Title: Statistical Methods for the Randomized Response Technique
Diff between rr versions 1.1 dated 2015-02-19 and 1.2 dated 2015-03-21
Description: Enables researchers to conduct multivariate statistical analyses of survey data with randomized response technique items from several designs, including mirrored question, forced question, and unrelated question. This includes regression with the randomized response as the outcome and logistic regression with the randomized response item as a predictor. In addition, tools for conducting power analysis for designing randomized response items are included. The package implements methods described in Blair, Imai, and Zhou (2015) ''Design and Analysis of the Randomized Response Technique,'' Working paper available at
Author: Graeme Blair
Maintainer: Graeme Blair
ChangeLog | 1 +
DESCRIPTION | 9 +++++----
MD5 | 22 ++++++++++++++--------
NAMESPACE | 16 +++++++++++++++-
R/onAttach.R | 8 --------
R/rr.R | 8 +++++---
R/rrBayes.R |only
R/rrreg.predictor.R | 2 +-
man/rr-package.Rd | 4 ++--
man/rrreg.bayes.Rd |only
src/R2models.c | 25 +++++++++++++++++--------
tests |only
12 files changed, 60 insertions(+), 35 deletions(-)
Title: Advanced Data Analysis of T-Cell Receptor Repertoires
Diff between tcR versions 1.1 dated 2015-01-10 and 1.3 dated 2015-03-21
Description: Platform for the advanced analysis of T-cell receptor repertoires data and visualisation of the analysis results.
Author: Vadim Nazarov, Mikhail Pogorelyy
Maintainer: Vadim Nazarov
tcR-1.1/tcR/data/human.alphabets.rda |only
tcR-1.1/tcR/data/mouse.alphabets.rda |only
tcR-1.1/tcR/data/segments.rda |only
tcR-1.1/tcR/man/parse.file.Rd |only
tcR-1.1/tcR/man/parse.file.list.Rd |only
tcR-1.3/tcR/DESCRIPTION | 16
tcR-1.3/tcR/MD5 | 119 +++----
tcR-1.3/tcR/NAMESPACE | 3
tcR-1.3/tcR/NEWS |only
tcR-1.3/tcR/R/crosses.R | 7
tcR-1.3/tcR/R/dataproc.R | 6
tcR-1.3/tcR/R/datatools.R | 63 +++
tcR-1.3/tcR/R/diversity.R | 55 ++-
tcR-1.3/tcR/R/docdata.R | 85 ++++-
tcR-1.3/tcR/R/filters.R | 2
tcR-1.3/tcR/R/graph.R |only
tcR-1.3/tcR/R/infoanalysis.R | 16
tcR-1.3/tcR/R/input.R | 449 ++++++++++++++++++----------
tcR-1.3/tcR/R/kmers.R | 32 +
tcR-1.3/tcR/R/measures.R | 15
tcR-1.3/tcR/R/plots.R | 207 +++++++++---
tcR-1.3/tcR/R/segments.R | 58 +--
tcR-1.3/tcR/R/shared.R | 10
tcR-1.3/tcR/R/spectrum.R | 8
tcR-1.3/tcR/R/stats.R | 137 ++++++--
tcR-1.3/tcR/R/strtools.R | 4
tcR-1.3/tcR/README.md | 9
tcR-1.3/tcR/data/datalist | 4
tcR-1.3/tcR/data/genesegments.rda |only
tcR-1.3/tcR/data/twa.rda |binary
tcR-1.3/tcR/data/twb.rda |binary
tcR-1.3/tcR/inst/crossanalysis.report.Rmd | 4
tcR-1.3/tcR/inst/doc/tcrvignette.R | 176 ++++++----
tcR-1.3/tcR/inst/doc/tcrvignette.Rnw | 218 ++++++++-----
tcR-1.3/tcR/inst/doc/tcrvignette.pdf |binary
