImageDimensions.R | 4 R/check_nifti.R | 8 R/check_nifti_header.R | 4 R/checkimg.R | 12 R/finite_img.R | 12 R/maskEmptyImageDimensions.R | 4 R/mask_vals.R | 4 R/minmax_img.R | 4 R/ortho2.R | 118 +++---- R/rescale_img.R | 13 R/robust_window.R | 14 R/separate_img.R | 4 README.md |only build/vignette.rds |binary inst/doc/neurobase.Rmd | 4 inst/doc/neurobase.html | 348 +++++++++++----------- inst/doc/nifti_basics.Rmd | 4 inst/doc/nifti_basics.html | 478 +++++++++++++++---------------- man/applyEmptyImageDimensions-methods.Rd | 23 - man/check_nifti-methods.Rd | 12 man/checkimg-methods.Rd | 12 man/colorbar.Rd | 3 man/dropEmptyImageDimensions.Rd | 4 man/finite_img-methods.Rd | 3 man/getEmptyImageDimensions.Rd | 3 man/maskEmptyImageDimensions-methods.Rd | 8 man/multi_overlay.Rd | 14 man/ortho2.Rd | 20 - man/ortho_diff.Rd | 5 man/replace_outside_surface.Rd | 4 man/rescale_img.Rd | 6 man/robust_window.Rd | 6 man/separate_img-methods.Rd | 3 man/subset_dti-methods.Rd | 17 - man/window_img.Rd | 4 man/zscore_img.Rd | 3 vignettes/neurobase.Rmd | 4 vignettes/nifti_basics.Rmd | 4 41 files changed, 656 insertions(+), 623 deletions(-)
Title: Multiple Mediation Analysis
Description: Used for general multiple mediation analysis.
The analysis method is described in Yu et al. (2014) <doi:10.4172/2155-6180.1000189> "General Multiple Mediation Analysis With an Application to Explore Racial Disparity in Breast Cancer Survival", published on Journal of Biometrics & Biostatistics, 5(2):189; and Yu et al.(2017) <DOI:10.1016/j.sste.2017.02.001> "Exploring racial disparity in obesity: a mediation analysis considering geo-coded environmental factors", published on Spatial and Spatio-temporal Epidemiology, 21, 13-23.
Author: Qingzhao Yu and Bin Li
Maintainer: Qingzhao Yu <qyu@lsuhsc.edu>
Diff between mma versions 6.1-0 dated 2018-03-08 and 7.0-0 dated 2018-11-20
DESCRIPTION | 8 MD5 | 26 R/mma.r | 1396 +++++++++++++++++++++++++++++++++++------------- man/boot.med.Rd | 8 man/boot.med.par.Rd | 6 man/data.org.Rd | 10 man/form.interaction.Rd |only man/med.Rd | 6 man/mma-package.Rd | 6 man/mma.Rd | 6 man/mma.par.Rd | 6 man/plot.med.Rd | 4 man/plot.mma.Rd | 2 man/summary.med_iden.Rd | 5 man/test.moderation.Rd |only 15 files changed, 1090 insertions(+), 399 deletions(-)
Title: Fishery Science Methods and Models
Description: Functions for applying a wide range of fisheries stock assessment methods.
Author: Gary A. Nelson <gary.nelson@mass.gov>
Maintainer: Gary A. Nelson <gary.nelson@mass.gov>
Diff between fishmethods versions 1.10-4 dated 2017-10-16 and 1.11-0 dated 2018-11-20
fishmethods-1.10-4/fishmethods/R/vblrt.R |only fishmethods-1.10-4/fishmethods/R/vbmultifit.R |only fishmethods-1.10-4/fishmethods/man/vblrt.Rd |only fishmethods-1.10-4/fishmethods/man/vbmultifit.Rd |only fishmethods-1.11-0/fishmethods/DESCRIPTION | 16 +- fishmethods-1.11-0/fishmethods/MD5 | 136 +++++++++---------- fishmethods-1.11-0/fishmethods/NAMESPACE | 2 fishmethods-1.11-0/fishmethods/R/M.empirical.R | 29 ++-- fishmethods-1.11-0/fishmethods/R/deplet.R | 9 - fishmethods-1.11-0/fishmethods/R/fpc.R |only fishmethods-1.11-0/fishmethods/R/growthlrt.R |only fishmethods-1.11-0/fishmethods/R/growthmultifit.R |only fishmethods-1.11-0/fishmethods/R/surveyref.R | 16 -- fishmethods-1.11-0/fishmethods/data/sole.rda |only fishmethods-1.11-0/fishmethods/man/M.empirical.Rd | 24 ++- fishmethods-1.11-0/fishmethods/man/agesurv.Rd | 2 fishmethods-1.11-0/fishmethods/man/agesurvcl.Rd | 2 fishmethods-1.11-0/fishmethods/man/alk.Rd | 2 fishmethods-1.11-0/fishmethods/man/alkD.Rd | 2 fishmethods-1.11-0/fishmethods/man/alkprop.Rd | 2 fishmethods-1.11-0/fishmethods/man/alkss.Rd | 2 fishmethods-1.11-0/fishmethods/man/bheq.Rd | 2 fishmethods-1.11-0/fishmethods/man/bhnoneq.Rd | 2 fishmethods-1.11-0/fishmethods/man/bt.log.Rd | 2 fishmethods-1.11-0/fishmethods/man/catch.select.Rd | 2 fishmethods-1.11-0/fishmethods/man/catchmsy.Rd | 2 fishmethods-1.11-0/fishmethods/man/catchsurvey.Rd | 2 fishmethods-1.11-0/fishmethods/man/clus.lf.Rd | 2 fishmethods-1.11-0/fishmethods/man/clus.mean.Rd | 2 fishmethods-1.11-0/fishmethods/man/clus.rho.Rd | 2 fishmethods-1.11-0/fishmethods/man/clus.rho.g.Rd | 2 fishmethods-1.11-0/fishmethods/man/clus.str.lf.Rd | 2 fishmethods-1.11-0/fishmethods/man/clus.t.test.Rd | 2 fishmethods-1.11-0/fishmethods/man/clus.vb.fit.Rd | 2 fishmethods-1.11-0/fishmethods/man/convmort.Rd | 2 fishmethods-1.11-0/fishmethods/man/cpuekapp.Rd | 2 fishmethods-1.11-0/fishmethods/man/dbsra.Rd | 2 fishmethods-1.11-0/fishmethods/man/deltadist.Rd | 2 fishmethods-1.11-0/fishmethods/man/deplet.Rd | 6 fishmethods-1.11-0/fishmethods/man/dlproj.Rd | 2 fishmethods-1.11-0/fishmethods/man/epr.Rd | 10 - fishmethods-1.11-0/fishmethods/man/fm_checkdesign.Rd | 2 fishmethods-1.11-0/fishmethods/man/fm_model_avg.Rd | 2 fishmethods-1.11-0/fishmethods/man/fm_telemetry.Rd | 2 fishmethods-1.11-0/fishmethods/man/fpc.Rd |only fishmethods-1.11-0/fishmethods/man/gap.Rd | 2 fishmethods-1.11-0/fishmethods/man/grotag.Rd | 2 fishmethods-1.11-0/fishmethods/man/growhamp.Rd | 2 fishmethods-1.11-0/fishmethods/man/growth.Rd | 2 fishmethods-1.11-0/fishmethods/man/growthlrt.Rd |only fishmethods-1.11-0/fishmethods/man/growthmultifit.Rd |only fishmethods-1.11-0/fishmethods/man/growtrans.Rd | 2 fishmethods-1.11-0/fishmethods/man/irm_cr.Rd | 2 fishmethods-1.11-0/fishmethods/man/irm_h.Rd | 2 fishmethods-1.11-0/fishmethods/man/lifetable.Rd | 2 fishmethods-1.11-0/fishmethods/man/mature.Rd | 2 fishmethods-1.11-0/fishmethods/man/mort.al.Rd | 2 fishmethods-1.11-0/fishmethods/man/mrN.single.Rd | 2 fishmethods-1.11-0/fishmethods/man/opt_slot.Rd | 2 fishmethods-1.11-0/fishmethods/man/opt_trophy.Rd | 2 fishmethods-1.11-0/fishmethods/man/pgen.Rd | 2 fishmethods-1.11-0/fishmethods/man/powertrend.Rd | 2 fishmethods-1.11-0/fishmethods/man/pwpop.Rd | 2 fishmethods-1.11-0/fishmethods/man/remp.Rd | 2 fishmethods-1.11-0/fishmethods/man/sbpr.Rd | 2 fishmethods-1.11-0/fishmethods/man/schnabel.Rd | 2 fishmethods-1.11-0/fishmethods/man/slca.Rd | 2 fishmethods-1.11-0/fishmethods/man/sole.Rd |only fishmethods-1.11-0/fishmethods/man/sr.Rd | 2 fishmethods-1.11-0/fishmethods/man/surveyfit.Rd | 2 fishmethods-1.11-0/fishmethods/man/surveyref.Rd | 14 - fishmethods-1.11-0/fishmethods/man/tag_model_avg.Rd | 2 fishmethods-1.11-0/fishmethods/man/vbfr.Rd | 4 fishmethods-1.11-0/fishmethods/man/ypr.Rd | 2 fishmethods-1.11-0/fishmethods/man/zt.Rd | 2 75 files changed, 187 insertions(+), 183 deletions(-)
Title: Non-Invasive Pretty Printing of R Code
Description: Pretty-prints R code without changing the
user's formatting intent.
