Title: Dynamic Generation of Scientific Reports
Description: The RSP markup language makes any text-based document come alive. RSP provides a powerful markup for controlling the content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g. 'Today's date is <%=Sys.Date()%>'. Contrary to many other literate programming languages, with RSP it is straightforward to loop over mixtures of code and text sections, e.g. in month-by-month summaries. RSP has also several preprocessing directives for incorporating static and dynamic contents of external files (local or online) among other things. Functions rstring() and rcat() make it easy to process RSP strings, rsource() sources an RSP file as it was an R script, while rfile() compiles it (even online) into its final output format, e.g. rfile('report.tex.rsp') generates 'report.pdf' and rfile('report.md.rsp') generates 'report.html'. RSP is ideal for self-contained scientific reports and R package vignettes. It's easy to use - if you know how to write an R script, you'll be up and running within minutes.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.rsp versions 0.43.0 dated 2018-08-26 and 0.43.1 dated 2019-02-05
DESCRIPTION | 12 +++--- MD5 | 43 +++++++++++------------ NEWS | 15 ++++++++ R/999.package.R | 3 - R/HttpDaemon.R | 2 - R/RspDirective.R | 5 ++ R/compileAsciiDoc.R | 3 + R/compileAsciiDocNoweb.R | 6 ++- R/readText.R | 5 ++ build/vignette.rds |binary inst/WORDLIST |only inst/doc/Dynamic_document_creation_using_RSP.pdf |binary inst/doc/RSP_intro.html | 11 +++-- inst/doc/RSP_intro.html.rsp | 2 - inst/doc/RSP_refcard.pdf |binary inst/doc/R_packages-LaTeX_vignettes.pdf |binary inst/doc/R_packages-RSP_vignettes.html | 2 - inst/doc/R_packages-Vignettes_prior_to_R300.pdf |binary man/R.rsp-package.Rd | 7 +-- man/compileAsciiDoc.Rd | 3 + man/compileAsciiDocNoweb.Rd | 6 ++- man/start.HttpDaemon.Rd | 2 - vignettes/RSP_intro.html.rsp | 2 - 23 files changed, 83 insertions(+), 46 deletions(-)
Title: Adding Progress Bar to '*apply' Functions
Description: A lightweight package that adds
progress bar to vectorized R functions
('*apply'). The implementation can easily be added
to functions where showing the progress is
useful (e.g. bootstrap). The type and style of the
progress bar (with percentages or remaining time)
can be set through options.
Supports several parallel processing backends.
Author: Peter Solymos [aut, cre], Zygmunt Zawadzki [aut]
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between pbapply versions 1.3-4 dated 2018-01-10 and 1.4-0 dated 2019-02-05
DESCRIPTION | 8 ++++---- MD5 | 10 ++++++---- NAMESPACE | 2 +- R/pblapply.R | 2 ++ R/pbmapply.R |only man/pbapply.Rd | 28 +++++++++++++++++++++++++--- tests |only 7 files changed, 38 insertions(+), 12 deletions(-)
Title: Routines for Logspline Density Estimation
Description: Contains routines for logspline density estimation.
The function oldlogspline() uses the same algorithm as the logspline package
version 1.0.x; i.e. the Kooperberg and Stone (1992)
algorithm (with an improved interface). The recommended routine logspline()
uses an algorithm from Stone et al (1997) <DOI:10.1214/aos/1031594728>.
Author: Charles Kooperberg <clk@fredhutch.org>
Maintainer: Charles Kooperberg <clk@fredhutch.org>
Diff between logspline versions 2.1.11 dated 2018-06-14 and 2.1.12 dated 2019-02-05
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- src/nlsd.c | 7 ++++++- 3 files changed, 13 insertions(+), 8 deletions(-)
More information about CongreveLamsdell2016 at CRAN
Permanent link
Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM
or Gibbs sampling, with optional kernel term and sampling techniques as described
by Xavier (2017) <doi:10.1186/s12859-017-1582-3>.
Author: Alencar Xavier, William Muir, Shizhong Xu, Katy Rainey.
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between bWGR versions 1.5.6 dated 2018-10-04 and 1.5.7 dated 2019-02-05
bWGR-1.5.6/bWGR/man/mkr.Rd |only bWGR-1.5.6/bWGR/src/wgr20180916.cpp |only bWGR-1.5.7/bWGR/DESCRIPTION | 8 - bWGR-1.5.7/bWGR/MD5 | 18 +- bWGR-1.5.7/bWGR/R/RcppExports.R | 234 ++++++++++++++++++------------------ bWGR-1.5.7/bWGR/R/cv.R | 4 bWGR-1.5.7/bWGR/R/mix.R | 9 - bWGR-1.5.7/bWGR/man/bWGR.Rd | 4 bWGR-1.5.7/bWGR/man/mvr.Rd |only bWGR-1.5.7/bWGR/man/wgr.Rd | 4 bWGR-1.5.7/bWGR/src/RcppExports.cpp | 26 +++- bWGR-1.5.7/bWGR/src/wgr20190205.cpp |only 12 files changed, 164 insertions(+), 143 deletions(-)
Title: Quantified Risk Assessment Toolkit
Description: An open source risk analysis toolkit based on the OpenFAIR taxonomy
<https://www2.opengroup.org/ogsys/catalog/C13K> and risk assessment standard
<https://www2.opengroup.org/ogsys/catalog/C13G>. Empowers an organization to
perform a quantifiable, repeatable, and data-driven risk review.
Author: David Severski [aut, cre] (<https://orcid.org/0000-0001-7867-0459>)
Maintainer: David Severski <davidski@deadheaven.com>
Diff between evaluator versions 0.3.1 dated 2018-10-18 and 0.3.2 dated 2019-02-05
DESCRIPTION | 12 MD5 | 30 +- NEWS.md | 20 + README.md | 9 build/vignette.rds |binary inst/doc/process.Rmd | 4 inst/doc/process.html | 32 ++ inst/doc/usage.Rmd | 6 inst/doc/usage.html | 82 ++++-- inst/openfair_example/tests/openfair_example-expected/001.json | 130 +++++----- inst/openfair_example/tests/openfair_example-expected/001.png |binary inst/openfair_example/tests/openfair_example.R | 4 inst/rmd/analyze_risk.Rmd | 17 - tests/testthat/test-summarize.R | 17 - vignettes/process.Rmd | 4 vignettes/usage.Rmd | 6 16 files changed, 222 insertions(+), 151 deletions(-)
Title: Estimation of Ego-Temporal Exponential Random Graph Models via
Expectation Maximization (EM)
Description: Estimation of ego-temporal exponential random graph models with two-stage estimation including initialization through k-means clustering on temporal exponential random graph model parameters and EM as per Campbell (2018) <doi:10.7910/DVN/TWHEZ9>.
