Title: The Official SolveBio API Client for R
Description: R language bindings for SolveBio's API.
SolveBio is a biomedical knowledge hub that enables life science
organizations to collect and harmonize the complex, disparate
"multi-omic" data essential for today's R&D and BI needs.
For more information, visit <https://www.solvebio.com>.
Author: David Caplan
Maintainer: David Caplan <dcaplan@solvebio.com>
Diff between solvebio versions 0.2.3 dated 2016-11-02 and 0.3.0 dated 2016-11-09
DESCRIPTION | 6 ++-- MD5 | 11 +++++--- NAMESPACE | 2 + NEWS.md |only R/dataset.R | 66 ++++++++++++++++++++++++++++++++++++++++++++++++++ README.md | 26 +++++++++---------- man/Dataset.count.Rd |only man/Dataset.facets.Rd |only 8 files changed, 90 insertions(+), 21 deletions(-)
Title: Robust Meta-Analysis and Meta-Regression
Description: Performs meta-analysis and meta-regression using standard and robust methods with confidence intervals based on the profile likelihood. Robust methods are based on alternative distributions for the random effect, either the t-distribution (Lee and Thompson, 2008 <doi:10.1002/sim.2897> or Baker and Jackson, 2008 <doi:10.1007/s10729-007-9041-8>) or mixtures of normals (Beath, 2014 <doi:10.1002/jrsm.1114>).
Author: Ken Beath [aut, cre], Ben Bolker [aut], R Development Core Team [aut]
Maintainer: Ken Beath <ken.beath@mq.edu.au>
Diff between metaplus versions 0.7-8 dated 2016-09-11 and 0.7-9 dated 2016-11-09
metaplus-0.7-8/metaplus/inst/doc/beath-examples.R |only metaplus-0.7-8/metaplus/inst/doc/index.html |only metaplus-0.7-9/metaplus/DESCRIPTION | 8 ++-- metaplus-0.7-9/metaplus/MD5 | 25 +++++++-------- metaplus-0.7-9/metaplus/R/metaplus.R | 2 - metaplus-0.7-9/metaplus/R/plot.outlierProbs.R | 12 +++---- metaplus-0.7-9/metaplus/R/profilemix.metaplus.R | 4 +- metaplus-0.7-9/metaplus/R/profilenorm.metaplus.R | 10 ++---- metaplus-0.7-9/metaplus/R/profilet.metaplus.R | 7 ++-- metaplus-0.7-9/metaplus/build/vignette.rds |binary metaplus-0.7-9/metaplus/inst/NEWS | 10 ++++++ metaplus-0.7-9/metaplus/inst/doc/metaplus-package-code.R |only metaplus-0.7-9/metaplus/inst/doc/metaplus-package.pdf |binary metaplus-0.7-9/metaplus/man/metaplus.Rd | 2 - metaplus-0.7-9/metaplus/man/summary.Rd | 2 - 15 files changed, 45 insertions(+), 37 deletions(-)
Title: Bayesian Analysis of qRT-PCR Data
Description: Quantitative RT-PCR data are analyzed using generalized linear mixed models based on lognormal-Poisson error distribution, fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). The package also implements a lognormal model for higher-abundance data and a "classic" model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. The detailed tutorial is available here: <http://bit.ly/1Nwo4CB>.
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz <matz@utexas.edu>
Diff between MCMC.qpcr versions 1.2.2 dated 2015-10-28 and 1.2.3 dated 2016-11-09
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/HPDplot.R | 6 ++++-- R/HPDpoints.R | 2 +- man/HPDplot.Rd | 3 ++- man/MCMC.qpcr-package.Rd | 4 ++-- 6 files changed, 19 insertions(+), 16 deletions(-)
Title: High-Performance Stemmer, Tokenizer, and Spell Checker for R
Description: A spell checker and morphological analyzer library designed for
languages with rich morphology and complex word compounding or character
encoding. The package can check and analyze individual words as well as
search for incorrect words within a text, latex, html or xml document. Use
the 'devtools' package to spell check R documentation with 'hunspell'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between hunspell versions 2.1 dated 2016-10-03 and 2.2 dated 2016-11-09
DESCRIPTION | 8 +-- MD5 | 12 ++--- NEWS | 3 + build/vignette.rds |binary inst/doc/intro.html | 109 ++++++++++++++++++++++++++-------------------------- man/hunspell.Rd | 14 +++--- src/utils.h | 15 ++++--- 7 files changed, 85 insertions(+), 76 deletions(-)
Title: HTML Widgets for R
Description: A framework for creating HTML widgets that render in various
contexts including the R console, 'R Markdown' documents, and 'Shiny'
web applications.