Author: Kirill Müller [aut],
Lorenz Walthert [cre, aut]
Maintainer: Lorenz Walthert <lorenz.walthert@icloud.com>
Diff between styler versions 1.0.2 dated 2018-06-26 and 1.1.0 dated 2018-11-20
styler-1.0.2/styler/inst/doc/character-width.R |only styler-1.0.2/styler/inst/doc/character-width.Rmd |only styler-1.0.2/styler/inst/doc/character-width.html |only styler-1.0.2/styler/inst/doc/data_structures.R |only styler-1.0.2/styler/inst/doc/data_structures.Rmd |only styler-1.0.2/styler/inst/doc/data_structures.html |only styler-1.0.2/styler/inst/doc/gsoc_contrib.R |only styler-1.0.2/styler/inst/doc/gsoc_contrib.Rmd |only styler-1.0.2/styler/inst/doc/gsoc_contrib.html |only styler-1.0.2/styler/inst/doc/manipulating_nested_parse_data.R |only styler-1.0.2/styler/inst/doc/manipulating_nested_parse_data.Rmd |only styler-1.0.2/styler/inst/doc/manipulating_nested_parse_data.html |only styler-1.0.2/styler/man/identify_r_raw_chunks.Rd |only styler-1.0.2/styler/man/parse_transform_serialize.Rd |only styler-1.0.2/styler/man/transform_rmd.Rd |only styler-1.0.2/styler/tests/testthat/indention_round_brackets/multi_line-out.R |only styler-1.1.0/styler/DESCRIPTION | 47 - styler-1.1.0/styler/MD5 | 283 ++++++---- styler-1.1.0/styler/NAMESPACE | 4 styler-1.1.0/styler/NEWS.md | 80 +- styler-1.1.0/styler/R/addins.R | 17 styler-1.1.0/styler/R/compat-dplyr.R | 3 styler-1.1.0/styler/R/environments.R |only styler-1.1.0/styler/R/expr-is.R | 10 styler-1.1.0/styler/R/indent.R | 15 styler-1.1.0/styler/R/io.R |only styler-1.1.0/styler/R/nested-to-tree.R | 16 styler-1.1.0/styler/R/parse.R | 15 styler-1.1.0/styler/R/reindent.R | 48 - styler-1.1.0/styler/R/relevel.R | 17 styler-1.1.0/styler/R/roxygen-examples-add-remove.R |only styler-1.1.0/styler/R/roxygen-examples-find.R |only styler-1.1.0/styler/R/roxygen-examples-parse.R |only styler-1.1.0/styler/R/roxygen-examples.R |only styler-1.1.0/styler/R/rules-line-break.R | 52 + styler-1.1.0/styler/R/rules-other.R | 24 styler-1.1.0/styler/R/rules-spacing.R | 27 styler-1.1.0/styler/R/scratch/new-style.R | 9 styler-1.1.0/styler/R/set-assert-args.R | 5 styler-1.1.0/styler/R/style-guides.R | 17 styler-1.1.0/styler/R/testing.R | 44 - styler-1.1.0/styler/R/token-create.R | 11 styler-1.1.0/styler/R/transform-code.R | 88 +-- styler-1.1.0/styler/R/transform-files.R | 119 +++- styler-1.1.0/styler/R/ui.R | 76 +- styler-1.1.0/styler/R/utils.R | 28 styler-1.1.0/styler/R/vertical.R | 23 styler-1.1.0/styler/R/zzz.R | 8 styler-1.1.0/styler/README.md | 117 +++- styler-1.1.0/styler/build/vignette.rds |binary styler-1.1.0/styler/inst/doc/customizing_styler.html | 12 styler-1.1.0/styler/inst/doc/introducing_styler.html | 4 styler-1.1.0/styler/man/construct_out.Rd | 6 styler-1.1.0/styler/man/context_to_terminals.Rd | 4 styler-1.1.0/styler/man/create_node_from_nested_root.Rd | 8 styler-1.1.0/styler/man/create_pos_ids.Rd | 1 styler-1.1.0/styler/man/create_tokens.Rd | 1 styler-1.1.0/styler/man/find_dont_seqs.Rd |only styler-1.1.0/styler/man/find_tokens_to_update.Rd | 8 styler-1.1.0/styler/man/get_knitr_pattern.Rd | 4 styler-1.1.0/styler/man/has_crlf_as_first_line_sep.Rd | 1 styler-1.1.0/styler/man/identify_insufficiently_parsed_stings.Rd | 2 styler-1.1.0/styler/man/identify_raw_chunks.Rd |only styler-1.1.0/styler/man/identify_start_to_stop_of_roxygen_examples_from_text.Rd |only styler-1.1.0/styler/man/is_code_chunk_header.Rd | 2 styler-1.1.0/styler/man/make_transformer.Rd | 5 styler-1.1.0/styler/man/match_stop_to_start.Rd |only styler-1.1.0/styler/man/parse_roxygen.Rd |only styler-1.1.0/styler/man/parse_transform_serialize_r.Rd |only styler-1.1.0/styler/man/parse_transform_serialize_roxygen.Rd |only styler-1.1.0/styler/man/parser_version_set.Rd |only styler-1.1.0/styler/man/post_parse_roxygen.Rd |only styler-1.1.0/styler/man/prettify_any.Rd | 9 styler-1.1.0/styler/man/print.vertical.Rd |only styler-1.1.0/styler/man/reindention.Rd | 4 styler-1.1.0/styler/man/remove_dont_mask.Rd |only styler-1.1.0/styler/man/remove_roxygen_header.Rd |only styler-1.1.0/styler/man/separate_chunks.Rd | 10 styler-1.1.0/styler/man/split_roxygen_segments.Rd |only styler-1.1.0/styler/man/style_dir.Rd | 12 styler-1.1.0/styler/man/style_file.Rd | 19 styler-1.1.0/styler/man/style_pkg.Rd | 12 styler-1.1.0/styler/man/style_roxygen_code_example.Rd |only styler-1.1.0/styler/man/style_roxygen_code_example_segment.Rd |only styler-1.1.0/styler/man/style_roxygen_example_snippet.Rd |only styler-1.1.0/styler/man/style_text.Rd | 7 styler-1.1.0/styler/man/styler_addins.Rd | 1 styler-1.1.0/styler/man/test_collection.Rd | 13 styler-1.1.0/styler/man/tidyverse_style.Rd | 2 styler-1.1.0/styler/man/transform_code.Rd | 15 styler-1.1.0/styler/man/transform_file.Rd | 14 styler-1.1.0/styler/man/transform_files.Rd | 5 styler-1.1.0/styler/man/transform_mixed.Rd |only styler-1.1.0/styler/man/transform_utf8.Rd |only styler-1.1.0/styler/man/two_cols_match.Rd | 1 styler-1.1.0/styler/man/update_indention.Rd | 10 styler-1.1.0/styler/man/update_indention_ref.Rd | 22 styler-1.1.0/styler/man/validate_new_pos_ids.Rd | 1 styler-1.1.0/styler/man/visit.Rd | 1 styler-1.1.0/styler/man/visit_one.Rd | 1 styler-1.1.0/styler/man/wrap_expr_in_curly.Rd | 4 styler-1.1.0/styler/man/wrap_subexpr_in_curly.Rd | 4 styler-1.1.0/styler/tests/testthat/indention_round_brackets/multi_line-no-indention-out.R |only styler-1.1.0/styler/tests/testthat/indention_round_brackets/multi_line-random-out.R |only styler-1.1.0/styler/tests/testthat/indention_round_brackets/one_line-nested-out.R |only styler-1.1.0/styler/tests/testthat/line_breaks_and_other/comma-in.R |only styler-1.1.0/styler/tests/testthat/line_breaks_and_other/comma-in_tree |only styler-1.1.0/styler/tests/testthat/line_breaks_and_other/comma-out.R |only styler-1.1.0/styler/tests/testthat/public-api/xyzdir-dirty/clean-reference-with-scope-tokens |binary styler-1.1.0/styler/tests/testthat/public-api/xyzdir-dirty/dirty-reference-with-scope-spaces |binary styler-1.1.0/styler/tests/testthat/public-api/xyzdir-dirty/dirty-reference-with-scope-tokens |binary 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styler-1.1.0/styler/tests/testthat/strict/strict-out.R | 3 styler-1.1.0/styler/tests/testthat/test-helpers.R | 8 styler-1.1.0/styler/tests/testthat/test-identify-roxygen-examples.R |only styler-1.1.0/styler/tests/testthat/test-line_breaks_and_other.R | 6 styler-1.1.0/styler/tests/testthat/test-parsing.R | 8 styler-1.1.0/styler/tests/testthat/test-public_api.R | 63 ++ styler-1.1.0/styler/tests/testthat/test-rmd.R | 6 styler-1.1.0/styler/tests/testthat/test-rnw.R |only styler-1.1.0/styler/tests/testthat/test-roxygen-examples-complete.R |only styler-1.1.0/styler/tests/testthat/test-serialize_tests.R | 11 styler-1.1.0/styler/tests/testthat/test-spacing.R | 6 styler-1.1.0/styler/tests/testthat/test-token_adding_removing.R | 8 styler-1.1.0/styler/tests/testthat/token_adding_removing/add_brackets_in_pipe-in.R |only styler-1.1.0/styler/tests/testthat/token_adding_removing/add_brackets_in_pipe-in_tree |only styler-1.1.0/styler/tests/testthat/token_adding_removing/add_brackets_in_pipe-out.R |only styler-1.1.0/styler/tests/testthat/token_adding_removing/if-else-comma-in.R |only styler-1.1.0/styler/tests/testthat/token_adding_removing/if-else-comma-in_tree |only styler-1.1.0/styler/tests/testthat/token_adding_removing/if-else-comma-out.R |only 142 files changed, 1136 insertions(+), 552 deletions(-)
Title: Download Public Domain Works from Wikisource
Description: Download public domain works from Wikisource <https://wikisource.org/>, a free library from the Wikimedia Foundation project.
