Title: Minimax and Minimax Projection Designs
Description: Provides two main functions, minimax() and miniMaxPro(), for computing minimax
and minimax projection designs using the minimax clustering algorithm in Mak and
Joseph (2018) <DOI:10.1080/10618600.2017.1302881>. Current design region options
include the unit hypercube ("hypercube"), the unit simplex ("simplex"), the unit ball
("ball"), as well as user-defined constraints on the unit hypercube ("custom"). Minimax
designs can also be computed on user-provided images using the function minimax.map().
Design quality can be assessed using the function mMdist(), which computes the minimax
(fill) distance of a design.
Author: Simon Mak
Maintainer: Simon Mak <smak6@gatech.edu>
Diff between minimaxdesign versions 0.1.3 dated 2017-12-11 and 0.1.4 dated 2019-05-06
minimaxdesign-0.1.3/minimaxdesign/man/mMcPSO.Rd |only minimaxdesign-0.1.3/minimaxdesign/man/mMcPSO_map.Rd |only minimaxdesign-0.1.4/minimaxdesign/DESCRIPTION | 23 minimaxdesign-0.1.4/minimaxdesign/MD5 | 29 - minimaxdesign-0.1.4/minimaxdesign/NAMESPACE | 5 minimaxdesign-0.1.4/minimaxdesign/R/RcppExports.R | 26 - minimaxdesign-0.1.4/minimaxdesign/R/criteria.R |only minimaxdesign-0.1.4/minimaxdesign/R/minimax.R | 241 ++++------ minimaxdesign-0.1.4/minimaxdesign/R/transform.R |only minimaxdesign-0.1.4/minimaxdesign/man/CtoB.Rd | 2 minimaxdesign-0.1.4/minimaxdesign/man/mMdist.Rd |only minimaxdesign-0.1.4/minimaxdesign/man/miniMaxPro.Rd | 41 - minimaxdesign-0.1.4/minimaxdesign/man/minimax.Rd |only minimaxdesign-0.1.4/minimaxdesign/man/minimax.map.Rd |only minimaxdesign-0.1.4/minimaxdesign/man/minimaxdesign-package.Rd | 52 +- minimaxdesign-0.1.4/minimaxdesign/src/Makevars | 2 minimaxdesign-0.1.4/minimaxdesign/src/RcppExports.cpp | 10 minimaxdesign-0.1.4/minimaxdesign/src/init.c | 32 - minimaxdesign-0.1.4/minimaxdesign/src/kmeanspso.cpp | 109 +++- 19 files changed, 320 insertions(+), 252 deletions(-)
Title: Cross-Platform File System Operations Based on 'libuv'
Description: A cross-platform interface to file system operations, built on
top of the 'libuv' C library.
Author: Jim Hester [aut, cre],
Hadley Wickham [aut],
libuv project contributors [cph] (libuv library),
Joyent, Inc. and other Node contributors [cph] (libuv library),
RStudio [cph, fnd]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between fs versions 1.3.0 dated 2019-05-02 and 1.3.1 dated 2019-05-06
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 6 ++++++ src/RcppExports.cpp | 4 ++-- src/dir.cc | 9 +++++++-- tests/testthat/helper.R | 6 +++++- tests/testthat/test-create.R | 1 + tests/testthat/test-list.R | 2 +- tests/testthat/test-path.R | 14 ++++++++++---- tests/testthat/test-sanitize.R | 2 +- 10 files changed, 45 insertions(+), 23 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 1.1.0 dated 2018-11-20 and 1.1.1 dated 2019-05-06
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Title: Semiparametric Competing Risks Regression under Interval
Censoring
Description: Semiparametric regression models on the cumulative incidence function with interval-censored competing risks data as described in Bakoyannis, Yu, & Yiannoutsos (2017) <doi:10.1002/sim.7350>. The main function fits the proportional subdistribution hazards model (Fine-Gray model), the proportional odds model, and other models that belong to the class of semiparametric generalized odds rate transformation models.
Author: Giorgos Bakoyannis <gbakogia@iu.edu>, Jun Park <jp84@iu.edu>
Maintainer: Jun Park <jp84@iu.edu>
Diff between intccr versions 1.1.2 dated 2019-04-29 and 1.1.3 dated 2019-05-06
intccr-1.1.2/intccr/inst/doc/vig_intccr.Rnw |only intccr-1.1.2/intccr/inst/doc/vig_intccr.pdf |only intccr-1.1.2/intccr/inst/vig_intccr.pdf |only intccr-1.1.2/intccr/vignettes/vig_intccr.Rnw |only intccr-1.1.3/intccr/DESCRIPTION | 10 +-- intccr-1.1.3/intccr/MD5 | 16 ++--- intccr-1.1.3/intccr/NAMESPACE | 4 - intccr-1.1.3/intccr/R/bssmle_se.R | 76 +++++++++------------------ intccr-1.1.3/intccr/build/vignette.rds |binary intccr-1.1.3/intccr/inst/doc/intccr.Rnw |only intccr-1.1.3/intccr/inst/doc/intccr.pdf |only intccr-1.1.3/intccr/inst/intccr.pdf |only intccr-1.1.3/intccr/vignettes/intccr.Rnw |only 13 files changed, 39 insertions(+), 67 deletions(-)
Title: Miscellaneous Functions from Alexey Shipunov
Description: A collection of functions for data manipulation, plotting and statistical computing, to use separately or with the book "Visual Statistics. Use R!": Shipunov (2019) <http://ashipunov.info/shipunov/software/r/r-en.htm>.
Most useful functions are probably Bclust(), Jclust() and BootA() which bootstrap hierarchical clustering; Recode...() which multiple recode in a fast, flexible and simple way; Misclass() which outputs confusion matrix even if classes are not concerted;
Overlap() which calculates overlaps of convex hulls from any projection; and Pleiad() which is fast and flexible correlogram. In fact, there are much more useful functions, please see documentation.
Author: Alexey Shipunov [aut, cre], Paul Murrell [ctb], Marcello D'Orazio [ctb], Stephen Turner [ctb], Eugeny Altshuler [ctb], Roland Rau [ctb], Marcus W Beck [ctb], Sebastian Gibb [ctb], Weiliang Qiu [ctb], Emmanuel Paradis [ctb], R Core Team [ctb]
Maintainer: Alexey Shipunov <dactylorhiza@gmail.com>
Diff between shipunov versions 1.0 dated 2019-04-01 and 1.1 dated 2019-05-06
shipunov-1.0/shipunov/man/Draw.arrow.Rd |only shipunov-1.0/shipunov/man/Histp.Rd |only shipunov-1.1/shipunov/DESCRIPTION | 19 + shipunov-1.1/shipunov/MD5 | 78 ++++--- shipunov-1.1/shipunov/NAMESPACE | 11 - shipunov-1.1/shipunov/NEWS | 19 + shipunov-1.1/shipunov/R/asmisc.r | 239 ---------------------- shipunov-1.1/shipunov/R/bclust.r |only shipunov-1.1/shipunov/R/class_sample.r |only shipunov-1.1/shipunov/R/classproj.r |only shipunov-1.1/shipunov/R/gencldata.r |only shipunov-1.1/shipunov/R/gmoon.r | 13 - shipunov-1.1/shipunov/R/gower_dist.r | 2 shipunov-1.1/shipunov/R/hulls.r |only shipunov-1.1/shipunov/R/infill.r | 2 shipunov-1.1/shipunov/R/jclust.r |only shipunov-1.1/shipunov/R/misclass.r |only shipunov-1.1/shipunov/R/overlap.r |only shipunov-1.1/shipunov/R/root1.r |only shipunov-1.1/shipunov/R/updist.r |only shipunov-1.1/shipunov/TODO | 54 ++++ shipunov-1.1/shipunov/inst/bin/Rresults | 4 shipunov-1.1/shipunov/man/Bclabels.Rd |only shipunov-1.1/shipunov/man/Bclust.Rd |only shipunov-1.1/shipunov/man/BestOverlap.Rd |only shipunov-1.1/shipunov/man/BootKNN.Rd | 1 shipunov-1.1/shipunov/man/Boxplots.Rd | 2 shipunov-1.1/shipunov/man/Class.sample.Rd |only shipunov-1.1/shipunov/man/Classproj.Rd |only shipunov-1.1/shipunov/man/Ellipses.Rd | 2 shipunov-1.1/shipunov/man/Files.Rd | 4 shipunov-1.1/shipunov/man/Gen.cl.data.Rd |only shipunov-1.1/shipunov/man/Hcl2mat.Rd |only shipunov-1.1/shipunov/man/Hcoords.Rd |only shipunov-1.1/shipunov/man/Histr.Rd | 2 shipunov-1.1/shipunov/man/Hulls.Rd | 30 ++ shipunov-1.1/shipunov/man/Jclust.Rd | 20 + shipunov-1.1/shipunov/man/Miney.Rd | 2 shipunov-1.1/shipunov/man/Misclass.Rd | 37 ++- shipunov-1.1/shipunov/man/Overlap.Rd | 23 +- shipunov-1.1/shipunov/man/Pleiad.Rd | 8 shipunov-1.1/shipunov/man/Ploth.Rd | 1 shipunov-1.1/shipunov/man/Recode.Rd | 1 shipunov-1.1/shipunov/man/Root1.Rd |only shipunov-1.1/shipunov/man/Rresults.Rd | 10 shipunov-1.1/shipunov/man/Rro.test.Rd | 3 shipunov-1.1/shipunov/man/Tobin.Rd | 2 shipunov-1.1/shipunov/man/Toclip.Rd | 2 shipunov-1.1/shipunov/man/Updist.Rd |only shipunov-1.1/shipunov/man/pairwise.Eff.Rd | 6 shipunov-1.1/shipunov/man/pairwise.Table2.test.Rd | 3 51 files changed, 244 insertions(+), 356 deletions(-)
Title: Bayesian Estimation of the Evolutionary Rate Matrix
Description: Estimates the evolutionary rate matrix (R) using Markov chain Monte Carlo (MCMC) as described in Caetano and Harmon (2017) <doi:10.1111/2041-210X.12826>. The package has functions to run MCMC chains, plot results, evaluate convergence, and summarize posterior distributions.