Author: Ramnath Vaidyanathan [aut, cph],
Yihui Xie [aut],
JJ Allaire [aut, cre],
Joe Cheng [aut],
Kenton Russell [aut, cph],
RStudio [cph]
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between htmlwidgets versions 0.7 dated 2016-08-02 and 0.8 dated 2016-11-09
DESCRIPTION | 8 ++++---- MD5 | 35 ++++++++++++++++++----------------- NAMESPACE | 1 + R/utils.R | 13 ++++++++++--- R/widgetid.R | 5 ++++- build/vignette.rds |binary inst/NEWS | 10 ++++++++++ inst/doc/develop_advanced.R | 8 +++++--- inst/doc/develop_advanced.Rmd | 8 ++++---- inst/doc/develop_advanced.html | 29 ++++++++++++++++++----------- inst/doc/develop_intro.Rmd | 4 ++-- inst/doc/develop_intro.html | 17 +++++++++++------ inst/doc/develop_sizing.Rmd | 2 +- inst/doc/develop_sizing.html | 15 ++++++++++----- inst/www/htmlwidgets.js | 2 +- man/getDependency.Rd |only vignettes/develop_advanced.Rmd | 8 ++++---- vignettes/develop_intro.Rmd | 4 ++-- vignettes/develop_sizing.Rmd | 2 +- 19 files changed, 106 insertions(+), 65 deletions(-)
Title: Penalized Regression Models with Overlapping Grouped Covariates
Description: Fit the regularization path of linear, logistic or Cox models with
overlapping grouped covariates based on the latent group lasso approach. Latent
group MCP/SCAD as well as bi-level selection methods, namely the group exponential
lasso and the composite MCP are also available. This package serves as an
extension of R package 'grpreg' (by Dr. Patrick Breheny <patrick-breheny@uiowa.edu>)
for grouped variable selection involving overlaps between groups.
Author: Yaohui Zeng, Patrick Breheny
Maintainer: Yaohui Zeng <yaohui-zeng@uiowa.edu>
Diff between grpregOverlap versions 1.0-1 dated 2015-09-14 and 2.1-1 dated 2016-11-09
grpregOverlap-1.0-1/grpregOverlap/tests |only grpregOverlap-2.1-1/grpregOverlap/DESCRIPTION | 14 - grpregOverlap-2.1-1/grpregOverlap/MD5 | 40 ++- grpregOverlap-2.1-1/grpregOverlap/NAMESPACE | 4 grpregOverlap-2.1-1/grpregOverlap/NEWS |only grpregOverlap-2.1-1/grpregOverlap/R/cv.grpsurvOverlap.R |only grpregOverlap-2.1-1/grpregOverlap/R/grpregOverlap.R | 101 +++++++--- grpregOverlap-2.1-1/grpregOverlap/R/overlapMatrix.R | 17 - grpregOverlap-2.1-1/grpregOverlap/R/plot.R | 36 ++- grpregOverlap-2.1-1/grpregOverlap/R/plot.cv.grpregOverlap.R |only grpregOverlap-2.1-1/grpregOverlap/R/predict.R | 44 +++- grpregOverlap-2.1-1/grpregOverlap/R/predict.grpsurvOverlap.R |only grpregOverlap-2.1-1/grpregOverlap/R/summary.cv.grpregOverlap.R | 8 grpregOverlap-2.1-1/grpregOverlap/README.md | 21 +- grpregOverlap-2.1-1/grpregOverlap/data/pathway.dat.RData |binary grpregOverlap-2.1-1/grpregOverlap/man/cv.grpregOverlap.Rd | 2 grpregOverlap-2.1-1/grpregOverlap/man/cv.grpsurvOverlap.Rd |only grpregOverlap-2.1-1/grpregOverlap/man/grpregOverlap-internal.Rd | 2 grpregOverlap-2.1-1/grpregOverlap/man/grpregOverlap-package.Rd | 2 grpregOverlap-2.1-1/grpregOverlap/man/grpregOverlap.Rd | 56 +++-- grpregOverlap-2.1-1/grpregOverlap/man/plot.cv.grpregOverlap.Rd |only grpregOverlap-2.1-1/grpregOverlap/man/predict.grpregOverlap.Rd | 16 - grpregOverlap-2.1-1/grpregOverlap/man/predict.grpsurvOverlap.Rd |only grpregOverlap-2.1-1/grpregOverlap/man/summary.cv.grpregOverlap.Rd | 2 24 files changed, 234 insertions(+), 131 deletions(-)
Title: Fungible Coefficients and Monte Carlo Functions
Description: Computes fungible coefficients and Monte Carlo data.
Underlying theory for these functions is described in the following publications:
Waller, N. (2008). Fungible Weights in Multiple Regression. Psychometrika, 73(4), 691-703, <DOI10.1007/s11336-008-9066-z>.
Waller, N. & Jones, J. (2009). Locating the Extrema of Fungible Regression Weights.
Psychometrika, 74(4), 589-602, <DOI10.1007/s11336-008-9087-7>.
Waller, N. G. (2016). Fungible Correlation Matrices:
A Method for Generating Nonsingular, Singular, and Improper Correlation Matrices for
Monte Carlo Research. Multivariate Behavioral Research, 51(4), 554-568, <DOI10.1080/00273171.2016.1178566>.
Jones, J. A. & Waller, N. G. (2015). The normal-theory and asymptotic distribution-free (ADF)
covariance matrix of standardized regression coefficients: theoretical extensions
and finite sample behavior. Psychometrika, 80, 365-378, <DOI10.1007/s11336-013-9380-y>.