Author: Félix Luginbuhl [aut, cre]
Maintainer: Félix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between wikisourcer versions 0.1.1 dated 2018-10-28 and 0.1.2 dated 2018-11-20
DESCRIPTION | 6 ++-- MD5 | 12 ++++---- README.md | 6 ++-- inst/doc/wikisourcer.R | 13 +++------ inst/doc/wikisourcer.Rmd | 26 +++++-------------- inst/doc/wikisourcer.html | 62 ++++++++++++++++++++-------------------------- vignettes/wikisourcer.Rmd | 26 +++++-------------- 7 files changed, 61 insertions(+), 90 deletions(-)
Title: Tools for Nuclear Magnetic Resonance (NMR) Spectra Alignment,
Peak Based Processing, Quantitative Analysis and Visualizations
Description: Makes Nuclear Magnetic Resonance spectroscopy (NMR spectroscopy) data analysis as easy as possible by only requiring a small set of functions to perform an entire analysis. 'speaq' offers the possibility of raw spectra alignment and quantitation but also an analysis based on features whereby the spectra are converted to peaks which are then grouped and turned into features. These features can be processed with any number of statistical tools either included in 'speaq' or available elsewhere on CRAN. More detail can be found in Vu et al. (2011) <doi:10.1186/1471-2105-12-405> and Beirnaert et al. (2018) <doi:10.1371/journal.pcbi.1006018>.
Author: Charlie Beirnaert, Trung Nghia Vu, Pieter Meysman, Kris Laukens and Dirk Valkenborg
Maintainer: Charlie Beirnaert <charlie_beirnaert@icloud.com>
Diff between speaq versions 2.3.3 dated 2018-07-03 and 2.4.0 dated 2018-11-20
DESCRIPTION | 16 MD5 | 86 NAMESPACE | 1 NEWS.md | 10 R/BWR.R | 2 R/HMDBsearchR.R | 2 R/PeakFilling.R | 6 R/PeakGrouper.R | 8 R/ROIplot.R | 3 R/SCANT.R | 4 R/SilhouetR.R | 62 R/createNullSampling.R | 2 R/detectSpecPeaks.R | 3 R/dohCluster.R | 6 R/dohClusterCustommedSegments.R | 6 R/drawBW.R | 2 R/drawSpec.R | 10 R/drawSpecPPM.R | 23 R/findRef.R | 10 R/findSegPeakList.R | 2 R/getWaveletPeaks.R | 17 R/hClustAlign.R | 2 R/hclust.grouping.R | 10 R/makeSimulatedData.R | 2 R/regroupR.R | 8 inst/doc/classic_speaq_vignette.R | 6 inst/doc/classic_speaq_vignette.Rmd | 10 inst/doc/classic_speaq_vignette.html | 238 inst/doc/speaq2_illustrations.R | 4 inst/doc/speaq2_illustrations.Rmd | 20 inst/doc/speaq2_illustrations.html | 8447 ----------------------------------- man/BuildRawDataMatrix.Rd | 3 man/HMDBsearchR.Rd | 2 man/PeakFilling.Rd | 4 man/SilhouetR.Rd | 14 man/dohCluster.Rd | 4 man/drawBW.Rd | 2 man/drawSpec.Rd | 2 man/drawSpecPPM.Rd | 12 man/findRef.Rd | 2 man/getWaveletPeaks.Rd | 11 man/hClustAlign.Rd | 2 vignettes/classic_speaq_vignette.Rmd | 10 vignettes/speaq2_illustrations.Rmd | 20 44 files changed, 282 insertions(+), 8834 deletions(-)
Title: Producing and Reproducing Results
Description: A system for embedded scientific computing and reproducible research with R.
The OpenCPU server exposes a simple but powerful HTTP api for RPC and data interchange
with R. This provides a reliable and scalable foundation for statistical services or
building R web applications. The OpenCPU server runs either as a single-user development
server within the interactive R session, or as a multi-user Linux stack based on Apache2.
The entire system is fully open source and permissively licensed. The OpenCPU website
has detailed documentation and example apps.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between opencpu versions 2.0.8 dated 2018-07-27 and 2.1 dated 2018-11-20
DESCRIPTION | 16 ++++++++-------- MD5 | 14 +++++++------- NEWS | 7 +++++++ R/apps.R | 4 ++-- R/devtools.R | 10 +++++++--- R/github.R | 28 ++++++++++++++++++++-------- R/utils.R | 4 ++-- inst/doc/opencpu-paper.pdf |binary 8 files changed, 53 insertions(+), 30 deletions(-)
Title: Continuous Time Structural Equation Modelling
Description: A hierarchical, multivariate, continuous (and discrete) time dynamic modelling
package for panel and time series data, using stochastic differential
equations. Contains a faster frequentist set of functions using OpenMx for
single subject and mixed-effects (random intercepts only) structural
equation models, or a hierarchical Bayesian implementation using Stan that
allows for random effects and non-linearity over all model parameters.
Allows for modelling of multiple noisy measurements of multiple stochastic
processes, time varying input / event covariates, and time invariant
covariates used to predict the parameters.
Author: Charles Driver [aut, cre, cph],
Manuel Voelkle [aut, cph],
Han Oud [aut, cph]
Maintainer: Charles Driver <driver@mpib-berlin.mpg.de>
Diff between ctsem versions 2.7.4 dated 2018-11-09 and 2.7.6 dated 2018-11-20
ctsem-2.7.4/ctsem/src/stan_files32 |only ctsem-2.7.4/ctsem/tests/fixedvalsunspot.R |only ctsem-2.7.4/ctsem/tests/testthat/bayesvsfreq.R |only ctsem-2.7.4/ctsem/tests/testthat/bayesvsfreqtrait.R |only ctsem-2.7.4/ctsem/tests/testthat/bayesvsfreqtraitdual.R |only ctsem-2.7.4/ctsem/tests/testthat/bayesvsfreqtraitdualoptim.R |only ctsem-2.7.6/ctsem/DESCRIPTION | 8 ctsem-2.7.6/ctsem/MD5 | 73 ctsem-2.7.6/ctsem/NAMESPACE | 6 ctsem-2.7.6/ctsem/R/ctDiscretiseData.R | 2 ctsem-2.7.6/ctsem/R/ctStanFit.R | 1389 +---------- ctsem-2.7.6/ctsem/R/ctStanGenerateData.R |only ctsem-2.7.6/ctsem/R/ctStanModelWriter.R |only ctsem-2.7.6/ctsem/R/ctStanParMatrices.R | 4 ctsem-2.7.6/ctsem/R/ctStanPostPredict.R | 110 ctsem-2.7.6/ctsem/R/ctStanSummary.R | 18 ctsem-2.7.6/ctsem/R/ctdataupdate.R | 1 ctsem-2.7.6/ctsem/R/ctsem.R | 3 ctsem-2.7.6/ctsem/R/ctsemUtils.R | 29 ctsem-2.7.6/ctsem/R/ctsmupdate.R | 15 ctsem-2.7.6/ctsem/R/optimstan.R | 23 ctsem-2.7.6/ctsem/R/stan_unconstrainsamples.R |only ctsem-2.7.6/ctsem/R/stanmodels.R | 3 ctsem-2.7.6/ctsem/data/ctstantestfit.rda |binary ctsem-2.7.6/ctsem/man/ctStanFit.Rd | 11 ctsem-2.7.6/ctsem/man/ctStanGenerateData.Rd |only ctsem-2.7.6/ctsem/man/ctStanParMatrices.Rd | 2 ctsem-2.7.6/ctsem/man/ctStanPostPredict.Rd | 7 ctsem-2.7.6/ctsem/man/stan_unconstrainsamples.Rd |only ctsem-2.7.6/ctsem/src/Makevars | 5 ctsem-2.7.6/ctsem/src/Makevars.win | 10 ctsem-2.7.6/ctsem/src/stan_files/ctsm.stan | 692 ----- ctsem-2.7.6/ctsem/src/stan_files/ctsmgen.stan |only ctsem-2.7.6/ctsem/tests/testthat.R |only ctsem-2.7.6/ctsem/tests/testthat/ctStanFitTests.R | 11 ctsem-2.7.6/ctsem/tests/testthat/differenttraits.R | 8 ctsem-2.7.6/ctsem/tests/testthat/fixedvalsunspot.R |only ctsem-2.7.6/ctsem/tests/testthat/kalmanVram.R | 1 ctsem-2.7.6/ctsem/tests/testthat/nonlinearVlinear.R | 6 ctsem-2.7.6/ctsem/tests/testthat/test-knownFits.R | 8 ctsem-2.7.6/ctsem/tests/testthat/test-objectiveEquiv.R | 2 ctsem-2.7.6/ctsem/tests/testthat/test-stantipred.R | 7 ctsem-2.7.6/ctsem/tests/testthat/ukfpoptest.R | 3 ctsem-2.7.6/ctsem/tools/make_cc.R | 6 44 files changed, 402 insertions(+), 2061 deletions(-)
Title: Integrator of Bioinformatics Resources
Description: Can be used to integrate massive bioinformatics resources, such as tool/script and database. It provides the R functions and Shiny web application. Hundreds of bioinformatics tool/script and database have been included.