Author: Daniel Caetano [aut, cre],
Luke Harmon [aut]
Maintainer: Daniel Caetano <caetanods1@gmail.com>
Diff between ratematrix versions 1.1 dated 2018-10-30 and 1.2 dated 2019-05-06
ratematrix-1.1/ratematrix/inst/doc/Intro_on_the_package.pdf |only ratematrix-1.1/ratematrix/inst/doc/Making_prior_on_ratematrix.pdf |only ratematrix-1.1/ratematrix/inst/doc/Set_custom_starting_point.pdf |only ratematrix-1.2/ratematrix/DESCRIPTION | 8 ratematrix-1.2/ratematrix/MD5 | 68 - ratematrix-1.2/ratematrix/R/RcppExports.R | 12 ratematrix-1.2/ratematrix/R/continueMCMC.R | 9 ratematrix-1.2/ratematrix/R/logAnalyzer.R | 2 ratematrix-1.2/ratematrix/R/mergePosterior.R | 6 ratematrix-1.2/ratematrix/R/multRegimeJointMCMC.R | 29 ratematrix-1.2/ratematrix/R/multRegimeMCMC.R | 24 ratematrix-1.2/ratematrix/R/multiplierProposal.R | 8 ratematrix-1.2/ratematrix/R/ratematrixJointMCMC.R | 18 ratematrix-1.2/ratematrix/R/ratematrixMCMC.R | 42 ratematrix-1.2/ratematrix/R/readMCMC.R | 6 ratematrix-1.2/ratematrix/R/singleRegimeMCMC.R | 8 ratematrix-1.2/ratematrix/README.md | 42 ratematrix-1.2/ratematrix/build/vignette.rds |binary ratematrix-1.2/ratematrix/data/anoles.RData |binary ratematrix-1.2/ratematrix/data/centrarchidae.RData |binary ratematrix-1.2/ratematrix/inst/doc/Intro_on_the_package.Rmd | 2 ratematrix-1.2/ratematrix/inst/doc/Intro_on_the_package.html |only ratematrix-1.2/ratematrix/inst/doc/Making_prior_on_ratematrix.Rmd | 2 ratematrix-1.2/ratematrix/inst/doc/Making_prior_on_ratematrix.html |only ratematrix-1.2/ratematrix/inst/doc/Set_custom_starting_point.Rmd | 4 ratematrix-1.2/ratematrix/inst/doc/Set_custom_starting_point.html |only ratematrix-1.2/ratematrix/man/logAnalyzer.Rd | 2 ratematrix-1.2/ratematrix/man/plotRatematrix.Rd | 4 ratematrix-1.2/ratematrix/man/plotRootValue.Rd | 8 ratematrix-1.2/ratematrix/man/ratematrixJointMCMC.Rd | 20 ratematrix-1.2/ratematrix/man/ratematrixMCMC.Rd | 23 ratematrix-1.2/ratematrix/man/readMCMC.Rd | 6 ratematrix-1.2/ratematrix/man/testRatematrix.Rd | 3 ratematrix-1.2/ratematrix/src/MultRegimeMCMC.cpp | 543 +++++----- ratematrix-1.2/ratematrix/src/RcppExports.cpp | 69 - ratematrix-1.2/ratematrix/vignettes/Intro_on_the_package.Rmd | 2 ratematrix-1.2/ratematrix/vignettes/Making_prior_on_ratematrix.Rmd | 2 ratematrix-1.2/ratematrix/vignettes/Set_custom_starting_point.Rmd | 4 38 files changed, 575 insertions(+), 401 deletions(-)
Title: Estimating Regional Trends of a Prevalence from a DHS
Description: Spatial estimation of a prevalence surface
or a relative risks surface, using data from a Demographic and Health
Survey (DHS) or an analog survey, see Larmarange et al. (2011)
<doi:10.4000/cybergeo.24606>.
Author: Joseph Larmarange [aut, cre] (<https://orcid.org/0000-0001-7097-700X>)
Maintainer: Joseph Larmarange <joseph.larmarange@ird.fr>
Diff between prevR versions 3.3 dated 2016-02-23 and 3.4.0 dated 2019-05-06
DESCRIPTION | 28 MD5 | 104 +-- NAMESPACE | 13 NEWS.md |only R/as.prevR.r | 4 R/changeproj.prevR.r | 1 R/create.boundary.prevR.r | 4 R/direct.label_prevR.r | 15 R/export.prevR.r | 25 R/eyefit.prevR.r | 1 R/import.dhs.prevR.r | 4 R/kde.prevR.r | 7 R/krige.prevR.r | 18 R/plot.prevR.r | 4 R/prevR-package.r | 14 R/print.prevR.r | 1 R/quick.prevR.r | 26 R/setClass.prevR.r | 2 R/show.prevR.r | 1 R/summary.prevR.r | 1 R/theme_prevR.r | 5 build |only data/TMWorldBorders.rda |binary data/fdhs.rda |binary inst/doc |only man/NA.outside.SpatialPolygons.Rd | 1 man/Noptim.Rd | 1 man/TMWorldBorders.Rd | 1 man/as.SpatialGrid.Rd | 6 man/as.data.frame.prevR.Rd | 3 man/as.prevR.Rd | 6 man/changeproj-prevR-method.Rd | 4 man/create.boundary.Rd | 1 man/direct.label_prevR.Rd | 1 man/export-prevR-method.Rd | 18 man/fdhs.Rd | 1 man/import.dhs.Rd | 3 man/is.prevR.Rd | 1 man/kde-prevR-method.Rd | 8 man/krige-ANY-prevR-method.Rd | 20 man/plot-prevR-missing-method.Rd | 9 man/point.in.SpatialPolygons.Rd | 1 man/prevR-class.Rd | 3 man/prevR-package.Rd | 21 man/prevR.colors.Rd | 6 man/print-prevR-method.Rd | 3 man/quick.prevR.Rd | 9 man/rings-prevR-method.Rd | 3 man/show-prevR-method.Rd | 3 man/summary-prevR-method.Rd | 9 man/theme_prevR.Rd | 1 man/xyz2dataframe.Rd | 1 po/R-fr.po | 1272 +++++++++++++++++++------------------- vignettes |only 54 files changed, 856 insertions(+), 838 deletions(-)
Title: Importing 'SVG' Graphics
Description: Functions for importing external vector images and
drawing them as part of 'R' plots. This package is different from the
'grImport' package because, where that package imports 'PostScript'
format images, this package imports 'SVG' format images. Furthermore,
this package imports a specific subset of 'SVG', so external images
must be preprocessed using a package like 'rsvg' to produce 'SVG'
that this package can import. 'SVG' features that are not supported
by 'R' graphics, e.g., gradient fills, can be imported and then
exported via the 'gridSVG' package.
Author: Simon Potter [aut],
Paul Murrell [ctb, cre] (<https://orcid.org/0000-0002-3224-8858>)
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between grImport2 versions 0.1-4 dated 2018-03-20 and 0.1-5 dated 2019-05-06
DESCRIPTION | 8 +++++--- MD5 | 14 +++++++------- R/grid.picture.R | 4 ++-- R/grobify.R | 4 ++-- R/grobs.R | 4 ++-- inst/NEWS.Rd | 8 ++++++++ man/grid.picture.Rd | 6 +++++- tests/test-paths.R | 19 +++++++++++++------ 8 files changed, 44 insertions(+), 23 deletions(-)
Title: Test Shiny Apps
Description: For automated testing of Shiny applications, using a headless
browser, driven through 'WebDriver'.
Author: Winston Chang [aut, cre],
Gábor Csárdi [aut]
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shinytest versions 1.3.0 dated 2018-05-07 and 1.3.1 dated 2019-05-06
DESCRIPTION | 10 MD5 | 65 +-- NEWS.md | 19 R/debugging.R | 19 R/initialize.R | 9 R/install.R | 6 R/recorder.R | 83 +--- R/set-inputs.R | 19 R/shiny-driver.R | 15 R/widget.R | 2 README.md | 2 inst/js/shiny-tracer.js | 39 + inst/recorder/app.R | 200 +++++++--- inst/recorder/recorder.js | 44 +- inst/recorder/www/inject-recorder.js | 53 +- man/ShinyDriver.Rd | 7 man/Widget.Rd | 2 man/dependenciesInstalled.Rd | 4 man/diffviewer_widget.Rd | 3 man/expectUpdate.Rd | 4 man/recordTest.Rd | 12 tests/testthat/recorded_tests/041-dynamic-ui/tests/mytest-expected/001.json | 3 tests/testthat/recorded_tests/041-dynamic-ui/tests/mytest-expected/002.json | 3 tests/testthat/recorded_tests/041-dynamic-ui/tests/mytest-expected/003.json | 3 tests/testthat/recorded_tests/041-dynamic-ui/tests/mytest-expected/004.json | 3 tests/testthat/recorded_tests/041-dynamic-ui/tests/mytest-expected/005.json | 4 tests/testthat/recorded_tests/041-dynamic-ui/tests/mytest-expected/006.json | 4 tests/testthat/recorded_tests/inline-img-src/tests/mytest-expected/001.json | 96 ++-- tests/testthat/recorded_tests/rmd-prerendered/tests/mytest-expected/001.json | 51 +- tests/testthat/recorded_tests/rmd-prerendered/tests/mytest-expected/002.json | 51 +- tests/testthat/recorded_tests/rmd/tests/mytest-expected/001.json | 54 +- tests/testthat/recorded_tests/rmd/tests/mytest-expected/002.json | 53 +- tests/testthat/test-helper-rng.R |only tests/testthat/test-list-widgets.R | 2 34 files changed, 591 insertions(+), 353 deletions(-)
Title: Tools for Data Manipulation and Testing
Description: This is a set of simple utilities for various data
manipulation and testing tasks. The goal is to use core R tools well,
without bringing in many dependencies. Main areas of interest are
semi-automated data frame manipulation, such as converting factors in
multiple binary indicator columns. There are testing functions which
provide 'testthat' expectations to permute arguments to function
calls. There are functions and data to test extreme numbers, dates,
and bad input of various kinds which should allow testing failure and
corner cases, which can be used for fuzzing your functions. The test
suite has many examples of usage.