Author: Benjamin W. Campbell [aut, cre],
Michael Salter-Townshend [ctb],
Thomas Brendan Murphy [ctb]
Maintainer: Benjamin W. Campbell <campbell.1721@osu.edu>
Diff between egoTERGM versions 2.0.1 dated 2018-10-12 and 2.1.0 dated 2019-02-05
DESCRIPTION | 10 +-- MD5 | 32 ++++++------ R/ego_ergm.R | 13 ++-- R/ego_tergm.R | 114 +++++++++++++++++++++++-------------------- R/interpret_ego_tergm.R | 3 - R/sim_egonets.R | 7 +- R/stability_validation.R | 41 +++++++++------ build/vignette.rds |binary inst/doc/KnechtVignette.R | 9 ++- inst/doc/KnechtVignette.Rmd | 13 +++- inst/doc/KnechtVignette.html | 54 ++++++++++---------- man/ego_ergm.Rd | 5 + man/ego_tergm.Rd | 6 +- man/plot_ego_tergm.Rd | 4 - man/sim_egonets.Rd | 7 +- vignettes/KnechtVignette.Rmd | 13 +++- vignettes/egoTERGM.bib | 2 17 files changed, 186 insertions(+), 147 deletions(-)
Title: Reads Fixed-Width ASCII Data Files (.txt or .dat) that Have
Accompanying Setup Files (.sps or .sas)
Description: Lets you open a fixed-width ASCII file (.txt or
.dat) that has an accompanying setup file (.sps or .sas). These file
combinations are sometimes referred to as .txt+.sps, .txt+.sas,
.dat+.sps, or .dat+.sas. This will only run in a txt-sps or txt-sas
pair in which the setup file contains instructions to open that text
file. It will NOT open other text files, .sav, .sas, or .por data
files. Fixed-width ASCII files with setup files are common in older
(pre-2000) government data.
Author: Jacob Kaplan [aut, cre]
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>
Diff between asciiSetupReader versions 2.0.0 dated 2019-02-04 and 2.0.1 dated 2019-02-05
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/helper.R | 3 +++ R/read_ascii_setup.R | 2 +- inst/doc/Introduction_to_asciiSetupReader.html | 4 ++-- inst/doc/making-an-sps-file.html | 4 ++-- inst/doc/parsing-an-sps-or-sas-file.html | 4 ++-- 8 files changed, 24 insertions(+), 17 deletions(-)
More information about asciiSetupReader at CRAN
Permanent link
Title: Functions and C++ Header Files for Computation on Manifolds
Description: We provide a number of algorithms to estimate fundamental statistics including Fréchet mean and geometric median for manifold-valued data. Also, C++ header files are contained that implement elementary operations on manifolds such as Sphere, Grassmann, and others. See Bhattacharya and Bhattacharya (2012) <doi:10.1017/CBO9781139094764> if you are interested in statistics on manifolds, and Absil et al (2007) <isbn:978-0-691-13298-3> on computational aspects of optimization on matrix manifolds.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyou@nd.edu>
Diff between RiemBase versions 0.2.1 dated 2018-11-29 and 0.2.2 dated 2019-02-05
DESCRIPTION | 6 ++-- MD5 | 33 ++++++++++++----------- NAMESPACE | 2 + NEWS.md | 8 ++++- R/RcppExports.R | 4 ++ R/RiemBase-package.R | 2 - R/auxiliary_checkers.R | 31 +++++++++++++++++++-- R/init.R |only R/rbase.curvedist.R |only R/rbase.mean.R | 24 ++++++++++++++++ R/rbase.median.R | 12 ++++++++ R/rbase.robust.R | 19 ++++++++++++- build/partial.rdb |binary inst/include/manifolds/riem_04stiefel.h | 2 - inst/include/manifolds/riem_05grassmann.h | 2 - inst/include/procedures/riemfunc_extdist.h | 2 - man/rbase.curvedist.Rd |only src/RcppExports.cpp | 16 +++++++++++ src/engines.cpp | 41 +++++++++++++++++++++++++++++ 19 files changed, 175 insertions(+), 29 deletions(-)
Title: An Interface to Google's 'BigQuery' 'API'
Description: Easily talk to Google's 'BigQuery' database from R.
Author: Hadley Wickham [aut, cre],
Kungliga Tekniska Högskolan [ctb] (strptime implementation),
The NetBSD Foundation, Inc. [ctb] (gmtime implementation),
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between bigrquery versions 1.0.0 dated 2018-04-24 and 1.1.0 dated 2019-02-05
DESCRIPTION | 12 ++-- MD5 | 91 ++++++++++++++++----------------- NAMESPACE | 2 NEWS.md | 37 +++++++++++++ R/bigrquery.R | 4 + R/bq-dataset.R | 8 ++ R/bq-download.R | 48 ++++++++++++++--- R/bq-job.R | 7 +- R/bq-perform.R | 8 +- R/bq-refs.R | 25 +++++---- R/bq-request.R | 5 + R/bq-test.R | 6 +- R/dbi-connection.R | 16 +++-- R/dbi-driver.R | 8 ++ R/dbi-result.R | 9 ++- R/dplyr.R | 6 +- R/old-job-upload.R | 5 + README.md | 57 ++++++++++---------- man/DBI.Rd | 6 +- man/api-dataset.Rd | 7 +- man/api-job.Rd | 4 - man/api-perform.Rd | 29 ++++------ man/bigquery.Rd | 8 ++ man/bigrquery-package.Rd | 3 - man/bq_field.Rd | 2 man/bq_query.Rd | 4 - man/bq_refs.Rd | 7 +- man/bq_table_download.Rd | 8 ++ man/bq_test_project.Rd | 4 - man/get_job.Rd | 1 man/insert_extract_job.Rd | 5 + man/insert_query_job.Rd | 1 man/insert_upload_job.Rd | 1 man/list_tabledata.Rd | 6 +- man/query_exec.Rd | 6 +- man/wait_for.Rd | 1 src/BqField.cpp | 27 ++++++++- src/RcppExports.cpp | 2 src/integer64.h |only tests/testthat/bg-refs-print.txt | 2 tests/testthat/test-bq-download.R | 35 ++++++++++++ tests/testthat/test-bq-parse.R | 57 ++++++++++++-------- tests/testthat/test-bq-refs.R | 12 ++-- tests/testthat/test-bq-table.R | 96 +++++++++++++++++++++++++---------- tests/testthat/test-dbi-connection.R | 11 ++++ tests/testthat/test-dbi-result.R | 13 +++- tests/testthat/test-gs-object.R | 1 47 files changed, 480 insertions(+), 233 deletions(-)
Title: Interpretable Machine Learning
Description: Interpretability methods to analyze the behavior and predictions of
any machine learning model.
Implemented methods are:
Feature importance described by Fisher et al. (2018) <arXiv:1801.01489>,
accumulated local effects plots described by Apley (2018) <arXiv:1612.08468>,
partial dependence plots described by Friedman (2001) <http://www.jstor.org/stable/2699986>,
individual conditional expectation ('ice') plots described by Goldstein et al. (2013) <doi:10.1080/10618600.2014.907095>,
local models (variant of 'lime') described by Ribeiro et. al (2016) <arXiv:1602.04938>,
the Shapley Value described by Strumbelj et. al (2014) <doi:10.1007/s10115-013-0679-x>,
feature interactions described by Friedman et. al <doi:10.1214/07-AOAS148> and
tree surrogate models.