Author: Jianfeng Li [aut, cre] (<https://orcid.org/0000-0003-2349-208X>)
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>
Diff between BioInstaller versions 0.3.6 dated 2018-08-22 and 0.3.7 dated 2018-11-20
BioInstaller-0.3.6/BioInstaller/man/check_shiny_dep.Rd |only BioInstaller-0.3.7/BioInstaller/ChangeLog | 29 BioInstaller-0.3.7/BioInstaller/DESCRIPTION | 8 BioInstaller-0.3.7/BioInstaller/MD5 | 123 +- BioInstaller-0.3.7/BioInstaller/NAMESPACE | 2 BioInstaller-0.3.7/BioInstaller/NEWS.md | 12 BioInstaller-0.3.7/BioInstaller/R/BioInstaller.R | 7 BioInstaller-0.3.7/BioInstaller/R/conda.R | 6 BioInstaller-0.3.7/BioInstaller/R/install_utils.R | 3 BioInstaller-0.3.7/BioInstaller/R/versions.R | 27 BioInstaller-0.3.7/BioInstaller/R/web.R | 126 -- BioInstaller-0.3.7/BioInstaller/README.md | 23 BioInstaller-0.3.7/BioInstaller/build/vignette.rds |binary BioInstaller-0.3.7/BioInstaller/inst/doc/BioInstaller.R | 2 BioInstaller-0.3.7/BioInstaller/inst/doc/BioInstaller.Rmd | 2 BioInstaller-0.3.7/BioInstaller/inst/doc/BioInstaller.html | 425 +++++----- BioInstaller-0.3.7/BioInstaller/inst/doc/download.R | 2 BioInstaller-0.3.7/BioInstaller/inst/doc/download.Rmd | 101 -- BioInstaller-0.3.7/BioInstaller/inst/doc/download.html | 111 -- BioInstaller-0.3.7/BioInstaller/inst/doc/items_description.R | 2 BioInstaller-0.3.7/BioInstaller/inst/doc/items_description.Rmd | 2 BioInstaller-0.3.7/BioInstaller/inst/doc/items_description.html | 112 +- BioInstaller-0.3.7/BioInstaller/inst/doc/plugins_of_BioInstaller_shiny.R | 2 BioInstaller-0.3.7/BioInstaller/inst/doc/plugins_of_BioInstaller_shiny.Rmd | 2 BioInstaller-0.3.7/BioInstaller/inst/doc/plugins_of_BioInstaller_shiny.html | 4 BioInstaller-0.3.7/BioInstaller/inst/doc/start_shiny_of_BioInstaller.R | 2 BioInstaller-0.3.7/BioInstaller/inst/doc/start_shiny_of_BioInstaller.Rmd | 2 BioInstaller-0.3.7/BioInstaller/inst/doc/start_shiny_of_BioInstaller.html | 4 BioInstaller-0.3.7/BioInstaller/inst/doc/write_configuration_file.R | 2 BioInstaller-0.3.7/BioInstaller/inst/doc/write_configuration_file.Rmd | 3 BioInstaller-0.3.7/BioInstaller/inst/doc/write_configuration_file.html | 7 BioInstaller-0.3.7/BioInstaller/inst/extdata/config/db/db_annovar.toml | 8 BioInstaller-0.3.7/BioInstaller/inst/extdata/config/db/db_main.toml | 73 + BioInstaller-0.3.7/BioInstaller/inst/extdata/config/db/db_meta.toml | 50 + BioInstaller-0.3.7/BioInstaller/inst/extdata/config/github/github.toml | 10 BioInstaller-0.3.7/BioInstaller/inst/extdata/config/nongithub/nongithub.toml | 16 BioInstaller-0.3.7/BioInstaller/inst/extdata/config/nongithub/nongithub_meta.toml | 5 BioInstaller-0.3.7/BioInstaller/inst/extdata/files |only BioInstaller-0.3.7/BioInstaller/inst/extdata/scripts/parse_version.R | 6 BioInstaller-0.3.7/BioInstaller/inst/extdata/shiny/app.R | 8 BioInstaller-0.3.7/BioInstaller/inst/extdata/shiny/deps.R |only BioInstaller-0.3.7/BioInstaller/inst/extdata/shiny/global_var.R | 4 BioInstaller-0.3.7/BioInstaller/inst/extdata/shiny/index.md | 13 BioInstaller-0.3.7/BioInstaller/man/BioInstaller.Rd | 10 BioInstaller-0.3.7/BioInstaller/man/change.info.Rd | 7 BioInstaller-0.3.7/BioInstaller/man/conda.Rd | 4 BioInstaller-0.3.7/BioInstaller/man/conda.env.create.Rd | 4 BioInstaller-0.3.7/BioInstaller/man/copy_configs.Rd | 2 BioInstaller-0.3.7/BioInstaller/man/copy_plugins.Rd | 5 BioInstaller-0.3.7/BioInstaller/man/crawl.all.versions.Rd | 14 BioInstaller-0.3.7/BioInstaller/man/del.info.Rd | 4 BioInstaller-0.3.7/BioInstaller/man/figures/design_of_bioInstaller.jpg |binary BioInstaller-0.3.7/BioInstaller/man/get.info.Rd | 4 BioInstaller-0.3.7/BioInstaller/man/install.bioinfo.Rd | 27 BioInstaller-0.3.7/BioInstaller/man/install.github.Rd | 8 BioInstaller-0.3.7/BioInstaller/man/install.nongithub.Rd | 7 BioInstaller-0.3.7/BioInstaller/man/new.bioinfo.Rd | 4 BioInstaller-0.3.7/BioInstaller/man/spack.Rd | 4 BioInstaller-0.3.7/BioInstaller/vignettes/BioInstaller.Rmd | 2 BioInstaller-0.3.7/BioInstaller/vignettes/download.Rmd | 101 -- BioInstaller-0.3.7/BioInstaller/vignettes/items_description.Rmd | 2 BioInstaller-0.3.7/BioInstaller/vignettes/plugins_of_BioInstaller_shiny.Rmd | 2 BioInstaller-0.3.7/BioInstaller/vignettes/start_shiny_of_BioInstaller.Rmd | 2 BioInstaller-0.3.7/BioInstaller/vignettes/write_configuration_file.Rmd | 3 64 files changed, 751 insertions(+), 811 deletions(-)
Title: Tools for Model Specification in the Latent Variable Framework
Description: Tools for model specification in the latent variable framework
(add-on to the 'lava' package). The package contains three main functionalities:
Wald tests/F-tests with improved control of the type 1 error in small samples,
adjustment for multiple comparisons when searching for local dependencies,
and adjustment for multiple comparisons when doing inference for multiple latent variable models.