Author: Niels G. Waller <nwaller@umn.edu> and Jeff Jones <jeff.jones@kornferry.com>
Maintainer: Niels G. Waller <nwaller@umn.edu>
Diff between fungible versions 1.3 dated 2016-01-23 and 1.5 dated 2016-11-09
DESCRIPTION | 20 +++++-- MD5 | 26 ++++++--- NAMESPACE | 2 R/eigGen.R |only R/fungibleR.R | 59 +++++++++++++-------- R/rGivens.R |only R/rMAP.R |only R/rcor.R |only R/tetcor.R | 118 +++++++++++++++++++++++++++---------------- inst/CITATION | 8 +- inst/doc/fungible-manual.pdf |binary man/eigGen.Rd |only man/fungibleExtrema.Rd | 2 man/fungibleR.Rd | 2 man/rGivens.Rd |only man/rMAP.Rd |only man/rcor.Rd |only man/tetcor.Rd | 9 +-- 18 files changed, 158 insertions(+), 88 deletions(-)
Title: Interface to 'Dygraphs' Interactive Time Series Charting Library
Description: An R interface to the 'dygraphs' JavaScript charting library
(a copy of which is included in the package). Provides rich facilities
for charting time-series data in R, including highly configurable
series- and axis-display and interactive features like zoom/pan and
series/point highlighting.
Author: Dan Vanderkam [aut, cph] (dygraphs library in htmlwidgets/lib,
http://dygraphs.com/),
JJ Allaire [aut, cre] (R interface),
RStudio [cph],
Jonathan Owen [aut, cph],
Daniel Gromer [aut, cph],
Petr Shevtsov [aut, cph],
Benoit Thieurmel [aut, cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/htmlwidgets/lib/jquery/AUTHORS.txt)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between dygraphs versions 1.1.1.2 dated 2016-09-14 and 1.1.1.3 dated 2016-11-09
dygraphs-1.1.1.2/dygraphs/R/plugin.R |only dygraphs-1.1.1.3/dygraphs/DESCRIPTION | 8 - dygraphs-1.1.1.3/dygraphs/MD5 | 74 +++++++++-------- dygraphs-1.1.1.3/dygraphs/NAMESPACE | 3 dygraphs-1.1.1.3/dygraphs/R/annotation.R | 2 dygraphs-1.1.1.3/dygraphs/R/axis.R | 2 dygraphs-1.1.1.3/dygraphs/R/candlestick.R |only dygraphs-1.1.1.3/dygraphs/R/css.R | 2 dygraphs-1.1.1.3/dygraphs/R/dependency.R |only dygraphs-1.1.1.3/dygraphs/R/dygraph.R | 2 dygraphs-1.1.1.3/dygraphs/R/event.R | 4 dygraphs-1.1.1.3/dygraphs/R/highlight.R | 2 dygraphs-1.1.1.3/dygraphs/R/legend.R | 2 dygraphs-1.1.1.3/dygraphs/R/options.R | 2 dygraphs-1.1.1.3/dygraphs/R/range-selector.R | 2 dygraphs-1.1.1.3/dygraphs/R/roller.R | 2 dygraphs-1.1.1.3/dygraphs/R/series.R | 2 dygraphs-1.1.1.3/dygraphs/R/shading.R | 2 dygraphs-1.1.1.3/dygraphs/inst/NEWS | 15 +++ dygraphs-1.1.1.3/dygraphs/inst/examples/plotters |only dygraphs-1.1.1.3/dygraphs/inst/examples/shiny/server.R | 17 ++- dygraphs-1.1.1.3/dygraphs/inst/examples/shiny/ui.R | 2 dygraphs-1.1.1.3/dygraphs/inst/htmlwidgets/dygraphs.js | 49 +++++++++-- dygraphs-1.1.1.3/dygraphs/inst/plugins |only dygraphs-1.1.1.3/dygraphs/man/dyAnnotation.Rd | 2 dygraphs-1.1.1.3/dygraphs/man/dyAxis.Rd | 2 dygraphs-1.1.1.3/dygraphs/man/dyCSS.Rd | 2 dygraphs-1.1.1.3/dygraphs/man/dyCandlestick.Rd |only dygraphs-1.1.1.3/dygraphs/man/dyDependency.Rd |only dygraphs-1.1.1.3/dygraphs/man/dyEvent.Rd | 2 dygraphs-1.1.1.3/dygraphs/man/dyHighlight.Rd | 2 dygraphs-1.1.1.3/dygraphs/man/dyLegend.Rd | 2 dygraphs-1.1.1.3/dygraphs/man/dyLimit.Rd | 2 dygraphs-1.1.1.3/dygraphs/man/dyOptions.Rd | 2 dygraphs-1.1.1.3/dygraphs/man/dyPlotter.Rd |only dygraphs-1.1.1.3/dygraphs/man/dyPlugin.Rd | 9 -- dygraphs-1.1.1.3/dygraphs/man/dyRangeSelector.Rd | 2 dygraphs-1.1.1.3/dygraphs/man/dyRoller.Rd | 2 dygraphs-1.1.1.3/dygraphs/man/dySeries.Rd | 2 dygraphs-1.1.1.3/dygraphs/man/dyShading.Rd | 2 dygraphs-1.1.1.3/dygraphs/man/dygraph.Rd | 2 41 files changed, 148 insertions(+), 81 deletions(-)
Title: Modelling Multivariate Data with Additive Bayesian Networks
Description: Bayesian network analysis is a form of probabilistic graphical models which derives from empirical data a directed acyclic graph, DAG, describing the dependency structure between random variables. An additive Bayesian network model consists of a form of a DAG where each node comprises a generalized linear model, GLM. Additive Bayesian network models are equivalent to Bayesian multivariate regression using graphical modelling, they generalises the usual multivariable regression, GLM, to multiple dependent variables. 'abn' provides routines to help determine optimal Bayesian network models for a given data set, where these models are used to identify statistical dependencies in messy, complex data. The additive formulation of these models is equivalent to multivariate generalised linear modelling (including mixed models with iid random effects). The usual term to describe this model selection process is structure discovery. The core functionality is concerned with model selection - determining the most robust empirical model of data from interdependent variables. Laplace approximations are used to estimate goodness of fit metrics and model parameters, and wrappers are also included to the INLA package which can be obtained from <http://www.r-inla.org>. It is recommended the testing version, which can be downloaded by running: source("http://www.math.ntnu.no/inla/givemeINLA-testing.R"). A comprehensive set of documented case studies, numerical accuracy/quality assurance exercises, and additional documentation are available from the 'abn' website.