Author: Christoph Molnar [aut, cre]
Maintainer: Christoph Molnar <christoph.molnar@gmail.com>
Diff between iml versions 0.8.1 dated 2019-01-02 and 0.9.0 dated 2019-02-05
DESCRIPTION | 11 +- MD5 | 72 +++++++++--------- NAMESPACE | 3 NEWS.md | 10 ++ R/FeatureEffect-ale.R | 1 R/FeatureEffect.R | 136 +++++++++++++++++++++++++---------- R/FeatureEffects.R |only R/FeatureImp.R | 8 -- R/Interaction.R | 22 ++--- R/InterpretationMethod.R | 26 +++--- R/LocalModel.R | 11 +- R/Predictor.R | 3 R/Shapley.R | 15 +-- R/TreeSurrogate.R | 8 -- R/utils.R | 23 +++++ inst/doc/intro.R | 6 + inst/doc/intro.Rmd | 10 ++ inst/doc/intro.html | 105 ++++++++++++++------------- inst/doc/parallel.R | 8 +- inst/doc/parallel.Rmd | 11 ++ inst/doc/parallel.html | 25 ++++-- man/FeatureEffect.Rd | 21 +++-- man/FeatureEffects.Rd |only man/FeatureImp.Rd | 4 - man/Interaction.Rd | 7 - man/LocalModel.Rd | 5 - man/Partial.Rd | 2 man/Shapley.Rd | 4 - man/TreeSurrogate.Rd | 4 - man/plot.FeatureEffect.Rd | 7 + man/plot.FeatureEffects.Rd |only man/plot.Interaction.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test-FeatureEffect.R | 45 +++++++++-- tests/testthat/test-FeatureEffects.R |only tests/testthat/test-LocalModel.R | 4 - tests/testthat/test-utils.R | 12 +++ vignettes/intro.Rmd | 10 ++ vignettes/parallel.Rmd | 11 ++ 39 files changed, 421 insertions(+), 231 deletions(-)
Title: Tools to Deal with Fuzzy Numbers
Description: S4 classes and methods
to deal with fuzzy numbers. They allow for computing any arithmetic
operations (e.g., by using the Zadeh extension principle),
performing approximation of arbitrary fuzzy numbers by trapezoidal
and piecewise linear ones, preparing plots for publications, computing
possibility and necessity values for comparisons, etc.
Author: Marek Gagolewski [aut, cre],
Jan Caha [ctb]
Maintainer: Marek Gagolewski <gagolews@rexamine.com>
Diff between FuzzyNumbers versions 0.4-5 dated 2019-01-16 and 0.4-6 dated 2019-02-05
DESCRIPTION | 10 +-- MD5 | 92 +++++++++++++++--------------- NEWS | 5 + R/FuzzyNumbers-package.R | 38 +++++------- R/auxiliary-convert.R | 4 - R/auxiliary-invert.R | 4 - R/class-01-FuzzyNumber.R | 4 - R/class-02-DiscontinuousFuzzyNumber.R | 4 - R/class-02-PiecewiseLinearFuzzyNumber.R | 9 +- R/class-02-PowerFuzzyNumber.R | 4 - R/class-02-TrapezoidalFuzzyNumber.R | 4 - R/methods-Arithmetic.R | 4 - R/methods-Extract.R | 4 - R/methods-alphaInterval.R | 6 - R/methods-alphacut.R | 12 +-- R/methods-ambiguity.R | 4 - R/methods-as.FuzzyNumber.R | 4 - R/methods-as.PiecewiseLinearFuzzyNumber.R | 4 - R/methods-as.PowerFuzzyNumber.R | 4 - R/methods-as.TrapezoidalFuzzyNumber.R | 4 - R/methods-as.character.R | 4 - R/methods-compare.R | 21 ++++++ R/methods-core.R | 4 - R/methods-distance.R | 4 - R/methods-evaluate.R | 4 - R/methods-expectedInterval.R | 4 - R/methods-expectedValue.R | 4 - R/methods-fapply.R | 4 - R/methods-integrate.R | 4 - R/methods-min_max.R | 4 - R/methods-piecewiseLinearApproximation.R | 4 - R/methods-plot.R | 4 - R/methods-show.R | 4 - R/methods-special_functions.R | 4 - R/methods-supp.R | 4 - R/methods-trapezoidalApproximation.R | 4 - R/methods-value.R | 4 - R/methods-weightedExpectedValue.R | 4 - R/methods-width.R | 4 - inst/CITATION | 4 - inst/doc/FuzzyNumbersTutorial.R | 4 - inst/doc/FuzzyNumbersTutorial.Rnw | 28 ++++----- inst/doc/FuzzyNumbersTutorial.pdf |binary man/FuzzyNumbers-package.Rd | 34 ++++------- man/alphaInterval-methods.Rd | 2 man/alphacut-methods.Rd | 6 - vignettes/FuzzyNumbersTutorial.Rnw | 28 ++++----- 47 files changed, 220 insertions(+), 203 deletions(-)
Title: Various Utilities for Microbial Genomics and Metagenomics
Description: A collection of functions for microbial ecology and other
applications of genomics and metagenomics. Companion package for the
Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016
<DOI:10.7287/peerj.preprints.1900v1>).
Author: Luis M. Rodriguez-R [aut, cre]
Maintainer: Luis M. Rodriguez-R <lmrodriguezr@gmail.com>
Diff between enveomics.R versions 1.4.3 dated 2019-01-06 and 1.4.4 dated 2019-02-05
enveomics.R-1.4.3/enveomics.R/man/enve.recplot2.aucp.Rd |only enveomics.R-1.4.4/enveomics.R/DESCRIPTION | 10 ++--- enveomics.R-1.4.4/enveomics.R/MD5 | 17 ++++----- enveomics.R-1.4.4/enveomics.R/NAMESPACE | 5 +- enveomics.R-1.4.4/enveomics.R/R/recplot.R | 5 +- enveomics.R-1.4.4/enveomics.R/R/recplot2.R | 18 +--------- enveomics.R-1.4.4/enveomics.R/README.md | 3 + enveomics.R-1.4.4/enveomics.R/man/enve.recplot.Rd | 4 +- enveomics.R-1.4.4/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd | 2 - enveomics.R-1.4.4/enveomics.R/man/z$-methods.Rd | 7 +-- 10 files changed, 27 insertions(+), 44 deletions(-)
Title: Models for Data from Unmarked Animals
Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates.