Author: Jack O. Wasey [aut, cre, cph] (<https://orcid.org/0000-0003-3738-4637>)
Maintainer: Jack O. Wasey <jack@jackwasey.com>
Diff between jwutil versions 1.2.1 dated 2018-06-11 and 1.2.3 dated 2019-05-06
jwutil-1.2.1/jwutil/R/get_na_fields.r |only jwutil-1.2.1/jwutil/R/zero_na.r |only jwutil-1.2.1/jwutil/inst/include |only jwutil-1.2.1/jwutil/man/allIsInteger.Rd |only jwutil-1.2.1/jwutil/man/allIsNumeric.Rd |only jwutil-1.2.1/jwutil/man/areNumeric.Rd |only jwutil-1.2.1/jwutil/man/asNumericNoWarn.Rd |only jwutil-1.2.1/jwutil/man/countNonNaPairs.Rd |only jwutil-1.2.1/jwutil/man/dropRowsWithNAField.Rd |only jwutil-1.2.1/jwutil/man/factor_to_df_logical.Rd |only jwutil-1.2.1/jwutil/man/getNAFields.Rd |only jwutil-1.2.1/jwutil/man/set_attr_in_place.Rd |only jwutil-1.2.1/jwutil/man/strMultiMatch.Rd |only jwutil-1.2.1/jwutil/man/stripForFormula.Rd |only jwutil-1.2.1/jwutil/src/attr.cpp |only jwutil-1.2.1/jwutil/src/omp.cpp |only jwutil-1.2.1/jwutil/src/omp.h |only jwutil-1.2.1/jwutil/src/registration.c |only jwutil-1.2.3/jwutil/DESCRIPTION | 45 - jwutil-1.2.3/jwutil/MD5 | 190 +++--- jwutil-1.2.3/jwutil/NAMESPACE | 34 - jwutil-1.2.3/jwutil/NEWS.md |only jwutil-1.2.3/jwutil/R/RcppExports.R | 62 -- jwutil-1.2.3/jwutil/R/as_char_no_warn.r | 12 jwutil-1.2.3/jwutil/R/char.r | 156 +++-- jwutil-1.2.3/jwutil/R/df.r | 62 +- jwutil-1.2.3/jwutil/R/drop_duplicate_fields.R | 26 jwutil-1.2.3/jwutil/R/env.r | 13 jwutil-1.2.3/jwutil/R/factor_nosort.r | 11 jwutil-1.2.3/jwutil/R/factor_to_df_logical.r | 74 +- jwutil-1.2.3/jwutil/R/file.r | 40 - jwutil-1.2.3/jwutil/R/filter_better.r | 12 jwutil-1.2.3/jwutil/R/get_factor_fields.r | 3 jwutil-1.2.3/jwutil/R/get_numeric_fields.r | 6 jwutil-1.2.3/jwutil/R/list.r | 37 + jwutil-1.2.3/jwutil/R/logical_to_binary.r | 96 ++- jwutil-1.2.3/jwutil/R/match_multi.R |only jwutil-1.2.3/jwutil/R/merge_better.r | 107 ++- jwutil-1.2.3/jwutil/R/na.r |only jwutil-1.2.3/jwutil/R/pgo.R |only jwutil-1.2.3/jwutil/R/print_percent.R |only jwutil-1.2.3/jwutil/R/read_zip_url.r | 22 jwutil-1.2.3/jwutil/R/scan-build.R |only jwutil-1.2.3/jwutil/R/testing.r | 88 +-- jwutil-1.2.3/jwutil/R/to_data_raw.r | 27 jwutil-1.2.3/jwutil/R/update_github_pkgs.r | 2 jwutil-1.2.3/jwutil/R/util.r | 458 ++++++++++------ jwutil-1.2.3/jwutil/README.md | 5 jwutil-1.2.3/jwutil/build/vignette.rds |binary jwutil-1.2.3/jwutil/inst/doc/testing.html | 347 ++++++++++-- jwutil-1.2.3/jwutil/man/affixFields.Rd | 4 jwutil-1.2.3/jwutil/man/as_numeric_nowarn.Rd |only jwutil-1.2.3/jwutil/man/bang_dollar.Rd |only jwutil-1.2.3/jwutil/man/binary_col_names.Rd | 48 + jwutil-1.2.3/jwutil/man/build_formula.Rd | 1 jwutil-1.2.3/jwutil/man/combn_subset.Rd | 5 jwutil-1.2.3/jwutil/man/countIsNa.Rd | 2 jwutil-1.2.3/jwutil/man/countNotNumeric.Rd | 2 jwutil-1.2.3/jwutil/man/drop_duplicate_fields.Rd | 12 jwutil-1.2.3/jwutil/man/drop_rows_with_na.Rd |only jwutil-1.2.3/jwutil/man/expect_that_combine_all_args.Rd | 22 jwutil-1.2.3/jwutil/man/factor_nosort.Rd | 7 jwutil-1.2.3/jwutil/man/factor_to_df.Rd |only jwutil-1.2.3/jwutil/man/fastIntToString.Rd | 8 jwutil-1.2.3/jwutil/man/fastIntToStringRcpp.Rd |only jwutil-1.2.3/jwutil/man/fix_na_ish.Rd |only jwutil-1.2.3/jwutil/man/get_na_fields.Rd |only jwutil-1.2.3/jwutil/man/get_non_ASCII.Rd |only jwutil-1.2.3/jwutil/man/isRowSorted.Rd |only jwutil-1.2.3/jwutil/man/is_na_ish.Rd |only jwutil-1.2.3/jwutil/man/is_numeric_str.Rd |only jwutil-1.2.3/jwutil/man/jw_scan_build.Rd |only jwutil-1.2.3/jwutil/man/jwutil-package.Rd | 22 jwutil-1.2.3/jwutil/man/list_named.Rd |only jwutil-1.2.3/jwutil/man/logical_to_binary.Rd | 17 jwutil-1.2.3/jwutil/man/lsp.Rd | 10 jwutil-1.2.3/jwutil/man/match_multi.Rd |only jwutil-1.2.3/jwutil/man/merge_better.Rd | 20 jwutil-1.2.3/jwutil/man/min_r_version.Rd | 17 jwutil-1.2.3/jwutil/man/npc.Rd |only jwutil-1.2.3/jwutil/man/opt_binary_brute.Rd | 19 jwutil-1.2.3/jwutil/man/percent_signif.Rd |only jwutil-1.2.3/jwutil/man/percentize.Rd |only jwutil-1.2.3/jwutil/man/permute.Rd | 23 jwutil-1.2.3/jwutil/man/permuteWithRepeats.Rd | 24 jwutil-1.2.3/jwutil/man/pgo_bench.Rd |only jwutil-1.2.3/jwutil/man/propNaPerField.Rd | 6 jwutil-1.2.3/jwutil/man/random_test_dates.Rd | 4 jwutil-1.2.3/jwutil/man/rm_r.Rd | 4 jwutil-1.2.3/jwutil/man/shuffle.Rd | 10 jwutil-1.2.3/jwutil/man/sort_clip_char.Rd |only jwutil-1.2.3/jwutil/man/source_purl.Rd | 10 jwutil-1.2.3/jwutil/man/str_extract.Rd |only jwutil-1.2.3/jwutil/man/str_match_all.Rd |only jwutil-1.2.3/jwutil/man/str_multi_match.Rd |only jwutil-1.2.3/jwutil/man/str_pair_match.Rd |only jwutil-1.2.3/jwutil/man/strip.Rd | 4 jwutil-1.2.3/jwutil/man/strip_for_formula.Rd |only jwutil-1.2.3/jwutil/man/two_cat_to_logical.Rd |only jwutil-1.2.3/jwutil/man/unzip_to_data_raw.Rd | 4 jwutil-1.2.3/jwutil/man/update_github_pkgs.Rd | 2 jwutil-1.2.3/jwutil/man/zero_na.Rd | 23 jwutil-1.2.3/jwutil/src/Makevars | 7 jwutil-1.2.3/jwutil/src/Makevars.win | 8 jwutil-1.2.3/jwutil/src/RcppExports.cpp | 252 ++------ jwutil-1.2.3/jwutil/src/get_current_stdlib.cpp |only jwutil-1.2.3/jwutil/src/jwomp.cpp |only jwutil-1.2.3/jwutil/src/jwomp.h |only jwutil-1.2.3/jwutil/src/jwutil_types.h |only jwutil-1.2.3/jwutil/src/prof |only jwutil-1.2.3/jwutil/src/rowsorted.cpp | 3 jwutil-1.2.3/jwutil/src/stdlib.cpp |only jwutil-1.2.3/jwutil/src/test-jwutil.cpp | 5 jwutil-1.2.3/jwutil/src/util.cpp | 11 jwutil-1.2.3/jwutil/tests/testthat/test-char.R | 141 ++-- jwutil-1.2.3/jwutil/tests/testthat/test-cpp.R | 2 jwutil-1.2.3/jwutil/tests/testthat/test-df.R | 216 ++++--- jwutil-1.2.3/jwutil/tests/testthat/test-list.R | 2 jwutil-1.2.3/jwutil/tests/testthat/test-merge.R | 136 ++-- jwutil-1.2.3/jwutil/tests/testthat/test-testing.R | 27 jwutil-1.2.3/jwutil/tests/testthat/test-util.R | 408 ++++++++------ 121 files changed, 2156 insertions(+), 1327 deletions(-)
Title: Seeking and Finding Clones in Copy Number and Sequencing Data
Description: Defines the classes and functions used to simulate and
to analyze data sets describing copy number variants and,
optionally, sequencing mutations in order to detect clonal subsets.
See Zucker et al. (2019) <doi:10.1093/bioinformatics/btz057>.
Author: Kevin R. Coombes, Mark Zucker
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between CloneSeeker versions 1.0.4 dated 2019-04-12 and 1.0.7 dated 2019-05-06
DESCRIPTION | 10 MD5 | 22 - R/sysdata.rda |binary build/vignette.rds |binary inst/doc/CloneSeeker.pdf |binary tests/test01-Simplex.R | 1 tests/test01-Simplex.Rout.save | 71 ++--- tests/test02-WV.Rout.save | 2 tests/test03-simulate.R | 1 tests/test03-simulate.Rout.save | 487 +++++++++++++++++------------------ tests/test04-algorithm.R | 1 tests/test04-algorithm.Rout.save | 539 +++++++++++++++++++-------------------- 12 files changed, 570 insertions(+), 564 deletions(-)
Title: Threshing and Reaping for Principal Components
Description: Defines the classes used to identify
outliers (threshing) and compute the number of significant principal
components and number of clusters (reaping) in a joint application
of PCA and hierarchical clustering. See Wang et al., 2018,
<doi:10.1186/s12859-017-1998-9>.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Thresher versions 1.1.1 dated 2019-04-23 and 1.1.2 dated 2019-05-06
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- build/vignette.rds |binary data/savedSims.rda |binary inst/doc/Thresher.pdf |binary tests/01-remap.R | 2 +- tests/01-remap.Rout.save | 8 ++++---- tests/02-thresh.R | 2 +- tests/02-thresh.Rout.save | 8 ++++---- tests/04-reap.R | 2 +- tests/04-reap.Rout.save | 8 ++++---- 11 files changed, 29 insertions(+), 29 deletions(-)
Title: Functions to Solve Quadratic Programming Problems
Description: This package contains routines and documentation for
solving quadratic programming problems.
Author: S original by Berwin A. Turlach <Berwin.Turlach@gmail.com> R
port by Andreas Weingessel <Andreas.Weingessel@ci.tuwien.ac.at>
Maintainer: Berwin A. Turlach <Berwin.Turlach@gmail.com>
Diff between quadprog versions 1.5-6 dated 2019-04-07 and 1.5-7 dated 2019-05-06
quadprog-1.5-6/quadprog/LICENSE.GPL-2 |only quadprog-1.5-6/quadprog/LICENSE.GPL-3 |only quadprog-1.5-7/quadprog/ChangeLog | 156 ++++++++++++++++++++++++++++++- quadprog-1.5-7/quadprog/DESCRIPTION | 10 - quadprog-1.5-7/quadprog/GPL-2 |only quadprog-1.5-7/quadprog/GPL-3 |only quadprog-1.5-7/quadprog/MD5 | 12 +- quadprog-1.5-7/quadprog/src/Makevars | 12 -- quadprog-1.5-7/quadprog/src/Makevars.win | 9 - 9 files changed, 168 insertions(+), 31 deletions(-)
Title: Finding the Number of Significant Principal Components
Description: Implements methods to automate the Auer-Gervini graphical
Bayesian approach for determining the number of significant
principal components. Automation uses clustering, change points, or
simple statistical models to distinguish "long" from "short" steps
in a graph showing the posterior number of components as a function
of a prior parameter. See <doi:10.1101/237883>.
Author: Kevin R. Coombes, Min Wang
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between PCDimension versions 1.1.10 dated 2019-04-23 and 1.1.11 dated 2019-05-06
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ build/vignette.rds |binary data/spca.rda |binary inst/doc/PCDimension.pdf |binary tests/00-auer.R | 2 +- tests/00-auer.Rout.save | 8 ++++---- 7 files changed, 15 insertions(+), 15 deletions(-)
Title: Integrating Multiple Modalities of High Throughput Assays Using
Item Response Theory
Description: Provides a systematic framework for
integrating multiple modalities of assays profiled on the same set of
samples. The goal is to identify genes that are altered in cancer
either marginally or consistently across different assays. The
heterogeneity among different platforms and different samples are
automatically adjusted so that the overall alteration magnitude can
be accurately inferred. See Tong and Coombes (2012)
<doi:10.1093/bioinformatics/bts561>.