Author: Fraser Ian Lewis [aut], Gilles Kratzer [cre, ctb], Marta Pittavino [ctb], Reinhard Furrer [ctb]
Maintainer: Gilles Kratzer <gilles.kratzer@math.uzh.ch>
Diff between abn versions 1.0 dated 2016-01-18 and 1.0.2 dated 2016-11-09
abn-1.0.2/abn/DESCRIPTION | 16 ++++++++-------- abn-1.0.2/abn/MD5 | 19 +++++++++++-------- abn-1.0.2/abn/build/vignette.rds |binary abn-1.0.2/abn/inst/doc/abn_v1.0.2.R |only abn-1.0.2/abn/inst/doc/abn_v1.0.2.Rnw |only abn-1.0.2/abn/inst/doc/abn_v1.0.2.pdf |only abn-1.0.2/abn/inst/tests |only abn-1.0.2/abn/man/build_score_cache.Rd | 4 ++-- abn-1.0.2/abn/vignettes/abn_v1.0.2-concordance.tex |only abn-1.0.2/abn/vignettes/abn_v1.0.2.Rnw |only abn-1.0/abn/inst/doc/abn_v1.0.R |only abn-1.0/abn/inst/doc/abn_v1.0.Rnw |only abn-1.0/abn/inst/doc/abn_v1.0.pdf |only abn-1.0/abn/vignettes/abn_v1.0.Rnw |only abn-1.0/abn/vignettes/abn_v10-newfile.pdf |only 15 files changed, 21 insertions(+), 18 deletions(-)
Title: A Simple Package for Testing R Packages
Description: Provides two convenience functions assert() and test_pkg() to
facilitate testing R packages.
Author: Yihui Xie
Maintainer: Yihui Xie <xie@yihui.name>
Diff between testit versions 0.5 dated 2016-02-17 and 0.6 dated 2016-11-09
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- NEWS | 12 ++++++++++++ R/testit.R | 26 ++++++++++++++++++-------- R/utils.R | 21 ++++++++++++++++++++- README.md | 5 +++-- man/test_pkg.Rd | 16 ++++++++++------ tests/test-all.R | 1 + tests/test-error |only tests/testit/test-assert.R | 17 +++++++++++++++++ tests/testit/test-utils.R | 5 ++++- 11 files changed, 99 insertions(+), 31 deletions(-)
Title: A Simple HTTP Server to Serve Static Files or Dynamic Documents
Description: Start an HTTP server in R to serve static files, or dynamic
documents that can be converted to HTML files (e.g., R Markdown) under a
given directory.
Author: Yihui Xie [aut, cre],
Carson Sievert [ctb],
Jesse Anderson [ctb],
Ramnath Vaidyanathan [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between servr versions 0.4 dated 2016-04-15 and 0.4.1 dated 2016-11-09
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 12 ++++++++++++ R/static.R | 6 ++++-- R/utils.R | 4 +++- README.md | 8 ++++---- 6 files changed, 32 insertions(+), 16 deletions(-)
Title: Scale Functions for Visualization
Description: Graphical scales map data to aesthetics, and provide
methods for automatically determining breaks and labels
for axes and legends.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between scales versions 0.4.0 dated 2016-02-26 and 0.4.1 dated 2016-11-09
DESCRIPTION | 8 ++--- LICENSE | 2 - MD5 | 29 +++++++++++--------- NAMESPACE | 1 NEWS.md | 9 ++++++ R/RcppExports.R | 2 - R/breaks.r | 8 ++++- R/scale-discrete.r | 21 +++++++++----- R/trans-date.r | 49 +++++++++++++++++++++++++++++++++- README.md | 2 - build/partial.rdb |binary man/hms_trans.Rd |only man/time_trans.Rd | 4 +- man/train_discrete.Rd | 4 ++ src/RcppExports.cpp | 26 +++++++++--------- tests/testthat/test-breaks-extended.R |only tests/testthat/test-discrete.R |only 17 files changed, 119 insertions(+), 46 deletions(-)
Title: Client for Various 'CrossRef' APIs
Description: Client for various 'CrossRef' APIs, including 'metadata' search
with their old and newer search APIs, get 'citations' in various formats
(including 'bibtex', 'citeproc-json', 'rdf-xml', etc.), convert 'DOIs'
to 'PMIDs', and 'vice versa', get citations for 'DOIs', and get links to
full text of articles when available.