Author: Brice Ozenne [aut, cre] (<https://orcid.org/0000-0001-9694-2956>)
Maintainer: Brice Ozenne <brice.ozenne@orange.fr>
Diff between lavaSearch2 versions 1.4 dated 2018-10-05 and 1.4.1 dated 2018-11-20
lavaSearch2-1.4.1/lavaSearch2/DESCRIPTION | 8 - lavaSearch2-1.4.1/lavaSearch2/MD5 | 63 +++------- lavaSearch2-1.4.1/lavaSearch2/NAMESPACE | 1 lavaSearch2-1.4.1/lavaSearch2/R/Utils-nlme.R |only lavaSearch2-1.4.1/lavaSearch2/R/calcDistMax.R | 29 ++-- lavaSearch2-1.4.1/lavaSearch2/R/calibrateType1.R | 11 - lavaSearch2-1.4.1/lavaSearch2/R/createContrast.R | 17 +- lavaSearch2-1.4.1/lavaSearch2/R/iidJack.R | 17 +- lavaSearch2-1.4.1/lavaSearch2/R/matrixPower.R | 17 +- lavaSearch2-1.4.1/lavaSearch2/R/modelsearch2.R | 18 +- lavaSearch2-1.4.1/lavaSearch2/R/sCorrect.R | 40 ++++-- lavaSearch2-1.4.1/lavaSearch2/inst/doc/overview.pdf |binary lavaSearch2-1.4.1/lavaSearch2/inst/tests |only lavaSearch2-1.4.1/lavaSearch2/inst/todo.org | 1 lavaSearch2-1.4.1/lavaSearch2/man/calibrateType1.Rd | 7 - lavaSearch2-1.4.1/lavaSearch2/man/coef2-internal.Rd | 2 lavaSearch2-1.4.1/lavaSearch2/man/createContrast.Rd | 13 +- lavaSearch2-1.4.1/lavaSearch2/man/getCluster2-internal.Rd | 2 lavaSearch2-1.4.1/lavaSearch2/man/getIndexOmega2-internal.Rd | 2 lavaSearch2-1.4.1/lavaSearch2/man/getVarCov2-internal.Rd | 2 lavaSearch2-1.4.1/lavaSearch2/man/iidJack.Rd | 9 - lavaSearch2-1.4.1/lavaSearch2/man/matrixPower.Rd | 3 lavaSearch2-1.4.1/lavaSearch2/tests/testthat/test1-sCorrect-validObjects.R | 4 lavaSearch2-1.4.1/lavaSearch2/tests/testthat/test3-multcomp.R | 10 - lavaSearch2-1.4.1/lavaSearch2/vignettes/overview.org | 46 ++++--- lavaSearch2-1.4/lavaSearch2/R/utils-nlme.R |only lavaSearch2-1.4/lavaSearch2/inst/vignettes |only lavaSearch2-1.4/lavaSearch2/tests/testthat/test1-calibrateType1.R |only 28 files changed, 176 insertions(+), 146 deletions(-)
More information about whiboclustering at CRAN
Permanent link
Title: Optional Types and Pattern Matching
Description: Introduces optional types with some() and none, as well as match_with() from functional languages.
Author: Antoine Champion
Maintainer: Antoine Champion <antoine.champion@outlook.com>
Diff between optional versions 1.1 dated 2018-05-06 and 2.0 dated 2018-11-20
optional-1.1/optional/man/optional.Rd |only optional-2.0/optional/DESCRIPTION | 10 optional-2.0/optional/MD5 | 30 +- optional-2.0/optional/NAMESPACE | 1 optional-2.0/optional/NEWS.md | 5 optional-2.0/optional/R/optional.R | 56 ++-- optional-2.0/optional/build/vignette.rds |binary optional-2.0/optional/inst/doc/UserGuide.R | 12 optional-2.0/optional/inst/doc/UserGuide.Rmd | 22 + optional-2.0/optional/inst/doc/UserGuide.html | 363 ++++++++++++++++++++------ optional-2.0/optional/man/make_opt.Rd | 6 optional-2.0/optional/man/match_with.Rd | 4 optional-2.0/optional/man/none.Rd | 2 optional-2.0/optional/man/opt_unwrap.Rd | 2 optional-2.0/optional/man/option.Rd |only optional-2.0/optional/man/some.Rd | 38 -- optional-2.0/optional/vignettes/UserGuide.Rmd | 22 + 17 files changed, 412 insertions(+), 161 deletions(-)
Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate
event history data <doi:10.1007/s10985-013-9244-x>. Including multivariate
cumulative incidence models <doi:10.1002/sim.6016>, and bivariate random
effects probit models (Liability models) <doi:10.1016/j.csda.2015.01.014>.
Also contains two-stage binomial modelling that can do pairwise odds-ratio
dependence modelling based marginal logistic regression models. This is an
alternative to the alternating logistic regression approach (ALR).
Author: Klaus K. Holst and Thomas Scheike
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between mets versions 1.2.4 dated 2018-08-13 and 1.2.5 dated 2018-11-20
mets-1.2.4/mets/man/concordance.Rd |only mets-1.2.5/mets/DESCRIPTION | 16 mets-1.2.5/mets/MD5 | 199 - mets-1.2.5/mets/NAMESPACE | 17 mets-1.2.5/mets/NEWS | 62 mets-1.2.5/mets/R/bicomprisk.R | 5 mets-1.2.5/mets/R/binomial.twostage.R | 244 - mets-1.2.5/mets/R/cor.R | 42 mets-1.2.5/mets/R/dreg.R | 52 mets-1.2.5/mets/R/dutils.R | 2 mets-1.2.5/mets/R/gof-phreg.R | 135 mets-1.2.5/mets/R/mets-package.R | 4 mets-1.2.5/mets/R/phreg.R | 727 +++- mets-1.2.5/mets/R/recurrent.marginal.R | 207 + mets-1.2.5/mets/R/sim.clayton.oakes.R | 48 mets-1.2.5/mets/R/twostage.R | 1497 ++++++++-- mets-1.2.5/mets/build/vignette.rds |binary mets-1.2.5/mets/inst/doc/basic-dutils.ltx | 207 + mets-1.2.5/mets/inst/doc/basic-dutils.pdf |binary mets-1.2.5/mets/inst/doc/binomial-case-control-ascertainment.ltx | 143 mets-1.2.5/mets/inst/doc/binomial-case-control-ascertainment.pdf |binary mets-1.2.5/mets/inst/doc/binomial-family.ltx | 52 mets-1.2.5/mets/inst/doc/binomial-family.pdf |binary mets-1.2.5/mets/inst/doc/binomial-twin.ltx | 59 mets-1.2.5/mets/inst/doc/binomial-twin.pdf |binary mets-1.2.5/mets/inst/doc/competing.ltx |only mets-1.2.5/mets/inst/doc/competing.pdf |only mets-1.2.5/mets/inst/doc/marginal-cox.ltx |only mets-1.2.5/mets/inst/doc/marginal-cox.pdf |only mets-1.2.5/mets/inst/doc/quantitative-twin.ltx | 161 - 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Title: Pathway Enrichment Analysis Utilizing Active Subnetworks
Description: Pathway enrichment analysis enables researchers to uncover mechanisms
underlying the phenotype. pathfindR is a tool for pathway enrichment analysis
utilizing active subnetworks. It identifies active subnetworks in a
protein-protein interaction network using user-provided a list of genes.
It performs pathway enrichment analyses on the identified subnetworks.
pathfindR also offers functionalities to cluster enriched pathways and identify
representative pathways and to score the pathways per sample. The method is
described in detail in Ulgen E, Ozisik O, Sezerman OU. 2018. pathfindR: An R
Package for Pathway Enrichment Analysis Utilizing Active Subnetworks. bioRxiv.
<doi:10.1101/272450>.
Author: Ege Ulgen, Ozan Ozisik
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between pathfindR versions 1.2.3 dated 2018-10-26 and 1.3.0 dated 2018-11-20
pathfindR-1.2.3/pathfindR/R/enrichment.R |only pathfindR-1.2.3/pathfindR/R/input_processing.R |only pathfindR-1.2.3/pathfindR/R/parseActive.R |only pathfindR-1.2.3/pathfindR/R/pathmap.R |only pathfindR-1.2.3/pathfindR/R/pwd.R |only pathfindR-1.2.3/pathfindR/R/wrapper.R |only pathfindR-1.2.3/pathfindR/inst/rmd/all_pathways.Rmd |only pathfindR-1.2.3/pathfindR/inst/rmd/clustering.Rmd |only pathfindR-1.2.3/pathfindR/inst/rmd/genes_table.Rmd |only pathfindR-1.2.3/pathfindR/man/calculate_pwd.Rd |only pathfindR-1.2.3/pathfindR/man/choose_clusters.Rd |only pathfindR-1.2.3/pathfindR/man/parseActiveSnwSearch.Rd |only pathfindR-1.2.3/pathfindR/man/pathmap.Rd |only pathfindR-1.3.0/pathfindR/.Rinstignore | 1 pathfindR-1.3.0/pathfindR/DESCRIPTION | 12 pathfindR-1.3.0/pathfindR/MD5 | 114 ++- pathfindR-1.3.0/pathfindR/NAMESPACE | 21 pathfindR-1.3.0/pathfindR/NEWS.md | 20 pathfindR-1.3.0/pathfindR/R/active_snw_functions.R |only pathfindR-1.3.0/pathfindR/R/clustering.R |only pathfindR-1.3.0/pathfindR/R/core_functions.R |only pathfindR-1.3.0/pathfindR/R/data.R | 57 + pathfindR-1.3.0/pathfindR/R/enrichment_functions.R |only pathfindR-1.3.0/pathfindR/R/pathfindR.R | 18 pathfindR-1.3.0/pathfindR/R/scores.R | 8 pathfindR-1.3.0/pathfindR/R/visualization_functions.R |only pathfindR-1.3.0/pathfindR/build/vignette.rds |binary pathfindR-1.3.0/pathfindR/data/RA_clustered.rda |binary pathfindR-1.3.0/pathfindR/data/datalist |only pathfindR-1.3.0/pathfindR/data/example_active_snws.rda |only pathfindR-1.3.0/pathfindR/data/go_all_genes.rda |only