Author: Pan Tong, Kevin R Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between integIRTy versions 1.0.5 dated 2017-07-11 and 1.0.6 dated 2019-05-06
DESCRIPTION | 10 +++++----- MD5 | 28 ++++++++++++++-------------- build/vignette.rds |binary data/OV.rda |binary inst/doc/integIRTy.pdf |binary man/calculatePermutedScoreByGeneSampling.Rd | 4 ++-- man/computeAbility.Rd | 4 ++-- man/dichotomize.Rd | 2 +- man/dichotomizeCN.Rd | 1 + man/dichotomizeExpr.Rd | 3 +-- man/dichotomizeMethy.Rd | 3 +-- man/fitOnSinglePlat.Rd | 3 +-- man/intIRTeasyRun.Rd | 3 +-- man/intIRTeasyRunFromRaw.Rd | 3 +-- man/simulateBinaryResponseMat.Rd | 3 +-- 15 files changed, 31 insertions(+), 36 deletions(-)
Title: Classes and Methods for Training and Using Binary Prediction
Models
Description: Defines classes and methods to learn models and use them
to predict binary outcomes. These are generic tools, but we also
include specific examples for many common classifiers.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Modeler versions 3.4.4 dated 2019-04-23 and 3.4.5 dated 2019-05-06
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- build/vignette.rds |binary inst/doc/Modeler.pdf |binary tests/t00-filter.R | 2 +- tests/t00-filter.Rout.save | 8 ++++---- tests/t00-pruner.R | 2 +- tests/t00-pruner.Rout.save | 8 ++++---- 8 files changed, 21 insertions(+), 21 deletions(-)
Title: 'purrr'-Like Apply Functions Over Input Elements
Description: An easy-to-use, dependency-free set of functions for iterating over
elements of various input objects. Functions are wrappers around base
apply()/lapply()/vapply() functions but designed to have similar
functionality to the mapping functions in the 'purrr' package
<https://purrr.tidyverse.org/>. Specifically, function names more explicitly
communicate the expected class of the output and functions also allow for
the convenient shortcut of '~ .x' instead of the more verbose
'function(.x) .x'.
Author: Michael W. Kearney [aut, cre] (<https://orcid.org/0000-0002-0730-4694>)
Maintainer: Michael W. Kearney <kearneymw@missouri.edu>
Diff between dapr versions 0.0.2 dated 2019-01-20 and 0.0.3 dated 2019-05-06
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- NEWS.md | 7 +++++++ R/assert.R |only R/dap.R | 21 +++++++++++++-------- R/lap.R | 3 ++- R/utils.R | 5 ++++- R/vap.R | 24 ++++++++---------------- README.md | 19 ++++++++----------- tests/testthat/test-purrr-map.R | 4 ++-- 10 files changed, 56 insertions(+), 50 deletions(-)
Title: Classes and Methods for Cross Validation of "Class Prediction"
Algorithms
Description: Defines classes and methods to cross-validate various
binary classification algorithms used for "class prediction"
problems.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between CrossValidate versions 2.3.3 dated 2019-04-23 and 2.3.4 dated 2019-05-06
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/CrossVal.pdf |binary tests/testCV.R | 2 +- tests/testCV.Rout.save | 8 ++++---- 6 files changed, 14 insertions(+), 14 deletions(-)
Title: Simulating Realistic Gene Expression Data
Description: The Ultimate Microrray Prediction, Reality and Inference
Engine (UMPIRE) is a package to facilitate the simulation of realistic
microarray data sets with link to associate outcomes. See Zhang and
Coombes (2012) <doi:10.1186/1471-2105-13-S13-S1>.
Author: Kevin R. Coombes, Jiexin Zhang
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Umpire versions 1.3.6 dated 2019-04-23 and 1.3.7 dated 2019-05-06
DESCRIPTION | 8 ++++---- MD5 | 36 ++++++++++++++++++------------------ build/vignette.rds |binary inst/doc/Umpire.pdf |binary tests/t01-indNormal.R | 2 +- tests/t01-indNormal.Rout.save | 8 ++++---- tests/t02-1-engine.R | 2 +- tests/t02-1-engine.Rout.save | 8 ++++---- tests/t02-indLogNorm.R | 2 +- tests/t02-indLogNorm.Rout.save | 8 ++++---- tests/t03-mvn.R | 2 +- tests/t03-mvn.Rout.save | 8 ++++---- tests/t05-noise.R | 2 +- tests/t05-noise.Rout.save | 8 ++++---- tests/t06-engineAct.R | 2 +- tests/t06-engineAct.Rout.save | 8 ++++---- tests/t07-cancerModel.R | 2 +- tests/t07-cancerModel.Rout.save | 11 +++++------ tests/t08-cancerEngine.Rout.save | 6 +++--- 19 files changed, 61 insertions(+), 62 deletions(-)
Title: TraMineR Extension
Description: Collection of ancillary functions and utilities to be used in conjunction with the 'TraMineR' package for sequence data exploration. Most of the functions are in test phase, lack systematic consistency check of the arguments and are subject to changes. Once fully checked, some of the functions of this collection could be included in a next release of 'TraMineR'.
Author: Gilbert Ritschard [aut, cre, ths, cph]
(<https://orcid.org/0000-0001-7776-0903>),
Matthias Studer [aut] (<https://orcid.org/0000-0002-6269-1412>),
Reto Buergin [aut],
Alexis Gabadinho [ctb],
Pierre-Alexandre Fonta [ctb],
Nicolas Muller [ctb],
Patrick Rousset [ctb]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineRextras versions 0.4.4 dated 2018-12-14 and 0.4.5 dated 2019-05-06
DESCRIPTION | 17 +++++----- MD5 | 34 ++++++++++----------- NAMESPACE | 7 ++++ R/seqedist.R | 12 +++---- R/seqedplot.R | 4 +- R/seqprec.states.check.R | 3 + R/seqprecarity.R | 31 +++++++++++++++---- R/seqprecorr.R | 66 +++++++++++++++++++++++++++--------------- R/seqprecstart.R | 19 +++++++----- R/seqstart.R | 2 - R/seqtabstocc.R | 27 +++++++++++------ inst/CITATION | 46 ++++++++++++++--------------- inst/NEWS | 24 ++++++++++++++- inst/NEWS.Rd | 33 +++++++++++++++++++++ man/TraMineRextras-package.Rd | 2 - man/seqprecarity.Rd | 41 +++++++++++++++++--------- man/seqprecstart.Rd | 18 +++++++---- man/seqtabstocc.Rd | 20 ++++++++++-- 18 files changed, 277 insertions(+), 129 deletions(-)
More information about TraMineRextras at CRAN
Permanent link
Title: Basic Functions for Pre-Processing Microarrays
Description: Provides classes to pre-process microarray gene
expression data as part of the OOMPA collection of packages
described at <http://oompa.r-forge.r-project.org/>.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between PreProcess versions 3.1.6 dated 2019-04-23 and 3.1.7 dated 2019-05-06
PreProcess-3.1.6/PreProcess/tests/test07-complete-channel.Rout |only PreProcess-3.1.7/PreProcess/DESCRIPTION | 8 +- PreProcess-3.1.7/PreProcess/MD5 | 28 +++++----- PreProcess-3.1.7/PreProcess/build/vignette.rds |binary PreProcess-3.1.7/PreProcess/inst/doc/oompa-prep.pdf |binary PreProcess-3.1.7/PreProcess/tests/test01-utility.R | 2 PreProcess-3.1.7/PreProcess/tests/test01-utility.Rout.save | 8 +- PreProcess-3.1.7/PreProcess/tests/test03-channel-type.Rout.save | 6 +- PreProcess-3.1.7/PreProcess/tests/test04-channel.R | 2 PreProcess-3.1.7/PreProcess/tests/test04-channel.Rout.save | 8 +- PreProcess-3.1.7/PreProcess/tests/test05-processor.R | 2 PreProcess-3.1.7/PreProcess/tests/test05-processor.Rout.save | 8 +- PreProcess-3.1.7/PreProcess/tests/test06-pipeline.R | 2 PreProcess-3.1.7/PreProcess/tests/test06-pipeline.Rout.save | 8 +- PreProcess-3.1.7/PreProcess/tests/test07-complete-channel.R | 2 PreProcess-3.1.7/PreProcess/tests/test07-complete-channel.Rout.save |only 16 files changed, 42 insertions(+), 42 deletions(-)
Title: Qualitative Palettes with Many Colors
Description: Tools for creating, viewing, and assessing qualitative
palettes with many (20-30 or more) colors.