Author: Scott Chamberlain [aut, cre],
Carl Boettiger [aut],
Ted Hart [aut],
Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rcrossref versions 0.5.8 dated 2016-08-26 and 0.6.0 dated 2016-11-09
rcrossref-0.5.8/rcrossref/man/cr_fundref.Rd |only rcrossref-0.5.8/rcrossref/man/cr_search.Rd |only rcrossref-0.5.8/rcrossref/man/cr_search_free.Rd |only rcrossref-0.5.8/rcrossref/man/crosscite.Rd |only rcrossref-0.5.8/rcrossref/tests/testthat/test_cr_fundref.R |only rcrossref-0.5.8/rcrossref/tests/testthat/test_cr_search.R |only rcrossref-0.5.8/rcrossref/tests/testthat/test_cr_search_free.R |only rcrossref-0.5.8/rcrossref/tests/testthat/test_pmd2doi.R |only rcrossref-0.6.0/rcrossref/DESCRIPTION | 8 rcrossref-0.6.0/rcrossref/MD5 | 130 ++--- rcrossref-0.6.0/rcrossref/NEWS.md | 36 + rcrossref-0.6.0/rcrossref/R/cr_cn.r | 4 rcrossref-0.6.0/rcrossref/R/cr_ft_links.R | 9 rcrossref-0.6.0/rcrossref/R/cr_ft_text.R | 65 +- rcrossref-0.6.0/rcrossref/R/cr_fundref.r | 26 - rcrossref-0.6.0/rcrossref/R/cr_journals.r | 13 rcrossref-0.6.0/rcrossref/R/cr_members.r | 13 rcrossref-0.6.0/rcrossref/R/cr_prefixes.r | 14 rcrossref-0.6.0/rcrossref/R/cr_r.r | 12 rcrossref-0.6.0/rcrossref/R/cr_search.r | 96 ---- rcrossref-0.6.0/rcrossref/R/cr_search_free.r | 53 -- rcrossref-0.6.0/rcrossref/R/cr_types.R | 14 rcrossref-0.6.0/rcrossref/R/cr_works.R | 118 +++-- rcrossref-0.6.0/rcrossref/R/crosscite.R | 55 -- rcrossref-0.6.0/rcrossref/R/deprecated_defunct.R | 47 +- rcrossref-0.6.0/rcrossref/R/extract_pdf.R | 5 rcrossref-0.6.0/rcrossref/R/filters.R | 7 rcrossref-0.6.0/rcrossref/R/rcrossref-package.R | 24 - rcrossref-0.6.0/rcrossref/R/tdmurl.R | 10 rcrossref-0.6.0/rcrossref/R/zzz.R | 39 + rcrossref-0.6.0/rcrossref/README.md | 226 +++++----- rcrossref-0.6.0/rcrossref/build/vignette.rds |binary rcrossref-0.6.0/rcrossref/inst/doc/crossref_vignette.Rmd | 26 - rcrossref-0.6.0/rcrossref/inst/doc/crossref_vignette.html | 26 - rcrossref-0.6.0/rcrossref/inst/examples/MairChamberlain2014RJournal.txt | 4 rcrossref-0.6.0/rcrossref/inst/vign/crossref_vignette.Rmd | 4 rcrossref-0.6.0/rcrossref/inst/vign/crossref_vignette.md | 26 - rcrossref-0.6.0/rcrossref/man/as.tdmurl.Rd | 9 rcrossref-0.6.0/rcrossref/man/cr_cn.Rd | 4 rcrossref-0.6.0/rcrossref/man/cr_ft_links.Rd | 11 rcrossref-0.6.0/rcrossref/man/cr_ft_text.Rd | 22 rcrossref-0.6.0/rcrossref/man/cr_funders.Rd |only rcrossref-0.6.0/rcrossref/man/cr_fundref-defunct.Rd |only rcrossref-0.6.0/rcrossref/man/cr_journals.Rd | 42 + rcrossref-0.6.0/rcrossref/man/cr_members.Rd | 42 + rcrossref-0.6.0/rcrossref/man/cr_prefixes.Rd | 43 + rcrossref-0.6.0/rcrossref/man/cr_r.Rd | 14 rcrossref-0.6.0/rcrossref/man/cr_search-defunct.Rd |only rcrossref-0.6.0/rcrossref/man/cr_search_free-defunct.Rd |only rcrossref-0.6.0/rcrossref/man/cr_types.Rd | 43 + rcrossref-0.6.0/rcrossref/man/cr_works.Rd | 54 +- rcrossref-0.6.0/rcrossref/man/crosscite-defunct.Rd |only rcrossref-0.6.0/rcrossref/man/extract_xpdf.Rd | 9 rcrossref-0.6.0/rcrossref/man/rcrossref-defunct.Rd | 10 rcrossref-0.6.0/rcrossref/man/rcrossref-deprecated.Rd | 24 - rcrossref-0.6.0/rcrossref/man/rcrossref-package.Rd | 26 - rcrossref-0.6.0/rcrossref/tests/testthat/test_as.tdmurl.R | 16 rcrossref-0.6.0/rcrossref/tests/testthat/test_cr_agency.R | 8 rcrossref-0.6.0/rcrossref/tests/testthat/test_cr_citation_count.R | 10 rcrossref-0.6.0/rcrossref/tests/testthat/test_cr_cn.R | 31 - rcrossref-0.6.0/rcrossref/tests/testthat/test_cr_ft_links.R | 12 rcrossref-0.6.0/rcrossref/tests/testthat/test_cr_ft_text.R | 73 +-- rcrossref-0.6.0/rcrossref/tests/testthat/test_cr_funders.R |only