Author: Ian Fiske, Richard Chandler, David Miller, Andy Royle, Marc Kery, Jeff Hostetler, Rebecca Hutchinson, Adam Smith, Ken Kellner
Maintainer: Andy Royle <aroyle@usgs.gov>
Diff between unmarked versions 0.12-2 dated 2017-05-15 and 0.12-3 dated 2019-02-05
unmarked-0.12-2/unmarked/README |only unmarked-0.12-3/unmarked/DESCRIPTION | 20 unmarked-0.12-3/unmarked/MD5 | 99 ++-- unmarked-0.12-3/unmarked/NAMESPACE | 10 unmarked-0.12-3/unmarked/NEWS | 7 unmarked-0.12-3/unmarked/R/boot.R | 62 ++ unmarked-0.12-3/unmarked/R/getDesign.R | 132 +++++ unmarked-0.12-3/unmarked/R/occuMulti.R |only unmarked-0.12-3/unmarked/R/ranef.R | 28 + unmarked-0.12-3/unmarked/R/unmarkedFit.R | 309 +++++++++++++- unmarked-0.12-3/unmarked/R/unmarkedFitList.R | 15 unmarked-0.12-3/unmarked/R/unmarkedFrame.R | 178 +++++++- unmarked-0.12-3/unmarked/R/utils.R | 190 +++++--- unmarked-0.12-3/unmarked/build/vignette.rds |binary unmarked-0.12-3/unmarked/inst/doc/cap-recap.R | 38 - unmarked-0.12-3/unmarked/inst/doc/cap-recap.Rnw | 3 unmarked-0.12-3/unmarked/inst/doc/cap-recap.pdf |binary unmarked-0.12-3/unmarked/inst/doc/colext.R | 44 - unmarked-0.12-3/unmarked/inst/doc/colext.Rnw | 1 unmarked-0.12-3/unmarked/inst/doc/colext.pdf |binary unmarked-0.12-3/unmarked/inst/doc/distsamp.R | 20 unmarked-0.12-3/unmarked/inst/doc/distsamp.Rnw | 3 unmarked-0.12-3/unmarked/inst/doc/distsamp.pdf |binary unmarked-0.12-3/unmarked/inst/doc/spp-dist.R | 18 unmarked-0.12-3/unmarked/inst/doc/spp-dist.Rnw | 5 unmarked-0.12-3/unmarked/inst/doc/spp-dist.pdf |binary unmarked-0.12-3/unmarked/inst/doc/unmarked.R | 24 - unmarked-0.12-3/unmarked/inst/doc/unmarked.Rnw | 3 unmarked-0.12-3/unmarked/inst/doc/unmarked.pdf |binary unmarked-0.12-3/unmarked/inst/unitTests/runit.occuMulti.R |only unmarked-0.12-3/unmarked/inst/unitTests/runit.parboot.R | 302 ++++++++----- unmarked-0.12-3/unmarked/inst/unitTests/runit.predict.R | 85 +++ unmarked-0.12-3/unmarked/inst/unitTests/runit.ranef.R | 63 ++ unmarked-0.12-3/unmarked/inst/unitTests/runit.utils.R | 211 ++++++++- unmarked-0.12-3/unmarked/man/fitted-methods.Rd | 1 unmarked-0.12-3/unmarked/man/formatWideLong.Rd | 11 unmarked-0.12-3/unmarked/man/getP-methods.Rd | 3 unmarked-0.12-3/unmarked/man/occuMulti.Rd |only unmarked-0.12-3/unmarked/man/occuRN.Rd | 24 - unmarked-0.12-3/unmarked/man/predict-methods.Rd | 1 unmarked-0.12-3/unmarked/man/ranef-methods.Rd | 1 unmarked-0.12-3/unmarked/man/simulate-methods.Rd | 1 unmarked-0.12-3/unmarked/man/unmarked-package.Rd | 6 unmarked-0.12-3/unmarked/man/unmarkedFit-class.Rd | 5 unmarked-0.12-3/unmarked/man/unmarkedFrame-class.Rd | 7 unmarked-0.12-3/unmarked/man/unmarkedFrameOccuMulti.Rd |only unmarked-0.12-3/unmarked/src/init.c | 2 unmarked-0.12-3/unmarked/src/nll_occuMulti.cpp |only unmarked-0.12-3/unmarked/src/nll_occuMulti.h |only unmarked-0.12-3/unmarked/vignettes/cap-recap.Rnw | 3 unmarked-0.12-3/unmarked/vignettes/colext.Rnw | 1 unmarked-0.12-3/unmarked/vignettes/distsamp.Rnw | 3 unmarked-0.12-3/unmarked/vignettes/spp-dist.Rnw | 5 unmarked-0.12-3/unmarked/vignettes/unmarked.Rnw | 3 54 files changed, 1572 insertions(+), 375 deletions(-)
Title: Interactive Graphics for QTL Experiments
Description: Web-based interactive charts (using D3.js) for the analysis of
experimental crosses to identify genetic loci (quantitative trait
loci, QTL) contributing to variation in quantitative traits.
Author: Karl W Broman [aut, cre],
Michael Bostock [ctb, cph] (d3.js library in htmlwidgets/lib,
https://d3js.org),
Justin Palmer [ctb, cph] (d3.tip library in htmlwidgets/lib,
https://github.com/caged/d3-tip),
Cynthia Brewer [cph] (ColorBrewer library in htmlwidgets/lib,
http://colorbrewer2.org),
Mark Harrower [cph] (ColorBrewer library in htmlwidgets/lib,
http://colorbrewer2.org),
The Pennsylvania State University [cph] (ColorBrewer library in
htmlwidgets/lib, http://colorbrewer2.org),
jQuery Foundation [cph] (jQuery library in htmlwidgets/lib,
https://jquery.com),
jQuery contributors [ctb] (jQuery library in htmlwidgets/lib; see
https://github.com/jquery/jquery/blob/master/AUTHORS.txt),
jQuery UI contributors [ctb] (jQuery UI library in htmlwidgets/lib; see
https://jqueryui.com/about)
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtlcharts versions 0.9-6 dated 2017-06-01 and 0.11-6 dated 2019-02-05
qtlcharts-0.11-6/qtlcharts/DESCRIPTION | 54 qtlcharts-0.11-6/qtlcharts/LICENSE | 22 qtlcharts-0.11-6/qtlcharts/MD5 | 245 ++-- qtlcharts-0.11-6/qtlcharts/NEWS.md |only qtlcharts-0.11-6/qtlcharts/R/grav-data.R | 4 qtlcharts-0.11-6/qtlcharts/R/scat2scat.R | 7 qtlcharts-0.11-6/qtlcharts/README.md |only qtlcharts-0.11-6/qtlcharts/data/geneExpr.rda |binary qtlcharts-0.11-6/qtlcharts/data/grav.rda |binary qtlcharts-0.11-6/qtlcharts/inst/LICENSE | 22 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/iboxplot.js | 15 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/iboxplot.yaml | 4 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/idotplot.js | 15 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/idotplot.yaml | 4 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/iheatmap.js | 15 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/iheatmap.yaml | 4 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/ipleiotropy.js | 15 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/ipleiotropy.yaml | 4 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/iplot.js | 15 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/iplot.yaml | 4 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/iplotCorr.js | 17 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/iplotCorr.yaml | 4 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/iplotCurves.js | 15 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/iplotCurves.yaml | 4 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/iplotMScanone.js | 15 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/iplotMScanone.yaml | 4 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/iplotMap.js | 17 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/iplotMap.yaml | 6 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/iplotRF.js | 15 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/iplotRF.yaml | 4 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/iplotScanone.js | 15 