Author: Kevin R. Coombes, Guy Brock
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Polychrome versions 1.2.1 dated 2019-04-23 and 1.2.2 dated 2019-05-06
DESCRIPTION | 8 MD5 | 28 +- build/vignette.rds |binary data/Dark24.rda |binary data/Light24.rda |binary data/alphabet.rda |binary data/colorsafe.rda |binary data/glasbey.rda |binary data/iscc.rda |binary data/palette36.rda |binary inst/doc/color-deficits.html | 425 ++++++++++---------------------------- inst/doc/creatingPalettes.html | 455 ++++++++++++----------------------------- inst/doc/polychrome.html | 361 ++++++++------------------------ tests/testXform.R | 2 tests/testXform.Rout.save | 10 15 files changed, 370 insertions(+), 919 deletions(-)
Title: Classes and Methods for "Class Discovery" with Microarrays or
Proteomics
Description: Defines the classes used for "class discovery" problems
in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class
discovery primarily consists of unsupervised clustering methods with
attempts to assess their statistical significance.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between ClassDiscovery versions 3.3.11 dated 2019-04-23 and 3.3.12 dated 2019-05-06
ClassDiscovery-3.3.11/ClassDiscovery/tests/test05-spca.Rout |only ClassDiscovery-3.3.12/ClassDiscovery/DESCRIPTION | 8 - ClassDiscovery-3.3.12/ClassDiscovery/MD5 | 50 +++++----- ClassDiscovery-3.3.12/ClassDiscovery/build/vignette.rds |binary ClassDiscovery-3.3.12/ClassDiscovery/inst/doc/maha-test.pdf |binary ClassDiscovery-3.3.12/ClassDiscovery/inst/doc/oompa-cd.pdf |binary ClassDiscovery-3.3.12/ClassDiscovery/tests/exprSet-example.R | 2 ClassDiscovery-3.3.12/ClassDiscovery/tests/exprSet-example.Rout.save | 8 - ClassDiscovery-3.3.12/ClassDiscovery/tests/test00-color.Rout.save | 6 - ClassDiscovery-3.3.12/ClassDiscovery/tests/test01-distance.R | 2 ClassDiscovery-3.3.12/ClassDiscovery/tests/test01-distance.Rout.save | 8 - ClassDiscovery-3.3.12/ClassDiscovery/tests/test02-cluster.R | 2 ClassDiscovery-3.3.12/ClassDiscovery/tests/test02-cluster.Rout.save | 8 - ClassDiscovery-3.3.12/ClassDiscovery/tests/test02.1-just.R | 2 ClassDiscovery-3.3.12/ClassDiscovery/tests/test02.1-just.Rout.save | 8 - ClassDiscovery-3.3.12/ClassDiscovery/tests/test03-boot.R | 2 ClassDiscovery-3.3.12/ClassDiscovery/tests/test03-boot.Rout.save | 8 - ClassDiscovery-3.3.12/ClassDiscovery/tests/test04-perturb.R | 2 ClassDiscovery-3.3.12/ClassDiscovery/tests/test04-perturb.Rout.save | 8 - ClassDiscovery-3.3.12/ClassDiscovery/tests/test04.1-gpca.R | 2 ClassDiscovery-3.3.12/ClassDiscovery/tests/test04.1-gpca.Rout.save | 8 - ClassDiscovery-3.3.12/ClassDiscovery/tests/test05-spca.R | 2 ClassDiscovery-3.3.12/ClassDiscovery/tests/test05-spca.Rout.save |only ClassDiscovery-3.3.12/ClassDiscovery/tests/test06-mosaic.R | 2 ClassDiscovery-3.3.12/ClassDiscovery/tests/test06-mosaic.Rout.save | 8 - ClassDiscovery-3.3.12/ClassDiscovery/tests/test07-pcanova.R | 2 ClassDiscovery-3.3.12/ClassDiscovery/tests/test07-pcanova.Rout.save | 8 - 27 files changed, 78 insertions(+), 78 deletions(-)
More information about ClassDiscovery at CRAN
Permanent link
Title: Classes and Methods for "Class Comparison" Problems on
Microarrays
Description: Defines the classes used for "class comparison" problems
in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class
comparison includes tests for differential expression; see Simon's
book for details on typical problem types.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between ClassComparison versions 3.1.7 dated 2019-04-23 and 3.1.8 dated 2019-05-06
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- build/vignette.rds |binary inst/doc/oompa-cc.pdf |binary tests/testBum.R | 2 +- tests/testBum.Rout.save | 8 ++++---- tests/testDiff.R | 2 +- tests/testDiff.Rout.save | 8 ++++---- 8 files changed, 21 insertions(+), 21 deletions(-)
More information about ClassComparison at CRAN
Permanent link
Title: The Bimodality Index
Description: Defines the functions used to compute the
bimodal index as defined by Wang et al. (2009)
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2730180/>,
<doi:10.4137/CIN.S2846>.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between BimodalIndex versions 1.1.8 dated 2019-04-23 and 1.1.9 dated 2019-05-06
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/bim.pdf |binary tests/test09-bimodal.R | 2 +- tests/test09-bimodal.Rout.save | 8 ++++---- 6 files changed, 14 insertions(+), 14 deletions(-)
Title: Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
Description: Statistical tools for Bayesian structure learning in undirected graphical models for continuous, discrete, and mixed data. The package is implemented the recent improvements in the Bayesian graphical models literature, including Mohammadi and Wit (2015) <doi:10.1214/14-BA889>, Letac et al. (2018) <arXiv:1706.04416>, Dobra and Mohammadi (2018) <doi:10.1214/18-AOAS1164>, Mohammadi et al. (2017) <doi:10.1111/rssc.12171>. To speed up the computations, the BDMCMC sampling algorithms are implemented in parallel using OpenMP in C++.
Author: Reza Mohammadi [aut, cre] <https://orcid.org/0000-0001-9538-0648>,
Ernst Wit [aut] <https://orcid.org/0000-0002-3671-9610>,
Adrian Dobra [ctb]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between BDgraph versions 2.58 dated 2019-04-15 and 2.59 dated 2019-05-06
BDgraph-2.58/BDgraph/build |only BDgraph-2.59/BDgraph/DESCRIPTION | 8 +- BDgraph-2.59/BDgraph/MD5 | 64 ++++++++++---------- BDgraph-2.59/BDgraph/NEWS | 12 ++- BDgraph-2.59/BDgraph/R/bdgraph.R | 4 - BDgraph-2.59/BDgraph/R/detect_cores.R | 23 ++++--- BDgraph-2.59/BDgraph/inst/CITATION | 88 +++++----------------------- BDgraph-2.59/BDgraph/inst/doc/BDgraph.pdf |binary BDgraph-2.59/BDgraph/inst/doc/vignette.pdf |binary BDgraph-2.59/BDgraph/man/BDgraph-package.Rd | 4 - BDgraph-2.59/BDgraph/man/bdgraph.Rd | 4 - BDgraph-2.59/BDgraph/man/bdgraph.mpl.Rd | 2 BDgraph-2.59/BDgraph/man/bdgraph.sim.Rd | 4 - BDgraph-2.59/BDgraph/man/bdgraph.ts.Rd | 4 - BDgraph-2.59/BDgraph/man/compare.Rd | 4 - BDgraph-2.59/BDgraph/man/graph.sim.Rd | 4 - BDgraph-2.59/BDgraph/man/pgraph.Rd | 4 - BDgraph-2.59/BDgraph/man/plinks.Rd | 4 - BDgraph-2.59/BDgraph/man/plot.bdgraph.Rd | 4 - BDgraph-2.59/BDgraph/man/plot.graph.Rd | 4 - BDgraph-2.59/BDgraph/man/plot.sim.Rd | 4 - BDgraph-2.59/BDgraph/man/plotcoda.Rd | 4 - BDgraph-2.59/BDgraph/man/plotroc.Rd | 4 - BDgraph-2.59/BDgraph/man/print.bdgraph.Rd | 4 - BDgraph-2.59/BDgraph/man/print.sim.Rd | 4 - BDgraph-2.59/BDgraph/man/rgcwish.Rd | 2 BDgraph-2.59/BDgraph/man/rgwish.Rd | 4 - BDgraph-2.59/BDgraph/man/rwish.Rd | 2 BDgraph-2.59/BDgraph/man/select.Rd | 4 - BDgraph-2.59/BDgraph/man/summary.bdgraph.Rd | 4 - BDgraph-2.59/BDgraph/man/surveyData.Rd | 2 BDgraph-2.59/BDgraph/man/traceplot.Rd | 4 - BDgraph-2.59/BDgraph/vignettes/BDgraph.pdf |binary BDgraph-2.59/BDgraph/vignettes/vignette.pdf |only 34 files changed, 117 insertions(+), 166 deletions(-)
Title: Generation of Virtual Species Distributions
Description: Provides a framework for generating virtual species distributions,
a procedure increasingly used in ecology to improve species distribution
models. This package integrates the existing methodological approaches with the
objective of generating virtual species distributions with increased ecological
realism.
Author: Boris Leroy [cre, aut], Christine N. Meynard [ctb], Celine Bellard [ctb], Franck Courchamp [ctb], Robin Delsol [ctb], Willson Gaul [ctb], David M. Kaplan [ctb]
Maintainer: Boris Leroy <leroy.boris@gmail.com>
Diff between virtualspecies versions 1.4-4.1 dated 2019-04-22 and 1.5 dated 2019-05-06
DESCRIPTION | 12 MD5 | 40 - NAMESPACE | 4 NEWS | 33 + R/convertToPA.R | 1112 ++++++++++++++++++++++++++++++------------ R/generateRandomSp.R | 9 R/generateSpFromFun.R | 34 + R/generateSpFromPCA.R | 7 R/genericfunctions.R | 36 + R/limitDistribution.R | 3 R/plotResponse.R | 15 R/plotSuitabilityToProba.R |only R/sampleOccurrences.R | 37 + R/utilityFunctions.R | 8 man/convertToPA.Rd | 161 +++++- man/generateRandomSp.Rd | 10 man/generateSpFromFun.Rd | 18 man/generateSpFromPCA.Rd | 3 man/limitDistribution.Rd | 3 man/plotResponse.Rd | 4 man/plotSuitabilityToProba.Rd |only man/sampleOccurrences.Rd | 25 22 files changed, 1190 insertions(+), 384 deletions(-)
More information about virtualspecies at CRAN
Permanent link
Title: Lightweight Access to the 'Geospatial Data Abstraction Library'
('GDAL')
Description: Provides low-level access to 'GDAL' functionality for R packages. The aim is to minimize
the level of interpretation put on the 'GDAL' facilities, to enable direct use of it for a variety of purposes.
'GDAL' is the 'Geospatial Data Abstraction Library' a translator for raster and vector geospatial data formats
that presents a single raster abstract data model and single vector abstract data model to the calling application
for all supported formats <http://gdal.org/>. Other available packages 'rgdal' and 'sf' also provide access to
the 'GDAL' library, but neither can be used for these lower level tasks, and both do many other tasks.
Author: Michael Sumner [aut, cre] (<https://orcid.org/0000-0002-2471-7511>),
Simon Wotherspoon [ctb] (figured out the mechanism for the resampling
algorithm),
Mark Padgham [ctb] (helped get started :)),
Edzer Pebesma [ctb] (wrote allocate_attribute, copied here from sf),
Roger Bivand [ctb] (wrote configure.ac, copied here from rgdal),
Jim Hester [ctb] (wrote CollectorList.h, copied here from fs package),
Timothy Keitt [ctb] (wrote GetPointsInternal copied here from rgdal2
package),
Jeroen Ooms [ctb] (tweaked build process)
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between vapour versions 0.1.0 dated 2018-08-14 and 0.2.0 dated 2019-05-06
vapour-0.1.0/vapour/R/yyy-deprecate.R |only vapour-0.2.0/vapour/DESCRIPTION | 20 vapour-0.2.0/vapour/MD5 | 84 vapour-0.2.0/vapour/NAMESPACE | 6 vapour-0.2.0/vapour/NEWS.md | 63 vapour-0.2.0/vapour/R/RcppExports.R | 36 vapour-0.2.0/vapour/R/raster-info.R | 53 vapour-0.2.0/vapour/R/raster-input.R | 22 vapour-0.2.0/vapour/R/sysdata.rda |only vapour-0.2.0/vapour/R/vapour-helpers.R |only vapour-0.2.0/vapour/R/vapour-package.R | 13 vapour-0.2.0/vapour/R/vapour_input_attributes.R | 103 - vapour-0.2.0/vapour/R/vapour_input_geometry.R | 37 vapour-0.2.0/vapour/README.md | 250 ++ vapour-0.2.0/vapour/build/vignette.rds |binary vapour-0.2.0/vapour/configure | 2 vapour-0.2.0/vapour/configure.ac | 2 vapour-0.2.0/vapour/inst/WORDLIST |only vapour-0.2.0/vapour/inst/benchmarks/limit_n.R |only vapour-0.2.0/vapour/inst/doc/vapour.R | 43 vapour-0.2.0/vapour/inst/doc/vapour.Rmd | 74 vapour-0.2.0/vapour/inst/doc/vapour.html | 741 ++++++-- vapour-0.2.0/vapour/inst/extdata/gcps |only vapour-0.2.0/vapour/inst/extdata/gdal |only vapour-0.2.0/vapour/inst/extdata/point3d.gpkg |only vapour-0.2.0/vapour/man/GDAL-library.Rd |only vapour-0.2.0/vapour/man/vapour-package.Rd | 13 vapour-0.2.0/vapour/man/vapour_geom_summary.Rd |only vapour-0.2.0/vapour/man/vapour_raster_gcp.Rd |only vapour-0.2.0/vapour/man/vapour_raster_info.Rd | 10 vapour-0.2.0/vapour/man/vapour_read_attributes.Rd | 14 vapour-0.2.0/vapour/man/vapour_read_geometry.Rd | 22 vapour-0.2.0/vapour/man/vapour_read_names.Rd | 14 vapour-0.2.0/vapour/man/vapour_read_raster.Rd | 16 vapour-0.2.0/vapour/man/vapour_report_attributes.Rd |only vapour-0.2.0/vapour/src/Makevars.win | 1 vapour-0.2.0/vapour/src/RcppExports.cpp | 98 + vapour-0.2.0/vapour/src/contourize.cpp |only vapour-0.2.0/vapour/src/gdal_utils.cpp |only vapour-0.2.0/vapour/src/gdal_warper.cpp |only vapour-0.2.0/vapour/src/init.c | 32 vapour-0.2.0/vapour/src/rasterio.cpp | 120 + vapour-0.2.0/vapour/src/sds_io.cpp | 2 vapour-0.2.0/vapour/src/vapour.cpp | 841 ++++++++-- vapour-0.2.0/vapour/tests/spelling.R |only vapour-0.2.0/vapour/tests/testthat/test-features.R | 141 + vapour-0.2.0/vapour/tests/testthat/test-helpers.R |only vapour-0.2.0/vapour/tests/testthat/test-limit_skip_n.R |only vapour-0.2.0/vapour/tests/testthat/test-names.R |only vapour-0.2.0/vapour/tests/testthat/test-raster-info.R |only vapour-0.2.0/vapour/tests/testthat/test-rasterio-resampling.R | 59 vapour-0.2.0/vapour/tests/testthat/test-utils.R |only vapour-0.2.0/vapour/vignettes/vapour.Rmd | 74 53 files changed, 2404 insertions(+), 602 deletions(-)
Title: Class Unions, Matrix Operations, and Color Schemes for OOMPA
Description: Provides the class unions that must be
preloaded in order for the basic tools in the OOMPA (Object-Oriented
Microarray and Proteomics Analysis) project to be defined and loaded.