rcrossref-0.6.0/rcrossref/tests/testthat/test_cr_journals.R | 16 rcrossref-0.6.0/rcrossref/tests/testthat/test_cr_licenses.R | 10 rcrossref-0.6.0/rcrossref/tests/testthat/test_cr_members.R | 20 rcrossref-0.6.0/rcrossref/tests/testthat/test_cr_members_cursor.R | 14 rcrossref-0.6.0/rcrossref/tests/testthat/test_cr_prefixes.R | 14 rcrossref-0.6.0/rcrossref/tests/testthat/test_cr_r.R | 10 rcrossref-0.6.0/rcrossref/tests/testthat/test_cr_types.R | 8 rcrossref-0.6.0/rcrossref/tests/testthat/test_cr_works.R | 44 + rcrossref-0.6.0/rcrossref/tests/testthat/test_cr_works_cursor.R | 10 rcrossref-0.6.0/rcrossref/vignettes/crossref_vignette.Rmd | 26 - 73 files changed, 1034 insertions(+), 751 deletions(-)
Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Yihui Xie [aut, cre],
Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Aron Atkins [ctb],
Aaron Wolen [ctb],
Ashley Manton [ctb],
Ben Baumer [ctb],
Brian Diggs [ctb],
Cassio Pereira [ctb],
David Robinson [ctb],
Donald Arseneau [ctb, cph] (the framed package at inst/misc/framed.sty),
Doug Hemken [ctb],
Duncan Murdoch [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Hiroaki Yutani [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jason Punyon [ctb],
Jeff Arnold [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
John Muschelli [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kaiyin Zhong [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Michael Friendly [ctb],
Michal Bojanowski [ctb],
Michel Kuhlmann [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Noam Ross [ctb],
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Robert Krzyzanowski [ctb],
Romain Francois [ctb],
Scott Kostyshak [ctb],
Sebastian Meyer [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Zachary Foster [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between knitr versions 1.14 dated 2016-08-13 and 1.15 dated 2016-11-09
DESCRIPTION | 20 +++--- MD5 | 73 ++++++++++++----------- NAMESPACE | 4 + R/block.R | 52 +++++++++++----- R/cache.R | 12 +++ R/citation.R | 11 ++- R/engine.R | 78 +++++++++++++++++++------ R/hooks-html.R | 9 ++ R/hooks-latex.R | 4 - R/hooks.R | 2 R/output.R | 18 ++++- R/package.R | 10 +++ R/parser.R | 6 - R/pattern.R | 8 +- R/plot.R | 6 + R/table.R | 18 ++++- R/utils-conversion.R | 2 R/utils-rd2html.R | 2 R/utils-vignettes.R | 8 +- R/utils.R | 121 ++++++++++++++++++++++++++++++++++++--- build/knitr.pdf |binary build/vignette.rds |binary inst/doc/knit_expand.html | 4 - inst/doc/knit_print.html | 23 +++---- inst/doc/knitr-intro.html | 10 +-- inst/doc/knitr-markdown.html | 2 inst/doc/knitr-refcard.pdf |binary inst/examples/Sweavel.sty |only inst/examples/knitr-packages.bib | 12 +-- man/all_labels.Rd | 2 man/clean_cache.Rd | 5 + man/kable.Rd | 6 + man/plot_crop.Rd | 2 man/raw_output.Rd |only man/write_bib.Rd | 5 + tests/testit/test-plot.R | 2 tests/testit/test-sql.R |only tests/testit/test-table.R | 8 ++ tests/testit/test-utils.R | 45 +++++++++++++- 39 files changed, 445 insertions(+), 145 deletions(-)
Title: General Purpose Interface to 'Elasticsearch'
Description: Connect to 'Elasticsearch', a 'NoSQL' database built on the 'Java'
Virtual Machine. Interacts with the 'Elasticsearch' 'HTTP' 'API'
(<https://www.elastic.co/products/elasticsearch>), including functions for
setting connection details to 'Elasticsearch' instances, loading bulk data,
searching for documents with both 'HTTP' query variables and 'JSON' based body
requests. In addition, 'elastic' provides functions for interacting with 'APIs'
for 'indices', documents, nodes, clusters, an interface to the cat 'API', and