pathfindR-1.3.0/pathfindR/data/go_all_pathways.rda |only pathfindR-1.3.0/pathfindR/data/go_bp_genes.rda |binary pathfindR-1.3.0/pathfindR/data/go_bp_pathways.rda |binary pathfindR-1.3.0/pathfindR/data/kegg_genes.rda |binary pathfindR-1.3.0/pathfindR/data/kegg_pathways.rda |binary pathfindR-1.3.0/pathfindR/data/reactome_genes.rda |binary pathfindR-1.3.0/pathfindR/data/reactome_pathways.rda |binary pathfindR-1.3.0/pathfindR/inst/doc/pathfindr_manual_exec.R |only pathfindR-1.3.0/pathfindR/inst/doc/pathfindr_manual_exec.Rmd |only pathfindR-1.3.0/pathfindR/inst/doc/pathfindr_manual_exec.html |only pathfindR-1.3.0/pathfindR/inst/doc/pathfindr_vignette.R | 22 pathfindR-1.3.0/pathfindR/inst/doc/pathfindr_vignette.Rmd | 46 - pathfindR-1.3.0/pathfindR/inst/doc/pathfindr_vignette.html | 323 ++++------ pathfindR-1.3.0/pathfindR/inst/rmd/conversion_table.Rmd |only pathfindR-1.3.0/pathfindR/inst/rmd/enriched_pathways.Rmd |only pathfindR-1.3.0/pathfindR/inst/rmd/results.Rmd | 8 pathfindR-1.3.0/pathfindR/man/RA_clustered.Rd | 4 pathfindR-1.3.0/pathfindR/man/RA_output.Rd | 6 pathfindR-1.3.0/pathfindR/man/active_snw_search.Rd |only pathfindR-1.3.0/pathfindR/man/annotate_pathway_DEGs.Rd |only pathfindR-1.3.0/pathfindR/man/calculate_pw_scores.Rd | 2 pathfindR-1.3.0/pathfindR/man/cluster_graph_vis.Rd |only pathfindR-1.3.0/pathfindR/man/cluster_pathways.Rd |only pathfindR-1.3.0/pathfindR/man/create_kappa_matrix.Rd |only pathfindR-1.3.0/pathfindR/man/enrichment.Rd | 9 pathfindR-1.3.0/pathfindR/man/enrichment_analyses.Rd |only pathfindR-1.3.0/pathfindR/man/enrichment_chart.Rd | 2 pathfindR-1.3.0/pathfindR/man/example_active_snws.Rd |only pathfindR-1.3.0/pathfindR/man/filterActiveSnws.Rd |only pathfindR-1.3.0/pathfindR/man/fuzzy_pw_clustering.Rd |only pathfindR-1.3.0/pathfindR/man/go_all_genes.Rd |only pathfindR-1.3.0/pathfindR/man/go_all_pathways.Rd |only pathfindR-1.3.0/pathfindR/man/hierarchical_pw_clustering.Rd |only pathfindR-1.3.0/pathfindR/man/hyperg_test.Rd |only pathfindR-1.3.0/pathfindR/man/input_processing.Rd | 15 pathfindR-1.3.0/pathfindR/man/input_testing.Rd | 8 pathfindR-1.3.0/pathfindR/man/kegg_genes.Rd | 4 pathfindR-1.3.0/pathfindR/man/kegg_pathways.Rd | 4 pathfindR-1.3.0/pathfindR/man/pathfindR.Rd | 18 pathfindR-1.3.0/pathfindR/man/reactome_genes.Rd | 4 pathfindR-1.3.0/pathfindR/man/reactome_pathways.Rd | 6 pathfindR-1.3.0/pathfindR/man/return_pin_path.Rd | 6 pathfindR-1.3.0/pathfindR/man/run_pathfindR.Rd | 95 +- pathfindR-1.3.0/pathfindR/man/summarize_enrichment_results.Rd |only pathfindR-1.3.0/pathfindR/man/visualize_hsa_KEGG.Rd |only pathfindR-1.3.0/pathfindR/man/visualize_pw_interactions.Rd |only pathfindR-1.3.0/pathfindR/man/visualize_pws.Rd |only pathfindR-1.3.0/pathfindR/vignettes/example_pw_vis.png |only pathfindR-1.3.0/pathfindR/vignettes/pathfindr_manual_exec.Rmd |only pathfindR-1.3.0/pathfindR/vignettes/pathfindr_vignette.Rmd | 46 - pathfindR-1.3.0/pathfindR/vignettes/pw_clustering.png |binary 82 files changed, 477 insertions(+), 402 deletions(-)
Title: Colour Palettes Based on the Scientific Colour-Maps
Description: Colour choice in information visualisation is important in order to
avoid being mislead by inherent bias in the used colour palette. The 'scico'
package provides access to the perceptually uniform and colour-blindness
friendly palettes developed by Fabio Crameri and released under the
"Scientific Colour-Maps" moniker. The package contains 24 different palettes
and includes both diverging and sequential types.
Author: Thomas Lin Pedersen [aut, cre],
Fabio Crameri [aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between scico versions 1.0.0 dated 2018-05-30 and 1.1.0 dated 2018-11-20
DESCRIPTION | 21 +++++------ MD5 | 18 +++++---- NAMESPACE | 3 + R/ggplot2_scales.R | 94 +++++++++++++++++++++++++++++++++++++++++++++++--- R/palette.R | 2 - R/scico-package.R |only R/sysdata.rda |binary README.md | 2 - man/ggplot2-scales.Rd | 42 +++++++++++++++++----- man/scico-package.Rd |only tests |only 11 files changed, 149 insertions(+), 33 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 2.6-0 dated 2018-11-05 and 2.6-1 dated 2018-11-20
DESCRIPTION | 10 +- MD5 | 14 +- R/getMeta.R | 10 ++ R/importSAQN.R | 137 +++++++-------------------- README.md | 216 +++++++++++++++++++++++++++----------------- man/importSAQN.Rd | 136 +++++++-------------------- tools/unnamed-chunk-6-1.png |binary tools/unnamed-chunk-7-1.png |binary 8 files changed, 228 insertions(+), 295 deletions(-)
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and
regression models.
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer,
Brenton Kenkel, the R Core Team, Michael Benesty, Reynald Lescarbeau,
Andrew Ziem, Luca Scrucca, Yuan Tang, Can Candan, and Tyler Hunt.
Maintainer: Max Kuhn <mxkuhn@gmail.com>
Diff between caret versions 6.0-80 dated 2018-05-26 and 6.0-81 dated 2018-11-20
DESCRIPTION | 10 - MD5 | 140 +++++++-------- R/findLinearCombos.R | 2 R/learning_curve.R | 69 ++++--- R/preProcess.R | 372 +++++++++++++++++++++--------------------- R/predict.train.R | 3 R/recipes.R | 12 - R/rfe.R | 11 - R/thresholder.R | 69 ++++++- R/train.default.R | 252 ++++++++++++++-------------- R/trainControl.R | 2 R/updates.R | 40 ++-- inst/NEWS.Rd | 14 + inst/doc/caret.Rmd | 2 inst/doc/caret.html | 4 inst/models/models.RData |binary man/BoxCoxTrans.Rd | 2 man/avNNet.Rd | 11 - man/bag.Rd | 16 - man/bagEarth.Rd | 12 - man/bagFDA.Rd | 10 - man/calibration.Rd | 8 man/caret-internal.Rd | 19 -- man/caretFuncs.Rd | 10 - man/caretSBF.Rd | 2 man/classDist.Rd | 6 man/confusionMatrix.Rd | 6 man/createDataPartition.Rd | 9 - man/diff.resamples.Rd | 6 man/dotplot.diff.resamples.Rd | 3 man/dummyVars.Rd | 8 man/gafs.default.Rd | 6 man/gafs_initial.Rd | 6 man/icr.formula.Rd | 2 man/knn3.Rd | 7 man/knnreg.Rd | 5 man/learing_curve_dat.Rd | 15 - man/lift.Rd | 6 man/maxDissim.Rd | 6 man/modelLookup.Rd | 2 man/nearZeroVar.Rd | 2 man/nullModel.Rd | 2 man/oneSE.Rd | 1 man/pcaNNet.Rd | 11 - man/plot.rfe.Rd | 6 man/plot.train.Rd | 5 man/plot.varImp.train.Rd | 1 man/plsda.Rd | 2 man/postResample.Rd | 5 man/prcomp.resamples.Rd | 1 man/preProcess.Rd | 12 - man/predict.train.Rd | 5 man/recall.Rd | 23 -- man/resamples.Rd | 10 - man/rfe.Rd | 12 - man/rfeControl.Rd | 9 - man/safs.Rd | 1 man/safsControl.Rd | 4 man/safs_initial.Rd | 5 man/sbf.Rd | 6 man/sbfControl.Rd | 4 man/sensitivity.Rd | 11 - man/spatialSign.Rd | 3 man/summary.bagEarth.Rd | 1 man/thresholder.Rd | 37 +++- man/train.Rd | 24 +- man/trainControl.Rd | 24 +- man/twoClassSim.Rd | 10 - man/varImp.Rd | 26 -- man/xyplot.resamples.Rd | 6 vignettes/caret.Rmd | 2 71 files changed, 691 insertions(+), 765 deletions(-)
Title: A Framework for Data-Driven Stochastic Disease Spread
Simulations
Description: Provides an efficient and very flexible framework to
conduct data-driven epidemiological modeling in realistic large
scale disease spread simulations. The framework integrates
infection dynamics in subpopulations as continuous-time Markov
chains using the Gillespie stochastic simulation algorithm and
incorporates available data such as births, deaths and movements
as scheduled events at predefined time-points. Using C code for
the numerical solvers and 'OpenMP' (if available) to divide work
over multiple processors ensures high performance when simulating
a sample outcome. One of our design goals was to make the package
extendable and enable usage of the numerical solvers from other R
extension packages in order to facilitate complex epidemiological
research. The package contains template models and can be extended
with user-defined models.