It also includes vectorized operations for row-by-row means,
variances, and t-tests. Finally, it provides new color schemes.
Details on the packages in the OOMPA project can be found at
<http://oompa.r-forge.r-project.org/>.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between oompaBase versions 3.2.7 dated 2019-04-23 and 3.2.8 dated 2019-05-06
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/oompa.pdf |binary tests/testMatrixOps.R | 2 +- tests/testMatrixOps.Rout.save | 8 ++++---- 6 files changed, 14 insertions(+), 14 deletions(-)
Title: Outright Tool for the Analysis of Spatial Inequalities and
Segregation
Description: A set of indexes and tests for the analysis of social segregation.
Author: Mihai Tivadar <mihai.tivadar@irstea.fr>
Maintainer: Mihai Tivadar <mihai.tivadar@irstea.fr>
Diff between OasisR versions 3.0.0 dated 2017-08-30 and 3.0.1 dated 2019-05-06
OasisR-3.0.0/OasisR/vignettes/Dimensions_of_segregation.md |only OasisR-3.0.1/OasisR/DESCRIPTION | 16 OasisR-3.0.1/OasisR/MD5 | 17 OasisR-3.0.1/OasisR/R/SegFunctions.R | 40 -- OasisR-3.0.1/OasisR/build/vignette.rds |binary OasisR-3.0.1/OasisR/inst/CITATION | 26 - OasisR-3.0.1/OasisR/inst/doc/Dimensions_of_segregation.html | 237 +++++++++--- OasisR-3.0.1/OasisR/man/Atkinson.Rd | 2 OasisR-3.0.1/OasisR/man/ResamplePlot.Rd | 7 OasisR-3.0.1/OasisR/man/ResampleTest.Rd | 18 10 files changed, 244 insertions(+), 119 deletions(-)
Title: Item Response Theory Modeling and Scoring for Judgment Data
Description: Psychometric analysis and scoring of judgment data using polytomous Item-Response Theory (IRT) models, as described in Myszkowski and Storme (2019) <doi:10.1037/aca0000225>. A convenience function is used to automatically compare and select models, as well as to present a variety of model-based statistics. Plotting functions are used to present category curves, as well as information, reliability and standard error functions.
Author: Nils Myszkowski [aut, cre]
Maintainer: Nils Myszkowski <nilsmyszkowskiscience@gmail.com>
Diff between jrt versions 1.0.0 dated 2019-01-04 and 1.0.1 dated 2019-05-06
DESCRIPTION | 14 +-- MD5 | 50 +++++++------ NEWS.md | 8 ++ R/info.plot.R | 16 ---- R/jcc.plot.R | 16 ---- R/jrt.R | 109 ++++++++++++++++++++++++------ README.md | 41 ++++++----- build/partial.rdb |binary data |only inst/doc/my-vignette.R | 17 +--- inst/doc/my-vignette.Rmd | 32 ++++---- inst/doc/my-vignette.html | 47 ++++++------ man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-3-2.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-4-2.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/info.plot.Rd | 16 ---- man/jcc.plot.Rd | 16 ---- man/jrt.Rd | 21 +---- man/ratings.Rd |only vignettes/my-vignette.Rmd | 32 ++++---- 27 files changed, 234 insertions(+), 201 deletions(-)
Title: Free Brazilian Repository for Open Soil Data
Description: Making the access to the Free Brazilian Repository for Open Soil Data <http://www.ufsm.br/febr/> as easy
as possible.
Author: Alessandro Samuel-Rosa [aut, cre]
(<https://orcid.org/0000-0003-0877-1320>),
Universidade Federal de Santa Maria [fnd],
Universidade Tecnológica Federal do Paraná [fnd]
Maintainer: Alessandro Samuel-Rosa <alessandrosamuelrosa@gmail.com>
Diff between febr versions 1.0.1 dated 2018-11-12 and 1.0.2 dated 2019-05-06
DESCRIPTION | 16 +- MD5 | 21 +- NEWS.md | 42 +++++ R/febr2spdf.R | 6 R/febrHelper.R | 22 +-- R/layersHelper.R | 76 ++++++---- R/observation.R | 3 R/unit.R | 6 build/vignette.rds |binary inst/WORDLIST |only inst/doc/febr.html | 387 ++++++++++++++++++++++++++++++++++++++++++----------- man/febr2spdf.Rd | 6 12 files changed, 441 insertions(+), 144 deletions(-)
Title: Modelling Actual, Potential and Reference Crop
Evapotranspiration
Description: Uses data and constants to calculate potential evapotranspiration (PET) and actual evapotranspiration (AET) from 21 different formulations including Penman, Penman-Monteith FAO 56, Priestley-Taylor and Morton formulations.
Author: Danlu Guo [aut, cre] <danlu.guo@adelaide.edu.au>, Seth Westra [aut] <swestra@civeng.adelaide.edu.au>, Tim Peterson [ctb] <timjp@unimelb.edu.au>
Maintainer: Danlu Guo <danlu.guo@unimelb.edu.au>
Diff between Evapotranspiration versions 1.12 dated 2017-10-28 and 1.13 dated 2019-05-06
DESCRIPTION | 9 MD5 | 18 NEWS | 21 R/Reading.R | 2204 +++++++++++++++++++++++++++-------------------- man/ET.MortonCRAE.Rd | 1 man/ET.MortonCRWE.Rd | 1 man/ET.Penman.Rd | 6 man/ET.PenmanMonteith.Rd | 6 man/climatedata.Rd | 2 man/constants.Rd | 2 10 files changed, 1338 insertions(+), 932 deletions(-)
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Title: Poisson-Tweedie Generalized Linear Mixed Model
Description: Fits Poisson-Tweedie generalized linear mixed model.
Likelihood approximation based on adaptive Gauss Hermite quadrature rule.
Author: Mirko Signorelli [aut, cre],
Pietro Spitali [aut],
Roula Tsonaka [aut]
Maintainer: Mirko Signorelli <m.signorelli@lumc.nl>
Diff between ptmixed versions 0.0.2 dated 2019-04-23 and 0.0.3 dated 2019-05-06
DESCRIPTION | 6 ++--- MD5 | 7 +++--- R/ptmixed.R | 54 ++++++++++++++++++++++++++++------------------------ R/starting-values.R | 6 ++--- inst |only 5 files changed, 40 insertions(+), 33 deletions(-)
Title: Bindings to Selected 'liblwgeom' Functions for Simple Features
Description: Access to selected functions found in 'liblwgeom' <https://github.com/postgis/postgis/tree/svn-trunk/liblwgeom>, the light-weight geometry library used by 'PostGIS' <http://postgis.net/>.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Colin Rundel [ctb],
Andy Teucher [ctb],
liblwgeom developers [cph]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between lwgeom versions 0.1-6 dated 2019-02-18 and 0.1-7 dated 2019-05-06
DESCRIPTION | 6 ++-- MD5 | 12 ++++---- R/split.R | 4 +- configure | 79 +++++++++++++++++++++++++++++++++++++++++++++---------- configure.ac | 61 ++++++++++++++++++++++++++++++++++++++++++ src/Makevars.win | 34 ++++++++++++----------- tools/winlibs.R | 8 +++-- 7 files changed, 161 insertions(+), 43 deletions(-)
Title: Some Latent Variable Models
Description: Includes some procedures for latent variable modeling with a
particular focus on multilevel data.
The 'LAM' package contains mean and covariance structure modelling
for multivariate normally distributed data (mlnormal(); Longford, 1987;
<doi:10.1093/biomet/74.4.817>), a general Metropolis-Hastings algorithm
(amh(); Roberts & Rosenthal, 2001, <doi:10.1214/ss/1015346320>) and
penalized maximum likelihood estimation (pmle(); Cole, Chu & Greenland,
2014; <doi:10.1093/aje/kwt245>).