more.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between elastic versions 0.7.6 dated 2016-08-25 and 0.7.8 dated 2016-11-09
elastic-0.7.6/elastic/tests/testthat/test-search.R |only elastic-0.7.8/elastic/DESCRIPTION | 10 elastic-0.7.8/elastic/MD5 | 123 +++--- elastic-0.7.8/elastic/NAMESPACE | 5 elastic-0.7.8/elastic/NEWS.md | 26 + elastic-0.7.8/elastic/R/Search_uri.R | 46 +- elastic-0.7.8/elastic/R/alias.R | 21 - elastic-0.7.8/elastic/R/cat.r | 2 elastic-0.7.8/elastic/R/cluster.R | 2 elastic-0.7.8/elastic/R/count.r | 1 elastic-0.7.8/elastic/R/docs_bulk.r | 242 +++--------- elastic-0.7.8/elastic/R/docs_bulk_plugins.R |only elastic-0.7.8/elastic/R/docs_bulk_prep.R |only elastic-0.7.8/elastic/R/docs_bulk_utils.R |only elastic-0.7.8/elastic/R/docs_create.R | 55 +- elastic-0.7.8/elastic/R/docs_delete.R | 23 - elastic-0.7.8/elastic/R/docs_get.r | 57 +- elastic-0.7.8/elastic/R/docs_mget.r | 88 ++-- elastic-0.7.8/elastic/R/docs_update.R |only elastic-0.7.8/elastic/R/explain.R | 17 elastic-0.7.8/elastic/R/httr-verbs.R | 56 +- elastic-0.7.8/elastic/R/index.R | 59 +- elastic-0.7.8/elastic/R/mapping.R | 14 elastic-0.7.8/elastic/R/msearch.R | 10 elastic-0.7.8/elastic/R/nodes.R | 79 +-- elastic-0.7.8/elastic/R/percolater.R | 121 ++---- elastic-0.7.8/elastic/R/ping.r | 5 elastic-0.7.8/elastic/R/scroll.R | 67 +++ elastic-0.7.8/elastic/R/search.r | 39 + elastic-0.7.8/elastic/R/search_body.R | 34 - elastic-0.7.8/elastic/R/search_template.R | 12 elastic-0.7.8/elastic/R/termvectors.R | 42 +- elastic-0.7.8/elastic/R/tokenizer_set.R | 8 elastic-0.7.8/elastic/R/zzz.r | 17 elastic-0.7.8/elastic/README.md | 10 elastic-0.7.8/elastic/build/vignette.rds |binary elastic-0.7.8/elastic/inst/examples/msearch_eg2.json | 5 elastic-0.7.8/elastic/man/Search.Rd | 120 ++++- elastic-0.7.8/elastic/man/Search_uri.Rd | 19 elastic-0.7.8/elastic/man/alias.Rd | 4 elastic-0.7.8/elastic/man/docs_bulk.Rd | 100 ++-- elastic-0.7.8/elastic/man/docs_bulk_prep.Rd |only elastic-0.7.8/elastic/man/docs_create.Rd | 38 + elastic-0.7.8/elastic/man/docs_delete.Rd | 13 elastic-0.7.8/elastic/man/docs_get.Rd | 32 + elastic-0.7.8/elastic/man/docs_mget.Rd | 59 ++ elastic-0.7.8/elastic/man/docs_update.Rd |only elastic-0.7.8/elastic/man/explain.Rd | 4 elastic-0.7.8/elastic/man/index.Rd | 6 elastic-0.7.8/elastic/man/mapping.Rd | 10 elastic-0.7.8/elastic/man/nodes.Rd | 44 +- elastic-0.7.8/elastic/man/percolate.Rd | 68 +-- elastic-0.7.8/elastic/man/scroll.Rd | 69 +++ elastic-0.7.8/elastic/man/search_body.Rd | 11 elastic-0.7.8/elastic/man/termvectors.Rd | 28 - elastic-0.7.8/elastic/tests/testthat/test-alias.R | 15 elastic-0.7.8/elastic/tests/testthat/test-cluster.R | 3 elastic-0.7.8/elastic/tests/testthat/test-docs.R | 60 ++ elastic-0.7.8/elastic/tests/testthat/test-docs_bulk.R | 18 elastic-0.7.8/elastic/tests/testthat/test-docs_bulk_prep.R |only elastic-0.7.8/elastic/tests/testthat/test-indices.R | 6 elastic-0.7.8/elastic/tests/testthat/test-mappings.R | 7 elastic-0.7.8/elastic/tests/testthat/test-msearch.R | 2 elastic-0.7.8/elastic/tests/testthat/test-nodes.R | 12 elastic-0.7.8/elastic/tests/testthat/test-search.r |only elastic-0.7.8/elastic/tests/testthat/test-search_template.R | 33 + elastic-0.7.8/elastic/tests/testthat/test-search_uri.R | 15 67 files changed, 1239 insertions(+), 853 deletions(-)
Title: Detection of Dichotomous Differential Item Functioning (DIF) by
Non- Linear Regression Function
Description: Detection of differential item functioning among dichotomously
scored items with non-linear regression procedure.