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/iplotScanone.yaml | 4 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/iplotScantwo.js | 21 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/iplotScantwo.yaml | 4 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/itriplot.js | 15 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/itriplot.yaml | 4 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/colorbrewer/bower.json |only qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/d3-tip/bower.json |only qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/d3/bower.json |only qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/d3/d3.min.js | 10 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/d3panels/ReadMe.md | 45 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/d3panels/d3panels.min.js | 6 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/d3panels/package.json |only qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/jquery-ui/bower.json |only qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-bg_glass_55_fbf9ee_1x400.png |binary qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-bg_glass_65_ffffff_1x400.png |binary qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-bg_glass_75_dadada_1x400.png |binary qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-bg_glass_75_e6e6e6_1x400.png |binary qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-bg_glass_95_fef1ec_1x400.png |binary qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-icons_222222_256x240.png |binary qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-icons_2e83ff_256x240.png |binary qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-icons_454545_256x240.png |binary qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-icons_888888_256x240.png |binary qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-icons_cd0a0a_256x240.png |binary qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-longname.png |binary qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/jquery-ui/themes/smoothness/jquery-ui.css | 554 +++++----- qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/jquery-ui/themes/smoothness/jquery-ui.min.css | 8 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/jquery-ui/themes/smoothness/theme.css | 99 + qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/jquery/bower.json |only qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/jquery/dist/jquery.min.js | 6 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iboxplot.coffee | 19 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iboxplot.js | 143 +- qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/idotplot.coffee | 19 qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/idotplot.js | 66 - 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Title: Modelling Functions that Work with the Pipe
Description: Functions for modelling that help you seamlessly
integrate modelling into a pipeline of data manipulation and
visualisation.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between modelr versions 0.1.2 dated 2018-05-10 and 0.1.3 dated 2019-02-05
DESCRIPTION | 33 +++++++++++++++++++-------------- MD5 | 24 ++++++++++++------------ NAMESPACE | 1 + NEWS.md | 11 +++++++++++ R/cross-validation.R | 37 +++++++++++++++++++++++++++++++------ R/predictions.R | 27 +++++++++++++++------------ R/typical.R | 4 ++-- README.md | 29 ++++++++++++++++++----------- man/add_predictions.Rd | 23 ++++++++++++++--------- man/crossv_mc.Rd | 18 ++++++++++++------ man/modelr-package.Rd | 11 +++++++---- tests/testthat/test-resampling.R | 19 +++++++++++++++++++ tests/testthat/test-typical.R | 8 ++++++++ 13 files changed, 169 insertions(+), 76 deletions(-)
Title: Non-Normal Repeated Measurements Models
Description: Various functions to fit models for non-normal repeated
measurements.
Author: Bruce Swihart [cre, aut],
Jim Lindsey [aut] (Jim created this package, Bruce is maintaining the
CRAN version),
T.R. Ten Have [ctb, cph] (Wrote Logit_bin_nest.f90 (in binnest.f).),
Richard Cook [ctb, cph] (Wrote calcs.c, calcs.h, calcs1.c, calcs1.h,
calcs2.c, calcs2.h, calcs3.c, calcs3.h, calcs4.c, calcs4.h; defs.h;
gaps.c, gaps.h.),
Iain MacDonald [ctb, cph] (Wrote chidden.f, cphidden.f, hidden.f.),
Walter Zucchini [ctb, cph] (Wrote chidden.f, cphidden.f, hidden.f.),
Burton Garbow [ctb, cph] (Wrote eigen.f.),
Euginia Zharichenko [ctb, cph] (Wrote logitord.f.)
Maintainer: Bruce Swihart <bruce.swihart@gmail.com>
Diff between repeated versions 1.1.0 dated 2016-11-30 and 1.1.1 dated 2019-02-05
DESCRIPTION | 10 ++--- MD5 | 97 ++++++++++++++++++++++++++-------------------------- NAMESPACE | 2 - NEWS.md | 10 +++++ R/binnest.r | 2 - R/chidden.r | 4 +- R/cphidden.r | 4 +- R/gar.r | 4 +- R/gausscop.r | 36 +++++++++---------- R/gnlmix.r | 12 +++--- R/gnlmm.r | 40 ++++++++++----------- R/gnlmm3.r | 6 +-- R/hidden.r | 6 +-- R/hnlmix.r | 8 ++-- R/kalcount.r | 8 ++-- R/kalseries.r | 8 ++-- R/logitord.r | 2 - man/binnest.Rd | 16 ++++---- man/biv.betab.Rd | 5 +- man/biv.binom.Rd | 9 ++-- man/capture.Rd | 1 man/catmiss.Rd | 1 man/chidden.Rd | 13 +++--- man/cphidden.Rd | 7 +-- man/gar.Rd | 28 +++++++-------- man/gausscop.Rd | 24 ++++++------ man/glmm.Rd | 5 +- man/gnlmix.Rd | 13 +++--- man/gnlmm.Rd | 12 +++--- man/gnlmm3.Rd | 5 +- man/hidden.Rd | 19 ++++------ man/hnlmix.Rd | 16 ++++---- man/kalcount.Rd | 20 +++++----- man/kalseries.Rd | 21 +++++------ man/logitord.Rd | 11 ++--- man/marg.hom.Rd | 1 man/nbkal.Rd | 14 +++---- src/binnest.f | 4 +- src/chidden.f | 4 +- src/cphidden.f | 4 +- src/dist.c | 34 +++++++++--------- src/dist.h | 32 ++++++++--------- src/gar.c | 22 +++++------ src/gausscop.f | 4 +- src/hidden.f | 4 +- src/kcountb.c | 8 ++-- src/kserieb.c | 8 ++-- src/logitord.f | 4 +- src/repeated_init.c |only src/romberg.c | 4 +- 50 files changed, 315 insertions(+), 317 deletions(-)
Title: Tools for Natural Language Processing in French
Description: Tools for Natural Language Processing in French and texts from Marcel Proust's collection
"A La Recherche Du Temps Perdu". The novels contained in this collection are
"Du cote de chez Swann ", "A l'ombre des jeunes filles en fleurs","Le Cote de Guermantes",
"Sodome et Gomorrhe I et II", "La Prisonniere", "Albertine disparue", and "Le Temps retrouve".