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between LAM versions 0.3-48 dated 2018-06-07 and 0.4-17 dated 2019-05-06
DESCRIPTION | 17 - MD5 | 214 +++++++++-------- NAMESPACE | 21 + R/RcppExports.R | 2 R/amh.R | 52 ++-- R/amh_compare_estimators.R | 18 - R/amh_eval_priors.R | 4 R/amh_ic.R | 10 R/amh_init_acceptance_parameters.R | 6 R/amh_loglike.R | 6 R/amh_posterior.R | 12 R/amh_proc_methods.R | 4 R/amh_proposal_refresh.R | 28 +- R/amh_sampling.R | 24 - R/clpm_to_ctm.R |only R/clpm_to_ctm_drift_to_paths.R |only R/clpm_to_ctm_estimating_function.R |only R/clpm_to_ctm_paths_to_drift.R |only R/coef.amh.R | 4 R/coef.mlnormal.R | 4 R/coef.pmle.R | 4 R/confint.amh.R | 16 - R/confint.mlnormal.R | 12 R/confint.pmle.R | 12 R/lam_add_increment.R |only R/lam_moving_average.R | 4 R/lam_vcov_linear_trafo.R |only R/lam_vcov_to_se.R |only R/loglike_mvnorm.R | 6 R/loglike_mvnorm_NA_pattern.R | 6 R/loglike_mvnorm_NA_pattern_R.R | 6 R/loglike_mvnorm_R.R | 14 - R/mlnormal.R | 188 +++++++-------- R/mlnormal_abs_approx.R | 16 - R/mlnormal_adjust_numdiff_parameter.R | 6 R/mlnormal_as_vector_names.R | 4 R/mlnormal_check_matrix_list_difference.R | 4 R/mlnormal_covmat_add_ridge.R | 4 R/mlnormal_create_disp.R | 8 R/mlnormal_equal_list_matrices.R | 10 R/mlnormal_equal_matrix.R | 10 R/mlnormal_eval_penalty.R | 8 R/mlnormal_eval_penalty_update_theta.R | 30 +- R/mlnormal_eval_priors.R | 4 R/mlnormal_eval_priors_derivative.R | 10 R/mlnormal_eval_priors_derivative2.R | 14 - R/mlnormal_fill_matrix_from_list.R | 8 R/mlnormal_fit_function_ml.R | 34 +- R/mlnormal_ic.R | 6 R/mlnormal_information_matrix_reml.R | 42 +-- R/mlnormal_linear_regression_bayes.R | 6 R/mlnormal_matrix2list.R | 8 R/mlnormal_parameter_change.R | 4 R/mlnormal_postproc_eval_posterior.R | 24 - R/mlnormal_postproc_parameters.R | 50 ++-- R/mlnormal_proc.R | 50 ++-- R/mlnormal_proc_control.R | 20 - R/mlnormal_proc_variance_shortcut.R | 34 +- R/mlnormal_proc_variance_shortcut_XY_R.R | 10 R/mlnormal_proc_variance_shortcut_XY_Rcpp.R | 4 R/mlnormal_proc_variance_shortcut_Z_R.R | 22 - R/mlnormal_proc_variance_shortcut_Z_Rcpp.R | 32 +- R/mlnormal_process_prior.R | 20 - R/mlnormal_soft_thresholding.R | 6 R/mlnormal_summary_round_helper.R | 10 R/mlnormal_update_V_R.R | 12 R/mlnormal_update_V_Rcpp.R | 12 R/mlnormal_update_beta.R | 52 ++-- R/mlnormal_update_beta_GLS.R | 6 R/mlnormal_update_beta_XVX_R.R | 14 - R/mlnormal_update_beta_XVX_Rcpp.R | 8 R/mlnormal_update_beta_iterations_penalty.R | 14 - R/mlnormal_update_beta_iterations_priors.R | 10 R/mlnormal_update_ml_derivative_V.R | 20 - R/mlnormal_update_theta_ml.R | 58 ++-- R/mlnormal_update_theta_newton_step.R | 10 R/mlnormal_verbose_f0.R | 4 R/mlnormal_verbose_f1.R | 6 R/mlnormal_verbose_f2.R | 22 - R/plot.amh.R | 132 +++++----- R/pmle.R | 74 ++---- R/pmle_data_proc.R | 12 R/pmle_eval_posterior.R | 12 R/pmle_eval_prior.R | 4 R/pmle_ic.R | 6 R/pmle_prior_extract_density.R | 14 - R/pmle_process_prior.R | 14 - R/print.mlnormal.R | 36 +- R/suff_stat_NA_pattern.R | 11 R/summary.amh.R | 76 +++--- R/summary.mlnormal.R | 62 ++--- R/summary.pmle.R | 60 ++-- R/vcov.amh.R | 4 R/vcov.mlnormal.R | 4 R/vcov.pmle.R | 4 R/vcov_linear_trafo.R |only R/zzz.R | 8 README.md | 2 build |only data/data.HT12.rda |binary inst/NEWS | 15 + man/LAM-package.Rd | 32 +- man/amh.Rd | 246 ++++++++++---------- man/clpm_to_ctm.Rd |only man/data.HT.Rd | 4 man/loglike_mvnorm.Rd | 31 +- man/mlnormal.Rd | 337 ++++++++++++++-------------- man/suff_stat_NA_pattern.Rd | 4 src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 2 src/lam_rcpp_loglike_mvnorm.cpp | 24 + src/lam_rcpp_mlnormal.cpp | 146 +++++------- 113 files changed, 1433 insertions(+), 1407 deletions(-)
Title: Beautiful Colour Maps for Oceanography
Description: Perceptually uniform palettes for commonly used
variables in oceanography as functions taking an integer
and producing character vectors of colours.
See Thyng, K.M., Greene, C.A., Hetland, R.D., Zimmerle, H.M.
and S.F. DiMarco (2016) <doi:10.5670/oceanog.2016.66> for
the guidelines adhered to when creating the palettes.
Author: Kristen Thyng [aut],
Clark Richards [ctb],
Ivan Krylov [cre]
Maintainer: Ivan Krylov <krylov.r00t@gmail.com>
Diff between cmocean versions 0.1-1 dated 2019-04-23 and 0.2 dated 2019-05-06
DESCRIPTION | 8 - MD5 | 16 +- NEWS |only R/cmocean.R | 4 R/sysdata.rda |binary README.md |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/cmocean.html | 6 man/cmocean.Rd | 303 ++++++++++++++++++++++++++------------------------ 10 files changed, 178 insertions(+), 159 deletions(-)
Title: Performs Common Linear Algebra Operations Used in Quantum
Computing and Implements Quantum Algorithms
Description: Contains basic structures and operations used frequently in quantum computing. Intended to be a convenient tool to help in practicing the linear algebra involved in quantum operations. Has functionality for the creation of arbitrarily sized kets, bras, matrices and implements quantum gates, inner products, and tensor products. Contains all commonly used quantum gates, creates arbitrarily controlled versions of all gates, and can simulate complete or partial measurements of kets. Implements modular arithmetic commonly found in quantum algorithms and can convert functions into equivalent quantum gates. It can also simulate larger applications, including Steane error correction <DOI:10.1103/physrevlett.77.793>, the Quantum Fourier Transform developed by Shor (1999), Shor's algorithm which factors numbers up to 21, Grover's algorithm (1996), the Quantum Approximation Optimization Algorithm (QAOA) (Farhi, Goldstone, and Gutmann 2014) <arXiv:1411.4028>, and the training of a quantum neural network developed by Schuld (2018) <arXiv:1804.00633> which can classify the MNIST dataset.
Author: Salonik Resch
Maintainer: Salonik Resch <resc0059@umn.edu>
Diff between QuantumOps versions 2.5.1 dated 2019-04-09 and 2.5.2 dated 2019-05-06
DESCRIPTION | 12 ++--- MD5 | 44 ++++++++++++------ NAMESPACE | 7 +++ NEWS.md |only R/QuantumMNIST256Classifier.R | 8 ++- R/SWAP.R | 1 R/Shor.R | 98 ++++++++++++------------------------------ R/Steane.R |only R/SteaneCorrect.R |only R/cntrld.R | 4 - R/compareQuantumState.R |only R/convert_bin2dec.R |only R/convert_dec2bin.R |only R/dirac.R | 9 +++ R/extractMNIST.R | 7 ++- R/intket.R | 38 +++++----------- R/measure.R | 7 ++- R/reduceMeasure.R | 7 ++- R/singleSWAP.R |only R/sphericalket.R |only R/swapTest.R |only man/Steane.Rd |only man/SteaneCorrect.Rd |only man/compareQuantumState.Rd |only man/convert_bin2dec.Rd |only man/convert_dec2bin.Rd |only man/intket.Rd | 10 +++- man/measure.Rd | 15 +++--- man/reduceMeasure.Rd | 15 +++--- man/singleSWAP.Rd |only man/swapTest.Rd |only 31 files changed, 138 insertions(+), 144 deletions(-)
Title: Text Mining of PubMed Abstracts
Description: Text mining of PubMed Abstracts (text and XML) from <http://www.ncbi.nlm.nih.gov/pubmed>.
Author: Jyoti Rani, S.Ramachandran, Ab Rauf Shah
Maintainer: S. Ramachandran <ramuigib@gmail.com>
Diff between pubmed.mineR versions 1.0.14 dated 2019-02-12 and 1.0.15 dated 2019-05-06
DESCRIPTION | 10 +++++----- MD5 | 18 ++++++++++-------- NAMESPACE | 1 + R/pubtator_function.R | 12 ++++++------ R/word_associations.R |only data/GeneToEntrez.rda |binary data/HGNC2UniprotID.rda |binary data/HGNCdata.rda |binary data/common_words_new.rda |binary man/pubtator_function.Rd | 3 +-- man/word_associations.Rd |only 11 files changed, 23 insertions(+), 21 deletions(-)
Title: Estimation of Multivariate Long-Memory Models Parameters
Description: Computation of an estimation of the long-memory parameters and
the long-run covariance matrix using a multivariate model
(Lobato (1999) <doi:10.1016/S0304-4076(98)00038-4>; Shimotsu (2007) <doi:10.1016/j.jeconom.2006.01.003>). Two semi-parametric methods are
implemented: a Fourier based approach (Shimotsu (2007) <doi:10.1016/j.jeconom.2006.01.003>) and a wavelet based
approach (Achard and Gannaz (2016) <doi:10.1111/jtsa.12170>).
Author: Sophie Achard [aut, cre],
Irene Gannaz [aut]
Maintainer: Sophie Achard <sophie.achard@gipsa-lab.fr>
Diff between multiwave versions 1.2 dated 2016-11-24 and 1.4 dated 2019-05-06
DESCRIPTION | 9 ++++---- MD5 | 51 +++++++++++++++++++++++------------------------ R/mww_wav_eval.R | 2 - R/psi_hat_exact.R | 2 - R/scaling_function.R | 2 - data/brainHCP.txt.gz |binary inst |only man/DWTexact.Rd | 5 ++++ man/K_eval.Rd | 3 ++ man/compute_nj.Rd | 3 ++ man/fivarma.Rd | 4 +++ man/mfw.Rd | 4 +++ man/mfw_cov_eval.Rd | 5 ++++ man/mfw_eval.Rd | 3 ++ man/multiwave-package.Rd | 3 ++ man/mww.Rd | 3 ++ man/mww_cov_eval.Rd | 3 ++ man/mww_eval.Rd | 4 +++ man/mww_wav.Rd | 3 ++ man/mww_wav_cov_eval.Rd | 4 +++ man/mww_wav_eval.Rd | 5 ++++ man/psi_hat_exact.Rd | 3 ++ man/scaling_filter.Rd | 4 +++ man/scaling_function.Rd | 3 ++ man/toeplitz_nonsym.Rd | 3 ++ man/varma.Rd | 4 +++ man/vfracdiff.Rd | 4 +++ 27 files changed, 107 insertions(+), 32 deletions(-)
Title: Efficient Phylogenetics on Large Trees
Description: Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>
Diff between castor versions 1.3.5 dated 2019-02-15 and 1.3.6 dated 2019-05-06
DESCRIPTION | 8 +- MD5 | 18 ++-- R/asr_max_parsimony.R | 30 ++++--- R/asr_mk_model.R | 4 - R/fit_musse.R | 139 +++++++++++++++++++++++-------------- R/hsp_mk_model.R | 14 +-- man/asr_max_parsimony.Rd | 3 man/fit_musse.Rd | 2 src/RcppExports.cpp | 2 src/phylogenetics_cpp_routines.cpp | 34 ++++----- 10 files changed, 145 insertions(+), 109 deletions(-)
Title: Radiation Safety
Description: Provides functions for radiation safety, also known as "radiation protection" and "radiological control". The science of radiation protection is called "health physics" and its engineering functions are called "radiological engineering". Functions in this package cover many of the computations needed by radiation safety professionals. Examples include: obtaining updated calibration and source check values for radiation monitors to account for radioactive decay in a reference source, simulating instrument readings to better understand measurement uncertainty, correcting instrument readings for geometry and ambient atmospheric conditions. Many of these functions are described in Johnson and Kirby (2011, ISBN-13: 978-1609134198). Utilities are also included for developing inputs and processing outputs with radiation transport codes, such as MCNP, a general-purpose Monte Carlo N-Particle code that can be used for neutron, photon, electron, or coupled neutron/photon/electron transport (Werner et. al. (2018) <doi:10.2172/1419730>).