Author: Adela Drabinova [aut, cre], Patricia Martinkova [aut], Karel Zvara [aut]
Maintainer: Adela Drabinova <adela.drabinova@gmail.com>
Diff between difNLR versions 0.1.0 dated 2016-06-21 and 0.2.0 dated 2016-11-09
difNLR-0.1.0/difNLR/inst |only difNLR-0.2.0/difNLR/DESCRIPTION | 16 difNLR-0.2.0/difNLR/MD5 | 51 + difNLR-0.2.0/difNLR/NAMESPACE | 38 - difNLR-0.2.0/difNLR/R/GMAT.R |only difNLR-0.2.0/difNLR/R/GMAT2.R |only difNLR-0.2.0/difNLR/R/GMAT2key.R |only difNLR-0.2.0/difNLR/R/GMAT2test.R |only difNLR-0.2.0/difNLR/R/GMATkey.R |only difNLR-0.2.0/difNLR/R/GMATtest.R |only difNLR-0.2.0/difNLR/R/difMedical.R |only difNLR-0.2.0/difNLR/R/difMedicalkey.R |only difNLR-0.2.0/difNLR/R/difMedicaltest.R |only difNLR-0.2.0/difNLR/R/difNLR-package.R |only difNLR-0.2.0/difNLR/R/difNLR.R | 766 +++++++++++++++------------- difNLR-0.2.0/difNLR/R/genNLR.R |only difNLR-0.2.0/difNLR/R/startNLR.R | 130 ++-- difNLR-0.2.0/difNLR/data/GMAT.rda |binary difNLR-0.2.0/difNLR/data/GMAT2.rda |only difNLR-0.2.0/difNLR/data/GMAT2key.rda |only difNLR-0.2.0/difNLR/data/GMAT2test.rda |only difNLR-0.2.0/difNLR/data/GMATkey.rda |binary difNLR-0.2.0/difNLR/data/GMATtest.rda |binary difNLR-0.2.0/difNLR/data/difMedical.rda |only difNLR-0.2.0/difNLR/data/difMedicalkey.rda |only difNLR-0.2.0/difNLR/data/difMedicaltest.rda |only difNLR-0.2.0/difNLR/man/GMAT.Rd | 48 + difNLR-0.2.0/difNLR/man/GMAT2.Rd |only difNLR-0.2.0/difNLR/man/GMAT2key.Rd |only difNLR-0.2.0/difNLR/man/GMAT2test.Rd |only difNLR-0.2.0/difNLR/man/GMATkey.Rd | 41 - difNLR-0.2.0/difNLR/man/GMATtest.Rd | 52 + difNLR-0.2.0/difNLR/man/difMedical.Rd |only difNLR-0.2.0/difNLR/man/difMedicalkey.Rd |only difNLR-0.2.0/difNLR/man/difMedicaltest.Rd |only difNLR-0.2.0/difNLR/man/difNLR-package.Rd | 40 - difNLR-0.2.0/difNLR/man/difNLR.Rd | 173 +++--- difNLR-0.2.0/difNLR/man/genNLR.Rd |only difNLR-0.2.0/difNLR/man/startNLR.Rd | 49 + 39 files changed, 797 insertions(+), 607 deletions(-)
Title: Plot a Correlogram
Description: Calculates correlation of variables and displays the results
graphically. Included panel functions can display points, shading, ellipses, and
correlation values with confidence intervals.
Author: Kevin Wright [aut, cre]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between corrgram versions 1.9 dated 2016-07-16 and 1.10 dated 2016-11-09
corrgram-1.10/corrgram/DESCRIPTION | 10 +- corrgram-1.10/corrgram/MD5 | 25 +++---- corrgram-1.10/corrgram/R/corrgram.r |only corrgram-1.10/corrgram/build/vignette.rds |binary corrgram-1.10/corrgram/inst/doc/corrgram_examples.Rmd | 11 +-- corrgram-1.10/corrgram/inst/doc/corrgram_examples.html | 39 +++++------ corrgram-1.10/corrgram/man/corrgram.Rd | 10 +- corrgram-1.10/corrgram/tests/friendly.R | 5 - corrgram-1.10/corrgram/tests/misc.R | 60 ++++++++++------- corrgram-1.10/corrgram/tests/shade.R | 4 - corrgram-1.10/corrgram/tests/spearman.R | 4 - corrgram-1.10/corrgram/tests/testthat |only corrgram-1.10/corrgram/tests/testthat.R |only corrgram-1.10/corrgram/vignettes/corrgram_examples.Rmd | 11 +-- corrgram-1.9/corrgram/NEWS |only corrgram-1.9/corrgram/R/corrgram.R |only 16 files changed, 99 insertions(+), 80 deletions(-)
Title: Analyze Bunching in a Kink or Notch Setting
Description: View and analyze data where bunching is expected. Estimate counter-
factual distributions. For earnings data, estimate the compensated
elasticity of earnings w.r.t. the net-of-tax rate.
Author: Itai Trilnick [aut, cre]
Maintainer: Itai Trilnick <itai.trilnick@berkeley.edu>
Diff between bunchr versions 1.0.0 dated 2016-08-08 and 1.0.1 dated 2016-11-09
DESCRIPTION | 6 ++-- MD5 | 14 +++++----- NEWS.md | 7 ++++- inst/doc/bunching_with_bunchr.R | 2 - inst/doc/bunching_with_bunchr.Rmd | 2 - inst/doc/bunching_with_bunchr.html | 48 +++++++++++++++---------------------- inst/doc/notch_estimation.html | 12 ++++----- vignettes/bunching_with_bunchr.Rmd | 2 - 8 files changed, 45 insertions(+), 48 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-11-08 0.5