Author: Colin Fay [aut, cre] (<https://orcid.org/0000-0001-7343-1846>)
Maintainer: Colin Fay <contact@colinfay.me>
Diff between proustr versions 0.2.1 dated 2017-10-04 and 0.4.0 dated 2019-02-05
proustr-0.2.1/proustr/R/pr_norm_punct.R |only proustr-0.2.1/proustr/R/sysdata.rda |only proustr-0.2.1/proustr/data/sentiments_polarity.rda |only proustr-0.2.1/proustr/data/sentiments_score.rda |only proustr-0.2.1/proustr/man/reexports.Rd |only proustr-0.2.1/proustr/man/sentiments_polarity.Rd |only proustr-0.2.1/proustr/man/sentiments_score.Rd |only proustr-0.4.0/proustr/DESCRIPTION | 22 proustr-0.4.0/proustr/MD5 | 79 - proustr-0.4.0/proustr/NAMESPACE | 11 proustr-0.4.0/proustr/NEWS.md | 29 proustr-0.4.0/proustr/R/globalVariables.R | 5 proustr-0.4.0/proustr/R/pr_detect_calendar.R | 18 proustr-0.4.0/proustr/R/pr_detect_pronouns.R | 30 proustr-0.4.0/proustr/R/pr_norm.R |only proustr-0.4.0/proustr/R/pr_stem.R | 20 proustr-0.4.0/proustr/R/proust_datasets.R | 17 proustr-0.4.0/proustr/R/proust_novels.R | 16 proustr-0.4.0/proustr/R/proust_random.R | 11 proustr-0.4.0/proustr/R/proust_sentiments.R | 27 proustr-0.4.0/proustr/R/proust_stop_words.R | 7 proustr-0.4.0/proustr/R/utils.R | 4 proustr-0.4.0/proustr/README.md | 285 +++--- proustr-0.4.0/proustr/build/vignette.rds |binary proustr-0.4.0/proustr/data/datalist | 3 proustr-0.4.0/proustr/data/proust_char.rda |binary proustr-0.4.0/proustr/data/stop_words.rda |only proustr-0.4.0/proustr/inst/doc/gettingstarted.R | 10 proustr-0.4.0/proustr/inst/doc/gettingstarted.Rmd | 32 proustr-0.4.0/proustr/inst/doc/gettingstarted.html | 535 ++++++++---- proustr-0.4.0/proustr/inst/hex-proustr.png |only proustr-0.4.0/proustr/man/albertinedisparue.Rd | 2 proustr-0.4.0/proustr/man/alombredesjeunesfillesenfleurs.Rd | 3 proustr-0.4.0/proustr/man/ducotedechezswann.Rd | 3 proustr-0.4.0/proustr/man/laprisonniere.Rd | 3 proustr-0.4.0/proustr/man/lecotedeguermantes.Rd | 3 proustr-0.4.0/proustr/man/letempretrouve.Rd | 3 proustr-0.4.0/proustr/man/pr_keep_only_alnum.Rd |only proustr-0.4.0/proustr/man/pr_normalize_punc.Rd | 2 proustr-0.4.0/proustr/man/pr_unacent.Rd |only proustr-0.4.0/proustr/man/proust_sentiments.Rd | 17 proustr-0.4.0/proustr/man/proust_stopwords.Rd | 6 proustr-0.4.0/proustr/man/sodomeetgomorrhe.Rd | 2 proustr-0.4.0/proustr/man/stop_words.Rd |only proustr-0.4.0/proustr/tests/testthat/test-clean-punc.R | 15 proustr-0.4.0/proustr/tests/testthat/test-init.R | 20 proustr-0.4.0/proustr/vignettes/gettingstarted.Rmd | 32 47 files changed, 753 insertions(+), 519 deletions(-)
Title: Approximate Bayesian Computations for Phylogenetic Comparative
Methods
Description: Fits by ABC, the parameters of a stochastic process modelling the phylogeny and evolution of a suite of traits following the tree. The user may define an arbitrary Markov process for the trait and phylogeny. Importantly, trait-dependent speciation models are handled and fitted to data. See K. Bartoszek, P. Lio' (2018) <arXiv:1812.03715>.
Author: Krzysztof Bartoszek <krzbar@protonmail.ch>, Pietro Lio'
Maintainer: Krzysztof Bartoszek <krzbar@protonmail.ch>
Diff between pcmabc versions 1.0 dated 2018-12-18 and 1.0.1 dated 2019-02-05
DESCRIPTION | 14 +++++++------- MD5 | 35 ++++++++++++++++++----------------- R/ABC.R | 2 +- R/ABCdist.R | 2 +- R/ABCmessage.R | 2 +- R/ABCupdate.R | 2 +- R/draw.R | 2 +- R/getTipSample.R | 2 +- R/rates.R | 2 +- R/simsde.R | 2 +- R/simtree.R | 4 ++-- inst/CITATION |only man/PCM_ABC.Rd | 4 ++++ man/draw_phylproc.Rd | 8 ++++++-- man/get_phylogenetic_sample.Rd | 6 ++++++ man/pcmabc-package.Rd | 8 ++++++-- man/simulate_phenotype_on_tree.Rd | 6 ++++++ man/simulate_phylproc.Rd | 4 ++++ man/simulate_sde_on_branch.Rd | 4 ++++ 19 files changed, 71 insertions(+), 38 deletions(-)
Title: Fast Truncated Singular Value Decomposition and Principal
Components Analysis for Large Dense and Sparse Matrices
Description: Fast and memory efficient methods for truncated singular value
decomposition and principal components analysis of large sparse and dense
matrices.
Author: Jim Baglama [aut, cph],
Lothar Reichel [aut, cph],
B. W. Lewis [aut, cre, cph]
Maintainer: B. W. Lewis <blewis@illposed.net>
Diff between irlba versions 2.3.2 dated 2018-01-11 and 2.3.3 dated 2019-02-05
irlba-2.3.2/irlba/README.md |only irlba-2.3.3/irlba/DESCRIPTION | 14 +++---- irlba-2.3.3/irlba/MD5 | 30 +++++++-------- irlba-2.3.3/irlba/R/irlba.R | 51 +++++++++++++++----------- irlba-2.3.3/irlba/R/prcomp.R | 4 +- irlba-2.3.3/irlba/R/ssvd.R | 24 ++---------- irlba-2.3.3/irlba/README |only irlba-2.3.3/irlba/build/vignette.rds |binary irlba-2.3.3/irlba/inst/doc/irlba.pdf |binary irlba-2.3.3/irlba/man/irlba.Rd | 7 ++- irlba-2.3.3/irlba/man/partial_eigen.Rd | 3 + irlba-2.3.3/irlba/man/prcomp_irlba.Rd | 1 irlba-2.3.3/irlba/man/ssvd.Rd | 19 +-------- irlba-2.3.3/irlba/man/summary.irlba_prcomp.Rd | 1 irlba-2.3.3/irlba/man/svdr.Rd | 1 irlba-2.3.3/irlba/src/irlb.c | 19 +++++++-- irlba-2.3.3/irlba/tests/test.R | 28 +++++++++++++- 17 files changed, 111 insertions(+), 91 deletions(-)
Title: Enhance Shiny Apps with Customizable Modules
Description: Provides highly customizable modules to enhance your shiny apps.
Includes layout independent collapsible boxes and value boxes, a very fast
autocomplete input, rhandsontable extensions for filtering and paging and
much more.
Author: Richard Kunze, Mirjam Rehr
Maintainer: Richard Kunze <richard.kunze@daqana.com>
Diff between dqshiny versions 0.0.2 dated 2019-01-29 and 0.0.3 dated 2019-02-05
DESCRIPTION | 6 MD5 | 40 NEWS.md | 9 R/autocomplete_input.R | 1 R/dq_handsontable.R | 59 - R/dqshiny.R | 11 R/filter_row.R | 161 +-- R/filtering.R | 4 R/js.R | 12 R/sorting.R | 2 README.md | 3 man/add_js.Rd | 8 man/dq_render_handsontable.Rd | 11 tests/testthat/shinytest/dq_handsontable/app.R | 2 tests/testthat/shinytest/dq_handsontable/tests/dq_handsontableTest-expected/001.json | 484 +++------ tests/testthat/shinytest/dq_handsontable/tests/dq_handsontableTest-expected/002.json | 136 +- tests/testthat/shinytest/dq_handsontable/tests/dq_handsontableTest-expected/003.json | 6 tests/testthat/shinytest/dq_handsontable/tests/dq_handsontableTest-expected/004.json | 508 +++++----- tests/testthat/test-dq_handsontable.R | 20 tests/testthat/test-filter_row.R | 55 - tests/testthat/test-js.R | 4 21 files changed, 773 insertions(+), 769 deletions(-)
Title: Matching Algorithms for Causal Inference with Clustered Data
Description: Provides functions to perform matching algorithms for causal inference with clustered data, as described in B. Arpino and M. Cannas (2016) <doi:10.1002/sim.6880>. Pure within-cluster and preferential within-cluster matching are implemented. Both algorithms provide causal estimates with cluster-adjusted estimates of standard errors.