tcR-1.3/tcR/inst/library.report.Rmd | 4
tcR-1.3/tcR/man/bootstrap.tcr.Rd | 6
tcR-1.3/tcR/man/clonal.space.homeostasis.Rd |only
tcR-1.3/tcR/man/column.summary.Rd | 4
tcR-1.3/tcR/man/entropy.Rd | 15
tcR-1.3/tcR/man/entropy.seg.Rd | 7
tcR-1.3/tcR/man/freq.segments.Rd | 28 -
tcR-1.3/tcR/man/generate.kmers.Rd | 2
tcR-1.3/tcR/man/generate.tcr.Rd | 9
tcR-1.3/tcR/man/get.inframes.Rd | 10
tcR-1.3/tcR/man/get.kmers.Rd | 2
tcR-1.3/tcR/man/group.clonotypes.Rd |only
tcR-1.3/tcR/man/intersect.Rd | 2
tcR-1.3/tcR/man/inverse.simpson.Rd | 19 -
tcR-1.3/tcR/man/kmer.profile.Rd | 9
tcR-1.3/tcR/man/kmer.table.Rd | 6
tcR-1.3/tcR/man/mitcr.stats.Rd | 13
tcR-1.3/tcR/man/mutated.neighbours.Rd |only
tcR-1.3/tcR/man/mutation.network.Rd |only
tcR-1.3/tcR/man/parse.cloneset.Rd |only
tcR-1.3/tcR/man/parse.folder.Rd | 83 ++++-
tcR-1.3/tcR/man/rarefaction.Rd | 4
tcR-1.3/tcR/man/segments.alphabets.Rd | 53 ++-
tcR-1.3/tcR/man/segments.list.Rd | 8
tcR-1.3/tcR/man/set.group.vector.Rd |only
tcR-1.3/tcR/man/set.people.vector.Rd |only
tcR-1.3/tcR/man/shared.repertoire.Rd | 4
tcR-1.3/tcR/man/vis.V.usage.Rd | 5
tcR-1.3/tcR/man/vis.clonal.space.Rd |only
tcR-1.3/tcR/man/vis.logo.Rd |only
tcR-1.3/tcR/man/vis.number.count.Rd | 3
tcR-1.3/tcR/src/RcppExports.cpp | 88 ++---
tcR-1.3/tcR/src/neighbour.search.cpp | 2
tcR-1.3/tcR/vignettes/tcrvignette.Rnw | 218 ++++++++-----
69 files changed, 1496 insertions(+), 811 deletions(-)
Title: Shrinkage t Statistic and Correlation-Adjusted t-Score
Diff between st versions 1.2.3 dated 2014-11-14 and 1.2.4 dated 2015-03-21
Description: Implements the "shrinkage t" statistic
introduced in Opgen-Rhein and Strimmer (2007) and a shrinkage estimate
of the "correlation-adjusted t-score" (CAT score) described in
Zuber and Strimmer (2009). It also offers a convenient interface
to a number of other regularized t-statistics commonly
employed in high-dimensional case-control studies.
Author: Rainer Opgen-Rhein, Verena Zuber, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 12 ++++++------
MD5 | 16 ++++++++--------
NEWS | 4 ++++
R/modt.R | 8 +++-----
R/sam.R | 6 ++----
man/choedata.Rd | 5 -----
man/regularizedt.Rd | 2 +-
man/shrinkcat.stat.Rd | 2 +-
man/shrinkt.stat.Rd | 2 +-
9 files changed, 26 insertions(+), 31 deletions(-)
Title: Shrinkage Discriminant Analysis and CAT Score Variable Selection
Diff between sda versions 1.3.5 dated 2014-11-18 and 1.3.6 dated 2015-03-21
Description: Provides an efficient framework for
high-dimensional linear and diagonal discriminant analysis with
variable selection. The classifier is trained using James-Stein-type
shrinkage estimators and predictor variables are ranked using
correlation-adjusted t-scores (CAT scores). Variable selection error
is controlled using false non-discovery rates or higher criticism.