Author: Stefan Widgren [aut, cre] (<https://orcid.org/0000-0001-5745-2284>),
Robin Eriksson [aut] (<https://orcid.org/0000-0002-4291-712X>),
Stefan Engblom [aut] (<https://orcid.org/0000-0002-3614-1732>),
Pavol Bauer [aut] (<https://orcid.org/0000-0003-4328-7171>),
Attractive Chaos [cph] (Author of 'kvec.h', a generic dynamic array)
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between SimInf versions 6.1.0 dated 2018-08-13 and 6.2.0 dated 2018-11-20
DESCRIPTION | 8 MD5 | 60 +++--- NEWS | 22 ++ R/SimInf_events.R | 1 R/SimInf_model.R | 229 ++++++++++++----------- R/SimInf_mparse.R | 329 ++++++++++++++++++++++------------ R/check_arguments.R | 15 + R/package_skeleton.R | 348 +++++++++++++++++++++++++++--------- R/run_outer.R | 6 build/vignette.rds |binary inst/CITATION | 4 inst/doc/SimInf.Rnw | 2 inst/doc/SimInf.pdf |binary man/mparse.Rd | 42 +++- man/run.Rd | 2 src/SimInf.c | 21 +- src/solvers/SimInf_solver.c | 139 +++++++++----- src/solvers/SimInf_solver.h | 8 src/solvers/aem/SimInf_solver_aem.c | 29 ++- src/solvers/ssm/SimInf_solver_ssm.c | 22 +- tests/SEIR.R | 16 + tests/SIR.R | 12 + tests/SISe.R | 24 ++ tests/SISe3.R | 29 ++- tests/SISe3_sp.R | 55 +++++ tests/SISe_sp.R | 47 ++++ tests/SimInf_events.R | 1 tests/SimInf_model.R | 5 tests/model_builder.R | 282 +++++++++++++++++++++++++++-- tests/package_skeleton.R | 21 +- vignettes/SimInf.Rnw | 2 31 files changed, 1326 insertions(+), 455 deletions(-)
Title: Canadian Census Data and Geography from the 'CensusMapper' API
Description: Integrated, convenient, and uniform access to Canadian
Census data and geography retrieved using the 'CensusMapper' API. This package produces analysis-ready
tidy data frames and spatial data in multiple formats, as well as convenience functions
for working with Census variables, variable hierarchies, and region selection. API
keys are freely available with free registration at <https://censusmapper.ca/api>.
Census data and boundary geometries are reproduced and distributed on an "as
is" basis with the permission of Statistics Canada (Statistics Canada 2006;
2011; 2016).
Author: Jens von Bergmann [aut] (API creator and maintainer),
Dmitry Shkolnik [aut, cre] (Package maintainer, responsible for
correspondence),
Aaron Jacobs [aut]
Maintainer: Dmitry Shkolnik <shkolnikd@gmail.com>
Diff between cancensus versions 0.1.7 dated 2018-02-04 and 0.1.8 dated 2018-11-20
DESCRIPTION | 8 MD5 | 24 NEWS.md | 88 R/cancensus.R | 48 README.md | 24 build/vignette.rds |binary inst/doc/Making_maps_with_cancensus.R | 71 inst/doc/Making_maps_with_cancensus.Rmd | 20 inst/doc/Making_maps_with_cancensus.html | 4559 ------------------------------- inst/doc/cancensus.R | 30 inst/doc/cancensus.html | 161 - man/get_census.Rd | 10 vignettes/Making_maps_with_cancensus.Rmd | 20 13 files changed, 276 insertions(+), 4787 deletions(-)
Title: Q-Kernel-Based and Conditionally Negative Definite Kernel-Based
Machine Learning Tools
Description: Nonlinear machine learning tool for classification, clustering
and dimensionality reduction. It integrates 12 q-kernel functions and
14 conditional negative definite kernel functions and includes the
q-kernel and conditional negative definite kernel version of
density-based spatial clustering of applications with noise,
spectral clustering, generalized discriminant analysis, principal
component analysis, multidimensional scaling, locally linear embedding,
Sammon's mapping and t-Distributed stochastic neighbor embedding.
Author: Yusen Zhang [aut, cre] (<https://orcid.org/0000-0003-3842-1153>),
Daolin Pang [ctb],
Jinghao Wang [ctb],
Jialin Zhang [ctb]
Maintainer: Yusen Zhang <yusenzhang@126.com>
Diff between qkerntool versions 1.17 dated 2018-11-16 and 1.18 dated 2018-11-20
qkerntool-1.17/qkerntool/tests/testthat/testdbscan_norm.R |only qkerntool-1.17/qkerntool/tests/testthat/testqgda_new.R |only qkerntool-1.17/qkerntool/tests/testthat/testqsammon_new.R |only qkerntool-1.18/qkerntool/DESCRIPTION | 10 - qkerntool-1.18/qkerntool/MD5 | 14 + qkerntool-1.18/qkerntool/NEWS.md |only qkerntool-1.18/qkerntool/R/qsammon.R | 108 ++++++-------- qkerntool-1.18/qkerntool/README.md |only qkerntool-1.18/qkerntool/man/qsammon.Rd | 22 +- qkerntool-1.18/qkerntool/tests/testthat/testdbscan.R |only qkerntool-1.18/qkerntool/tests/testthat/testqgda.R |only qkerntool-1.18/qkerntool/tests/testthat/testqsammon.R |only 12 files changed, 73 insertions(+), 81 deletions(-)
Title: Multivariate Methods Based on the Oja Median and Related
Concepts
Description: Functions to calculate the Oja median, Oja signs and ranks and methods based upon them.
Author: Daniel Fischer, Karl Mosler, Jyrki Möttönen, Klaus Nordhausen, Oleksii Pokotylo, Daniel Vogel
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between OjaNP versions 0.9-10 dated 2018-07-13 and 0.9-12 dated 2018-11-20
DESCRIPTION | 8 +++---- MD5 | 8 +++---- man/OjaNP-package.Rd | 4 +-- src/bounded_search.cpp | 2 - src/matrix.h | 56 +++++++++++++++++++++++-------------------------- 5 files changed, 38 insertions(+), 40 deletions(-)
Title: Data Structures, Summaries, and Visualisations for Missing Data
Description: Missing values are ubiquitous in data and need to be explored and
handled in the initial stages of analysis. 'naniar' provides data structures
and functions that facilitate the plotting of missing values and examination
of imputations. This allows missing data dependencies to be explored with
minimal deviation from the common work patterns of 'ggplot2' and tidy data.
Author: Nicholas Tierney [aut, cre] (<https://orcid.org/0000-0003-1460-8722>),
Di Cook [aut] (<https://orcid.org/0000-0002-3813-7155>),
Miles McBain [aut] (<https://orcid.org/0000-0003-2865-2548>),
Colin Fay [aut] (<https://orcid.org/0000-0001-7343-1846>),
Mitchell O'Hara-Wild [ctb],
Jim Hester [ctb],
Luke Smith [ctb]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>
Diff between naniar versions 0.4.0.0 dated 2018-09-10 and 0.4.1 dated 2018-11-20
DESCRIPTION | 8 +-- MD5 | 56 ++++++++++++------------ NEWS.md | 9 +++ R/add-cols.R | 64 +++++----------------------- R/add-n-prop-miss.R | 8 --- R/cast-shadows.R | 14 +----- R/nabular.R | 2 R/shadow-recode.R | 10 +--- R/shadows.R | 6 -- R/utils.R | 23 +++------- inst/doc/exploring-imputed-values.html | 14 ++---- inst/doc/getting-started-w-naniar.html | 14 ++---- inst/doc/naniar-visualisation.Rmd | 2 inst/doc/naniar-visualisation.html | 16 +++---- inst/doc/replace-with-na.html | 14 ++---- inst/doc/special-missing-values.html | 14 ++---- man/figures/README-facet-by-month-1.png |binary man/figures/README-geom-miss-point-1.png |binary man/figures/README-gg-miss-span-1.png |binary man/figures/README-gg-miss-upset-1.png |binary man/figures/README-gg-miss-var-1.png |binary man/figures/README-regular-geom-point-1.png |binary man/figures/README-shadow-impute-1.png |binary man/figures/README-shadow-w-ggplot-1.png |binary man/gg_miss_upset.Rd | 2 man/impute_below_at.Rd | 2 man/scoped-impute_mean.Rd | 2 man/scoped-impute_median.Rd | 2 vignettes/naniar-visualisation.Rmd | 2 29 files changed, 112 insertions(+), 172 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-09-19 2.1
2017-05-16 2.0
2016-12-29 1.3.1
2016-06-03 1.1
2016-03-03 0.3
Title: Number of Newly Discovered Rare Species Estimation
Description: A Bayesian-weighted estimator and two unweighted estimators are
developed to estimate the number of newly found rare species in additional
ecological samples. Among these methods, the Bayesian-weighted estimator
and an unweighted (Chao-derived) estimator are of high accuracy and
recommended for practical applications.