Author: Massimo Cannas [aut, cre],
Bruno Arpino [ctb],
Elena Colicino [ctb]
Maintainer: Massimo Cannas <massimo.cannas@unica.it>
Diff between CMatching versions 2.2.1 dated 2018-10-05 and 2.3.0 dated 2019-02-05
DESCRIPTION | 12 ++--- MD5 | 12 ++--- R/CMatch.R | 103 +++++++++++++++++++++++++++++------------------ build/partial.rdb |binary man/CMatching-package.Rd | 57 ++++++++++++++++++++------ man/MatchPW.Rd | 6 +- man/MatchW.Rd | 2 7 files changed, 127 insertions(+), 65 deletions(-)
Title: JSON for Linking Data
Description: JSON-LD is a light-weight syntax for expressing linked data. It is primarily
intended for web-based programming environments, interoperable web services and for
storing linked data in JSON-based databases. This package provides bindings to the
JavaScript library for converting, expanding and compacting JSON-LD documents.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
rOpenSci [fnd] (https://ropensci.org)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between jsonld versions 2.0 dated 2018-05-06 and 2.1 dated 2019-02-05
DESCRIPTION | 6 ++-- MD5 | 8 ++--- NEWS | 3 ++ R/wrappers.R | 34 +++++++++++++++++++--- inst/js/wrappers.js | 78 ++++++++++------------------------------------------ 5 files changed, 54 insertions(+), 75 deletions(-)
Title: Combine Data from Positive and Negative Ionization Mode Finding
Common Entities
Description: Find common entities detected in both positive and negative
ionization mode, delete this entity in the less sensible mode and combine both
matrices.
Author: Monica Calderon-Santiago
Maintainer: Monica Calderon-Santiago <b42casam@uco.es>
Diff between MScombine versions 1.3 dated 2019-01-24 and 1.4 dated 2019-02-05
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/FindCommon.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-12 0.1-6
2018-04-10 0.1-5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-11-14 0.1-79
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-01 2.2-7
2016-12-21 2.0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-08-17 1.0.2
2018-05-31 1.0.1
Title: Multi-Category Classification Accuracy
Description: It contains six common multi-category classification accuracy evaluation measures:
Hypervolume Under Manifold (HUM), described in
Li and Fine (2008) <doi:10.1093/biostatistics/kxm050>.
Correct Classification Percentage (CCP), Integrated Discrimination Improvement (IDI), Net Reclassification Improvement (NRI), R-Squared Value (RSQ), described in
Li, Jiang and Fine (2013) <doi:10.1093/biostatistics/kxs047>.
Polytomous Discrimination Index (PDI), described in
Van Calster et al. (2012) <doi:10.1007/s10654-012-9733-3>.
Li et al. (2018) <doi:10.1177/0962280217692830>.
We described all these above measures and our mcca package in
Li, Gao and D'Agostino (2019) <doi:10.1002/sim.8103>.
Author: Ming Gao, Jialiang Li
Maintainer: Ming Gao <gaoming@umich.edu>
Diff between mcca versions 0.4.0 dated 2018-09-14 and 0.5.0 dated 2019-02-05
DESCRIPTION | 12 ++++++++---- MD5 | 10 +++++----- R/hum.R | 18 +++++++++--------- man/ccp.Rd | 2 +- man/mcca-package.Rd | 17 ++++++++++++----- man/rsq.Rd | 2 +- 6 files changed, 36 insertions(+), 25 deletions(-)
Title: Build Common Tables of Summary Statistics for Reports
Description: Mainly used to build tables that are commonly presented for
bio-medical/health research, such as basic characteristic tables or
descriptive statistics.
Author: Luke Johnston [aut, cre] (<https://orcid.org/0000-0003-4169-2616>)
Maintainer: Luke Johnston <lwjohnst@gmail.com>
Diff between carpenter versions 0.2.1 dated 2017-05-22 and 0.2.2 dated 2019-02-05
DESCRIPTION | 17 - LICENSE | 5 MD5 | 47 ++-- NAMESPACE | 4 NEWS.md | 12 + R/add_rows.R | 13 - R/build_table.R | 73 +++--- R/carpenter-package.R | 10 R/outline_table.R | 2 R/renaming.R | 6 R/stats.R | 4 R/utils-pipe.R |only README.md | 67 +++-- build/vignette.rds |binary inst/doc/carpenter.Rmd | 1 inst/doc/carpenter.html | 434 ++++++++++++++++++++++++++++--------- man/add_rows.Rd | 11 man/build_table.Rd | 8 man/carpenter.Rd | 10 man/figures |only man/outline_table.Rd | 6 man/pipe.Rd |only man/renaming.Rd | 8 man/table_stats.Rd | 8 tests/testthat/test-build_tables.R | 43 ++- vignettes/carpenter.Rmd | 1 26 files changed, 551 insertions(+), 239 deletions(-)
Title: Open Population Capture-Recapture
Description: Functions for non-spatial and spatial open-population capture-recapture analysis.
Author: Murray Efford [aut, cre] (<https://orcid.org/0000-0001-5231-5184>)
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between openCR versions 1.3.2 dated 2018-12-09 and 1.3.4 dated 2019-02-05
openCR-1.3.2/openCR/inst/doc/openCR-manual.pdf |only openCR-1.3.4/openCR/DESCRIPTION | 10 +++++----- openCR-1.3.4/openCR/MD5 | 17 ++++++++--------- openCR-1.3.4/openCR/NEWS | 18 ++++++++++++++++++ openCR-1.3.4/openCR/R/openCR.design.R | 2 ++ openCR-1.3.4/openCR/R/openCR.make.newdata.R | 4 +++- openCR-1.3.4/openCR/R/summary.R | 11 ++++++++--- openCR-1.3.4/openCR/inst/doc/openCR-vignette.pdf |binary openCR-1.3.4/openCR/man/classMembership.Rd | 2 +- openCR-1.3.4/openCR/man/openCR-package.Rd | 7 +++---- 10 files changed, 48 insertions(+), 23 deletions(-)
Title: Quiver Plots for 'ggplot2'
Description: An extension of 'ggplot2' to provide quiver plots to visualise vector fields.
This functionality is implemented using a geom to produce a new graphical layer, which
allows aesthetic options. This layer can be overlaid on a map to improve visualisation
of mapped data.