Author: Miika Ahdesmaki, Verena Zuber, Sebastian Gibb, and Korbinian Strimmer
Maintainer: Korbinian Strimmer
DESCRIPTION | 12 ++++++------
MD5 | 10 +++++-----
NAMESPACE | 2 ++
NEWS | 5 +++++
man/khan2001.Rd | 6 ++----
man/singh2002.Rd | 2 +-
6 files changed, 21 insertions(+), 16 deletions(-)
Title: Tools for Descriptive Statistics
Diff between DescTools versions 0.99.9 dated 2015-01-20 and 0.99.10 dated 2015-03-21
Description: A collection of basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains as well functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Ken Aho, Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Ben Bolker, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Clint Cummins, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Jeff Enos, Claus Ekstrom, Martin Elff, Richard W. Farebrother, John Fox, Michael Friendly, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Michael Hoehle, Christian W. Hoffmann, Torsten Hothorn, Markus Huerzeler, Wallace W. Hui, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Matthias Kohl, Mikko Korpela, Max Kuhn, Detlew Labes, Friederich Leisch, Jim Lemon, Dong Li, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Giovanni Millo, Yongyi Min, David Mitchell, Markus Naepflin, Daniel Navarro, Klaus Nordhausen, Derek Ogle, Hong Ooi, Nick Parsons, Sandrine Pavoine, Roland Rapold, William Revelle, Tyler Rinker, Brian D. Ripley, Caroline Rodriguez, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Werner A. Stahel, Mark Stevenson, Yves Tille, Adrian Trapletti, Simon Urbanek, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Rand R. Wilcox, Peter Wolf, Daniel Wollschlaeger, Thomas Yee, Achim Zeileis
Maintainer: Andri Signorell
DescTools-0.99.10/DescTools/DESCRIPTION | 12
DescTools-0.99.10/DescTools/MD5 | 205 +++++------
DescTools-0.99.10/DescTools/NAMESPACE | 121 ++++++
DescTools-0.99.10/DescTools/NEWS | 36 +
DescTools-0.99.10/DescTools/R/AscToChar.R | 2
DescTools-0.99.10/DescTools/R/CatTable.R | 2
DescTools-0.99.10/DescTools/R/CharToAsc.R | 5
DescTools-0.99.10/DescTools/R/ColorLegend.R | 2
DescTools-0.99.10/DescTools/R/Day.R | 2
DescTools-0.99.10/DescTools/R/Desc.Date.R | 40 +-
DescTools-0.99.10/DescTools/R/Desc.Lc.R | 2
DescTools-0.99.10/DescTools/R/Desc.data.frame.R | 2
DescTools-0.99.10/DescTools/R/Desc.factor.R | 2
DescTools-0.99.10/DescTools/R/Desc.integer.R | 2
DescTools-0.99.10/DescTools/R/Desc.list.R | 2
DescTools-0.99.10/DescTools/R/Desc.logical.R | 2
DescTools-0.99.10/DescTools/R/Desc.numeric.R | 11
DescTools-0.99.10/DescTools/R/Desc.table.R | 55 +--
DescTools-0.99.10/DescTools/R/DescNumFact.R | 8
DescTools-0.99.10/DescTools/R/DescNumNum.R | 12
DescTools-0.99.10/DescTools/R/DescTools-internal.R | 309 +++++++++--------
DescTools-0.99.10/DescTools/R/DescWrd.data.frame.R | 4
DescTools-0.99.10/DescTools/R/DescWrd.default.R | 11
DescTools-0.99.10/DescTools/R/DescWrd.formula.R | 8
DescTools-0.99.10/DescTools/R/DescWrd.list.R | 4
DescTools-0.99.10/DescTools/R/DrawBand.R | 18
DescTools-0.99.10/DescTools/R/DunnettTest.formula.R | 13
DescTools-0.99.10/DescTools/R/DurbinWatsonTest.R |only
DescTools-0.99.10/DescTools/R/Explore.R |only
DescTools-0.99.10/DescTools/R/FindColor.R | 2