Author: Mark Hogue <mark.hogue.chp@gmail.com>
Maintainer: Mark Hogue <mark.hogue.chp@gmail.com>
Diff between radsafer versions 1.0.0 dated 2019-04-04 and 2.0.0 dated 2019-05-06
radsafer-1.0.0/radsafer/R/data |only radsafer-1.0.0/radsafer/R/data-raw |only radsafer-1.0.0/radsafer/R/dk_pct_to_num_t_h.R |only radsafer-1.0.0/radsafer/R/man |only radsafer-1.0.0/radsafer/R/mcnp_energy_hist.R |only radsafer-1.0.0/radsafer/R/mcnp_rot_transform.R |only radsafer-1.0.0/radsafer/R/mcnp_scan2spec.df.R |only radsafer-1.0.0/radsafer/R/radsafer.R |only radsafer-1.0.0/radsafer/R/tests |only radsafer-1.0.0/radsafer/man/dk_pct_to_num_t_h.Rd |only radsafer-1.0.0/radsafer/man/plot_spec_from_hist.Rd |only radsafer-1.0.0/radsafer/man/radsafer.Rd |only radsafer-1.0.0/radsafer/man/rot_fun.Rd |only radsafer-1.0.0/radsafer/man/si_hist.Rd |only radsafer-1.0.0/radsafer/man/sp_hist.Rd |only radsafer-1.0.0/radsafer/man/tan_d2.Rd |only radsafer-1.0.0/radsafer/man/tau_est.Rd |only radsafer-2.0.0/radsafer/DESCRIPTION | 11 radsafer-2.0.0/radsafer/MD5 | 167 +++---- radsafer-2.0.0/radsafer/NAMESPACE | 27 - radsafer-2.0.0/radsafer/R/RN_Spec_Act.R |only radsafer-2.0.0/radsafer/R/RN_index_screen.R |only radsafer-2.0.0/radsafer/R/RN_info.R |only radsafer-2.0.0/radsafer/R/RN_plt.R |only radsafer-2.0.0/radsafer/R/air_dens_cf.R | 1 radsafer-2.0.0/radsafer/R/bin_screen_phot.R |only radsafer-2.0.0/radsafer/R/disk_to_disk_solid_angle.R | 234 +++++----- radsafer-2.0.0/radsafer/R/dk_activity.R | 16 radsafer-2.0.0/radsafer/R/dk_cf.R | 26 - radsafer-2.0.0/radsafer/R/dk_pct_to_num_half_life.R | 9 radsafer-2.0.0/radsafer/R/dk_reverse.R | 12 radsafer-2.0.0/radsafer/R/dk_time.R | 9 radsafer-2.0.0/radsafer/R/half_life_2pt.R | 1 radsafer-2.0.0/radsafer/R/mcnp_cone_angle.R | 44 + radsafer-2.0.0/radsafer/R/mcnp_est_nps.R |only radsafer-2.0.0/radsafer/R/mcnp_matrix_rotations.R |only radsafer-2.0.0/radsafer/R/mcnp_plot_out_spec.R | 40 - radsafer-2.0.0/radsafer/R/mcnp_scan2spec.R |only radsafer-2.0.0/radsafer/R/mcnp_si_hist.R |only radsafer-2.0.0/radsafer/R/mcnp_si_sp_RD.R |only radsafer-2.0.0/radsafer/R/mcnp_sp_hist.R |only radsafer-2.0.0/radsafer/R/neutron_geom_cf.R | 1 radsafer-2.0.0/radsafer/R/ratemeter_sim.R | 3 radsafer-2.0.0/radsafer/R/scaler_sim.R | 1 radsafer-2.0.0/radsafer/R/search_alpha_by_E.R |only radsafer-2.0.0/radsafer/R/search_beta_by_E.R |only radsafer-2.0.0/radsafer/R/search_phot_by_E.R |only radsafer-2.0.0/radsafer/R/spec_0.1_0.3.R |only radsafer-2.0.0/radsafer/R/stay_time.R | 1 radsafer-2.0.0/radsafer/R/tau_estimate.R | 7 radsafer-2.0.0/radsafer/R/utils-pipe.R |only radsafer-2.0.0/radsafer/README.md | 211 +++++++-- radsafer-2.0.0/radsafer/data/spec_0.1_0.3.rda |only radsafer-2.0.0/radsafer/man/RN_Spec_Act.Rd |only radsafer-2.0.0/radsafer/man/RN_index_screen.Rd |only radsafer-2.0.0/radsafer/man/RN_info.Rd |only radsafer-2.0.0/radsafer/man/RN_plt.Rd |only radsafer-2.0.0/radsafer/man/air_dens_cf.Rd | 6 radsafer-2.0.0/radsafer/man/bin_screen_phot.Rd |only radsafer-2.0.0/radsafer/man/disk_to_disk_solid_angle.Rd | 29 - radsafer-2.0.0/radsafer/man/dk_activity.Rd | 16 radsafer-2.0.0/radsafer/man/dk_cf.Rd | 17 radsafer-2.0.0/radsafer/man/dk_pct_to_num_half_life.Rd | 6 radsafer-2.0.0/radsafer/man/dk_reverse.Rd | 21 radsafer-2.0.0/radsafer/man/dk_time.Rd | 11 radsafer-2.0.0/radsafer/man/figures/README-unnamed-chunk-12-1.png |binary radsafer-2.0.0/radsafer/man/figures/README-unnamed-chunk-13-1.png |binary radsafer-2.0.0/radsafer/man/figures/README-unnamed-chunk-16-1.png |binary radsafer-2.0.0/radsafer/man/figures/README-unnamed-chunk-19-1.png |only radsafer-2.0.0/radsafer/man/figures/README-unnamed-chunk-9-1.png |binary radsafer-2.0.0/radsafer/man/half_life_2pt.Rd | 1 radsafer-2.0.0/radsafer/man/mcnp_cone_angle.Rd |only radsafer-2.0.0/radsafer/man/mcnp_est_nps.Rd |only radsafer-2.0.0/radsafer/man/mcnp_matrix_rotations.Rd |only radsafer-2.0.0/radsafer/man/mcnp_plot_out_spec.Rd |only radsafer-2.0.0/radsafer/man/mcnp_scan2spec.Rd |only radsafer-2.0.0/radsafer/man/mcnp_si_hist.Rd |only radsafer-2.0.0/radsafer/man/mcnp_si_sp_RD.Rd |only radsafer-2.0.0/radsafer/man/mcnp_sp_hist.Rd |only radsafer-2.0.0/radsafer/man/neutron_geom_cf.Rd | 6 radsafer-2.0.0/radsafer/man/pipe.Rd |only radsafer-2.0.0/radsafer/man/rate_meter_sim.Rd | 3 radsafer-2.0.0/radsafer/man/scaler_sim.Rd | 6 radsafer-2.0.0/radsafer/man/scan2spec.df.Rd | 2 radsafer-2.0.0/radsafer/man/search_alpha_by_E.Rd |only radsafer-2.0.0/radsafer/man/search_beta_by_E.Rd |only radsafer-2.0.0/radsafer/man/search_phot_by_E.Rd |only radsafer-2.0.0/radsafer/man/spec_0.1_0.3.Rd |only radsafer-2.0.0/radsafer/man/tau_estimate.Rd |only 89 files changed, 612 insertions(+), 333 deletions(-)
Title: Estimation of Marginal Treatment Effects using Local
Instrumental Variables
Description: In the generalized Roy model, the marginal treatment effect (MTE) can be used as
a building block for constructing conventional causal parameters such as the average treatment
effect (ATE) and the average treatment effect on the treated (ATT) (Heckman, Urzua, and Vytlacil 2006
<doi:10.1162/rest.88.3.389>). Given a treatment selection model and an outcome model, the function mte()
estimates the MTE via a semiparametric local instrumental variables method (or via a normal selection model).
The function eval_mte() evaluates MTE at any combination of covariates x and latent resistance u, and the
function eval_mte_tilde() evaluates MTE projected onto the estimated propensity score (Zhou and Xie 2019
<https://www.journals.uchicago.edu/doi/abs/10.1086/702172>). The object returned by mte() can be used to
estimate conventional parameters such as ATE and ATT (via average()) or marginal policy-relevant
treatment effects (via mprte()).
Author: Xiang Zhou [aut, cre]
Maintainer: Xiang Zhou <xiang_zhou@fas.harvard.edu>
Diff between localIV versions 0.2.0 dated 2019-04-28 and 0.2.1 dated 2019-05-06
DESCRIPTION | 9 ++++---- MD5 | 18 ++++++++-------- R/eval_mte.R | 21 ++++++++++++++----- R/eval_mte_tilde.R | 53 +++++++++++++++++++++++++++++++++----------------- R/mprte.R | 5 ++-- R/mte.R | 11 ++++++++++ man/eval_mte.Rd | 12 +++++++---- man/eval_mte_tilde.Rd | 41 ++++++++++++++++++++++++++------------ man/mprte.Rd | 6 +++-- man/mte.Rd | 12 +++++++++++ 10 files changed, 131 insertions(+), 57 deletions(-)
Title: Redraw Base Graphics Using 'grid' Graphics
Description: Functions to convert a page of plots drawn with the
'graphics' package into identical output drawn with the 'grid' package.
The result looks like the original 'graphics'-based plot, but consists
of 'grid' grobs and viewports that can then be manipulated with
'grid' functions (e.g., edit grobs and revisit viewports).
Author: Paul Murrell [cre, aut],
Zhijian Wen [aut]
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between gridGraphics versions 0.3-0 dated 2018-04-03 and 0.4-0 dated 2019-05-06
DESCRIPTION | 8 +- MD5 | 24 +++---- NAMESPACE | 3 R/axis.R | 128 +++++++++++++++++++++++------------------- R/box.R | 14 ++++ R/convert.R | 14 ++++ R/graphics.R | 17 ++++- R/mtext.R | 8 +- R/par.R | 20 +++--- R/persp.R | 21 ++++-- inst/NEWS.Rd | 32 ++++++++++ inst/test-scripts/test-axis.R | 29 +++++++++ man/grid.echo.Rd | 11 +++ 13 files changed, 233 insertions(+), 96 deletions(-)