Technical details of the proposed estimators have been well described
in the following paper: Shen TJ, Chen YH (2018) A Bayesian
weighted approach to predicting the number of newly discovered
rare species. Conservation Biology, In press.
Author: Youhua Chen,Tsung-Jen Shen
Maintainer: Youhua Chen <haydi@126.com>
Diff between RSE versions 1.2 dated 2018-10-19 and 1.3 dated 2018-11-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/RSE.R | 25 ++++++++++++++----------- build/partial.rdb |binary 4 files changed, 21 insertions(+), 18 deletions(-)
Title: Interface to the 'Handsontable.js' Library
Description: An R interface to the 'Handsontable' JavaScript library, which is a
minimalist Excel-like data grid editor. See <https://handsontable.com/> for details.
Author: Jonathan Owen [aut, cre, cph],
Jeff Allen [ctb],
Yihui Xie [ctb],
Enzo Martoglio [ctb],
Inberg Ger [ctb],
Warpechowski Marcin [ctb, cph] (Handsontable.js library),
Handsoncode sp. z o.o. [ctb, cph] (Handsontable.js library),
Aisch Gregor [ctb, cph] (Chroma.js library),
Företagsplatsen [ctb, cph] (Numbro.js library),
Draper Adam [ctb, cph] (Numeral.js library),
Wood Tim [ctb, cph] (Moment.js library),
Chernev Iskren [ctb, cph] (Moment.js library),
Moment.js contributors [ctb, cph] (Moment.js library),
Bushell David [ctb, cph] (Pikaday.js library),
jQuery Foundation [ctb, cph] (jQuery.js library),
Splunk Inc [ctb, cph] (Sparkline.js library),
Russell Kent [ctb, cph] (Sparkline.js library),
Rohan Jon [ctb, cph] (ZeroClipboard library),
Greene James [ctb, cph] (ZeroClipboard library)
Maintainer: Jonathan Owen <jonathanro@gmail.com>
Diff between rhandsontable versions 0.3.6 dated 2018-01-27 and 0.3.7 dated 2018-11-20
rhandsontable-0.3.6/rhandsontable/inst/htmlwidgets/lib/numbro/languages.js |only rhandsontable-0.3.7/rhandsontable/DESCRIPTION | 8 rhandsontable-0.3.7/rhandsontable/MD5 | 40 +- rhandsontable-0.3.7/rhandsontable/NEWS | 7 rhandsontable-0.3.7/rhandsontable/R/rhandsontable.R | 73 ++--- rhandsontable-0.3.7/rhandsontable/R/zzz.R |only rhandsontable-0.3.7/rhandsontable/build/vignette.rds |binary rhandsontable-0.3.7/rhandsontable/inst/doc/intro_rhandsontable.Rmd | 2 rhandsontable-0.3.7/rhandsontable/inst/doc/intro_rhandsontable.html | 137 +++++----- rhandsontable-0.3.7/rhandsontable/inst/htmlwidgets/lib/handsontable/all.min.js |only rhandsontable-0.3.7/rhandsontable/inst/htmlwidgets/lib/handsontable/handsontable.full.min.css | 10 rhandsontable-0.3.7/rhandsontable/inst/htmlwidgets/lib/handsontable/handsontable.full.min.js | 15 - rhandsontable-0.3.7/rhandsontable/inst/htmlwidgets/lib/numbro/languages.min.js |only rhandsontable-0.3.7/rhandsontable/inst/htmlwidgets/rhandsontable.js | 23 + rhandsontable-0.3.7/rhandsontable/inst/htmlwidgets/rhandsontable.yaml | 12 rhandsontable-0.3.7/rhandsontable/man/hot_col.Rd | 7 rhandsontable-0.3.7/rhandsontable/man/hot_context_menu.Rd | 5 rhandsontable-0.3.7/rhandsontable/man/hot_heatmap.Rd | 4 rhandsontable-0.3.7/rhandsontable/man/hot_row.Rd | 11 rhandsontable-0.3.7/rhandsontable/man/hot_rows.Rd | 3 rhandsontable-0.3.7/rhandsontable/man/hot_table.Rd | 8 rhandsontable-0.3.7/rhandsontable/man/hot_validate_numeric.Rd | 4 rhandsontable-0.3.7/rhandsontable/vignettes/intro_rhandsontable.Rmd | 2 23 files changed, 196 insertions(+), 175 deletions(-)
Title: Quality Control Charts for 'ggplot'
Description: Plot single and faceted type quality control charts
for 'ggplot'.
Author: Kenith Grey
Maintainer: Kenith Grey <kenithgrey@r-bar.net>
Diff between ggQC versions 0.0.2 dated 2018-01-30 and 0.0.3 dated 2018-11-20
DESCRIPTION | 8 MD5 | 61 +++-- NAMESPACE | 16 + R/02_QC_FUN_Capability.R |only R/03_Summay_FUNs.R | 6 R/03_Summay__Capability_FUNs.R |only R/04_facet_qc_violations.R | 35 ++- R/04_stat_mR.r | 5 R/04_stat_qc.R | 360 ++++++++++++++++++++++++++++--- R/04_stat_qc_capability.R |only R/04_stat_qc_violations.r | 45 +++ build/vignette.rds |binary inst/doc/XbarR_HOTTO.html | 16 - inst/doc/XmR_HOWTO.R | 31 +- inst/doc/XmR_HOWTO.Rmd | 33 +- inst/doc/XmR_HOWTO.html | 61 ++--- man/Cp.Rd |only man/Cpk.Rd |only man/DNS.Rd |only man/LD.Rd |only man/Pp.Rd |only man/Ppk.Rd |only man/QC_Capability.Rd |only man/QC_Lines.Rd | 8 man/UD.Rd |only man/capability.summary.Rd |only man/process_tolerance.Rd |only man/stat_QC.Rd | 82 +++++-- man/stat_QC_CAPA.Rd |only man/stat_QC_Capability.Rd |only man/stat_QC_cap_hlabels.Rd |only man/stat_QC_cap_hlines.Rd |only man/stat_QC_cap_summary.Rd |only man/stat_QC_cap_vlabels.Rd |only man/stat_QC_cap_vlines.Rd |only man/stat_QC_labels.Rd | 46 ++- man/stat_mR.Rd | 34 +- man/stat_pareto.Rd | 38 +-- man/stat_qc_violations.Rd | 50 ++-- tests/testthat/Wheeler118_result.csv |only tests/testthat/test_capability_methods.r |only tests/testthat/wheeler_USPC_118.csv |only vignettes/XmR_HOWTO.Rmd | 33 +- 43 files changed, 725 insertions(+), 243 deletions(-)
Title: Easy Use of 'GADM' Shapefiles
Description: Manipulate, assemble, export <http://www.gadm.org> shapefiles. Create choropleth, heatmaps, dots plot, proportional dots and more.
Author: Jean Pierre Decorps [aut, cre],
Morgane Vallee [ctb]
Maintainer: Jean Pierre Decorps <jp.decorps@epiconcept.fr>
Diff between GADMTools versions 2.2-2 dated 2018-07-04 and 3.0-1 dated 2018-11-20
DESCRIPTION | 13 - MD5 | 46 +++- NAMESPACE | 9 NEWS | 27 ++ R/01_GADMTools.R | 400 +++++++++++++----------------------------- R/05_choropleth.R | 50 +++-- R/06_json.choropleth.R | 4 R/07_fast.choropleth.R | 4 R/09_dots.R |only R/11_propDots.R |only R/12_isopleth.R |only R/getBackground.R |only README.md | 23 +- build/vignette.rds |binary inst/doc/Using_GADMTools.R | 31 +++ inst/doc/Using_GADMTools.Rmd | 100 ++++++++++ inst/doc/Using_GADMTools.pdf |binary man/GADMTools-package.Rd | 4 man/dots.Rd | 3 man/figures |only man/gadm.getBackground.Rd |only man/gadm.longTo360.Rd |only man/gadm.union.Rd |only man/isopleth.Rd | 8 man/subset.Rd | 5 vignettes/Rplot05.5.png |only vignettes/Rplot_7.7.png |only vignettes/Rplot_8.8.png |only vignettes/Rplot_8.9.png |only vignettes/Using_GADMTools.Rmd | 100 ++++++++++ 30 files changed, 482 insertions(+), 345 deletions(-)
Title: Data from the GLM Book by Dobson and Barnett
Description: Example datasets from the book "An Introduction to Generalised Linear Models" (Year: 2018, ISBN:9781138741515) by Dobson and Barnett.
Author: Adrian Barnett [aut, cre]
Maintainer: Adrian Barnett <a.barnett@qut.edu.au>
Diff between dobson versions 0.3 dated 2018-05-09 and 0.4 dated 2018-11-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- data/plant.dried.rda |binary man/plant.dried.Rd | 12 ++++-------- 4 files changed, 10 insertions(+), 14 deletions(-)