Author: Mitchell O'Hara-Wild [aut, cre]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between ggquiver versions 0.1.0 dated 2017-08-15 and 0.2.0 dated 2019-02-05
ggquiver-0.1.0/ggquiver/man/figure |only ggquiver-0.2.0/ggquiver/DESCRIPTION | 14 ++-- ggquiver-0.2.0/ggquiver/MD5 | 26 +++---- ggquiver-0.2.0/ggquiver/NAMESPACE | 1 ggquiver-0.2.0/ggquiver/NEWS.md | 4 + ggquiver-0.2.0/ggquiver/R/geom-quiver.r | 49 +++++++------- ggquiver-0.2.0/ggquiver/R/ggquiver.R | 3 ggquiver-0.2.0/ggquiver/R/stat-quiver.r | 27 ++++--- ggquiver-0.2.0/ggquiver/README.md | 33 ++++++--- ggquiver-0.2.0/ggquiver/man/figures |only ggquiver-0.2.0/ggquiver/man/geom_quiver.Rd | 45 ++++++------ ggquiver-0.2.0/ggquiver/man/ggquiver-package.Rd | 8 +- ggquiver-0.2.0/ggquiver/tests/testthat/test-geom_quiver.R | 31 +++++--- 13 files changed, 140 insertions(+), 101 deletions(-)
Title: Distance Measure Based Judgment and Learning
Description: Implements various decision support tools related to the Econometrics & Technometrics.
Subroutines include correlation reliability test, Mahalanobis distance measure for outlier detection, combinatorial search (all possible subset regression), non-parametric efficiency analysis measures: DDF (directional distance function), DEA (data envelopment analysis), HDF (hyperbolic distance function), SBM (slack-based measure), and SF (shortage function), benchmarking, Malmquist productivity analysis, risk analysis, technology adoption model, new product target setting, etc.
Author: Dong-Joon Lim, PhD
Maintainer: Dong-Joon Lim <tgno3.com@gmail.com>
Diff between DJL versions 2.8 dated 2018-12-09 and 2.9 dated 2019-02-05
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 12 ++++++++++++ R/roc.dea.R | 2 +- R/target.spec.dea.R | 48 +++++++++++++++++++++++++----------------------- man/target.spec.dea.Rd | 2 +- 6 files changed, 48 insertions(+), 34 deletions(-)
Title: Taking the Pain Out of Catching and Handling Conditions
Description: R has a unique way of dealing with warnings, errors, messages,
and other conditions, but it can often be troublesome to users coming
from different programming backgrounds. The purpose of this package is
to provide flexible and useful tools for handling R conditions with
less hassle. In order to lower the barrier of entry, keep code clean
and readable, and reduce the amount of typing required, `catchr` uses
a very simple domain-specific language that simplifies things on the
front-end.
This package aims to maintain a continuous learning curve that lets new
users jump straight in to condition-handling, while simultaneously
offering depth and complexity for more advanced users.
Author: Zachary Burchill [aut, cre, cph]
Maintainer: Zachary Burchill <zach.burchill.code@gmail.com>
Diff between catchr versions 0.1.0 dated 2018-12-30 and 0.2.0 dated 2019-02-05
catchr-0.1.0/catchr/R/code.R |only catchr-0.1.0/catchr/man/col_cond_page.Rd |only catchr-0.1.0/catchr/man/print_helpers.Rd |only catchr-0.1.0/catchr/man/raising_conds.Rd |only catchr-0.1.0/catchr/man/signal_custom_condition.Rd |only catchr-0.2.0/catchr/DESCRIPTION | 29 + catchr-0.2.0/catchr/MD5 | 50 ++- catchr-0.2.0/catchr/NAMESPACE | 48 ++ catchr-0.2.0/catchr/NEWS.md | 27 + catchr-0.2.0/catchr/R/arg-wrangling.R |only catchr-0.2.0/catchr/R/catching-n-plans.R |only catchr-0.2.0/catchr/R/check-n-clean.R |only catchr-0.2.0/catchr/R/help-docs.R |only catchr-0.2.0/catchr/R/make-handlers.R |only catchr-0.2.0/catchr/R/options.R |only catchr-0.2.0/catchr/R/printing.R |only catchr-0.2.0/catchr/R/zzz.R |only catchr-0.2.0/catchr/README.md | 349 +++++++++++++-------- catchr-0.2.0/catchr/build |only catchr-0.2.0/catchr/inst |only catchr-0.2.0/catchr/man/args_and_kwargs.Rd |only catchr-0.2.0/catchr/man/beep_with.Rd |only catchr-0.2.0/catchr/man/catchers.Rd |only catchr-0.2.0/catchr/man/catchr-DSL.Rd |only catchr-0.2.0/catchr/man/catchr_opts.Rd |only catchr-0.2.0/catchr/man/collecting-conditions.Rd |only catchr-0.2.0/catchr/man/default_catchr_options.Rd |only catchr-0.2.0/catchr/man/default_plan.Rd |only catchr-0.2.0/catchr/man/dispense_collected.Rd |only catchr-0.2.0/catchr/man/extract_display_string.Rd |only catchr-0.2.0/catchr/man/first_muffle_restart.Rd |only catchr-0.2.0/catchr/man/give_newline.Rd |only catchr-0.2.0/catchr/man/has_handler_args.Rd |only catchr-0.2.0/catchr/man/is_catchr_plan.Rd |only catchr-0.2.0/catchr/man/make_plans.Rd |only catchr-0.2.0/catchr/man/reserved-conditions.Rd |only catchr-0.2.0/catchr/man/user_displays.Rd |only catchr-0.2.0/catchr/man/user_exits.Rd |only catchr-0.2.0/catchr/man/view-plans.Rd |only catchr-0.2.0/catchr/man/with_ordered_handlers.Rd |only catchr-0.2.0/catchr/tests |only catchr-0.2.0/catchr/vignettes |only 42 files changed, 348 insertions(+), 155 deletions(-)
Title: 'AWS' Athena 'DBI' Wrapper
Description: 'RJDBC' based 'DBI' driver to Amazon Athena, which is an interactive
query service to analyze data in Amazon 'S3' using standard 'SQL'.
Author: Neal Fultz <nfultz@gmail.com>, Gergely Daróczi <gergely@system1.com>
Maintainer: Neal Fultz <nfultz@gmail.com>
Diff between AWR.Athena versions 1.1.0-1 dated 2017-11-19 and 2.0.6-1 dated 2019-02-05
AWR.Athena-1.1.0-1/AWR.Athena/man/AthenaResult-class.Rd |only AWR.Athena-1.1.0-1/AWR.Athena/man/dbSendQuery-AthenaConnection-character-method.Rd |only AWR.Athena-1.1.0-1/AWR.Athena/man/fetch-AthenaResult-numeric-method.Rd |only AWR.Athena-2.0.6-1/AWR.Athena/DESCRIPTION | 8 - AWR.Athena-2.0.6-1/AWR.Athena/MD5 | 17 +- AWR.Athena-2.0.6-1/AWR.Athena/NAMESPACE | 4 AWR.Athena-2.0.6-1/AWR.Athena/R/athena.R | 69 +--------- AWR.Athena-2.0.6-1/AWR.Athena/R/zzz.R | 6 AWR.Athena-2.0.6-1/AWR.Athena/README.md | 2 AWR.Athena-2.0.6-1/AWR.Athena/inst/java/log4j.properties | 3 AWR.Athena-2.0.6-1/AWR.Athena/man/Athena.Rd | 10 - 11 files changed, 33 insertions(+), 86 deletions(-)