DescTools-0.99.10/DescTools/R/Format.default.R | 30 +
DescTools-0.99.10/DescTools/R/GetPairs.R | 2
DescTools-0.99.10/DescTools/R/HighLow.R | 21 -
DescTools-0.99.10/DescTools/R/HuberM.R | 2
DescTools-0.99.10/DescTools/R/Impute.R | 2
DescTools-0.99.10/DescTools/R/Keywords.R | 25 -
DescTools-0.99.10/DescTools/R/Large.R | 36 +
DescTools-0.99.10/DescTools/R/MHChisqTest.R | 5
DescTools-0.99.10/DescTools/R/MeanCI.R | 10
DescTools-0.99.10/DescTools/R/MedianCI.R | 2
DescTools-0.99.10/DescTools/R/Month.R | 16
DescTools-0.99.10/DescTools/R/PalDescTools.R | 51 +-
DescTools-0.99.10/DescTools/R/PasswordDlg.R | 4
DescTools-0.99.10/DescTools/R/PlotACF.R | 2
DescTools-0.99.10/DescTools/R/PlotArea.R | 2
DescTools-0.99.10/DescTools/R/PlotDesc.Date.R | 2
DescTools-0.99.10/DescTools/R/PlotDesc.factor.R | 30 +
DescTools-0.99.10/DescTools/R/PlotDesc.table.R | 2
DescTools-0.99.10/DescTools/R/PlotGACF.R | 2
DescTools-0.99.10/DescTools/R/PlotMar.R | 2
DescTools-0.99.10/DescTools/R/PlotMonth.R | 2
DescTools-0.99.10/DescTools/R/PlotQQ.R | 31 +
DescTools-0.99.10/DescTools/R/PlotRCol.R | 4
DescTools-0.99.10/DescTools/R/PlotTernary.R | 3
DescTools-0.99.10/DescTools/R/PpPlot.R | 19 -
DescTools-0.99.10/DescTools/R/PpText.R | 2
DescTools-0.99.10/DescTools/R/SampleWord.R |only
DescTools-0.99.10/DescTools/R/SaveAs.R |only
DescTools-0.99.10/DescTools/R/ScheffeTest.aov.R | 4
DescTools-0.99.10/DescTools/R/SiegelTukeyRank.R | 23 -
DescTools-0.99.10/DescTools/R/Small.R | 36 +
DescTools-0.99.10/DescTools/R/SpreadOut.R | 5
DescTools-0.99.10/DescTools/R/Str.R | 2
DescTools-0.99.10/DescTools/R/StrTrunc.R | 2
DescTools-0.99.10/DescTools/R/StrVal.R | 4
DescTools-0.99.10/DescTools/R/ToLong.R | 17
DescTools-0.99.10/DescTools/R/Week.R | 56 ++-
DescTools-0.99.10/DescTools/R/Weekday.R | 16
DescTools-0.99.10/DescTools/R/WrdPlot.R | 5
DescTools-0.99.10/DescTools/R/WrdR.R | 2
DescTools-0.99.10/DescTools/R/WrdText.R | 2
DescTools-0.99.10/DescTools/R/XLGetRange.R | 3
DescTools-0.99.10/DescTools/R/Year.R | 2
DescTools-0.99.10/DescTools/R/YearDay.R | 3
DescTools-0.99.10/DescTools/R/YearMonth.R | 3
DescTools-0.99.10/DescTools/R/fastPOSIXct.R |only
DescTools-0.99.10/DescTools/inst/doc/DescTools.pdf |binary
DescTools-0.99.10/DescTools/man/AddMonths.Rd | 2
DescTools-0.99.10/DescTools/man/CochranArmitageTest.Rd | 2
DescTools-0.99.10/DescTools/man/CoefVar.Rd | 7
DescTools-0.99.10/DescTools/man/ConnLines.Rd | 2
DescTools-0.99.10/DescTools/man/CramerV.Rd | 5
DescTools-0.99.10/DescTools/man/DateFunctions.Rd | 28 -
DescTools-0.99.10/DescTools/man/Desc.Date.Rd | 7
DescTools-0.99.10/DescTools/man/Desc.Rd | 47 +-
DescTools-0.99.10/DescTools/man/DescTools-package.Rd | 7
DescTools-0.99.10/DescTools/man/DrawBand.Rd | 4
DescTools-0.99.10/DescTools/man/DurbinWatsonTest.Rd |only
DescTools-0.99.10/DescTools/man/Explore.Rd |only
DescTools-0.99.10/DescTools/man/Format.Rd | 3
DescTools-0.99.10/DescTools/man/GoodmanKruskalTauA.Rd | 2
DescTools-0.99.10/DescTools/man/KappaM.Rd |only
DescTools-0.99.10/DescTools/man/MeanCI.Rd | 7
DescTools-0.99.10/DescTools/man/MultinomCI.Rd | 9
DescTools-0.99.10/DescTools/man/OddsRatio.Rd | 10
DescTools-0.99.10/DescTools/man/PlotDesc.Rd | 4
DescTools-0.99.10/DescTools/man/PlotTernary.Rd | 6
DescTools-0.99.10/DescTools/man/RndPairs.Rd | 8
DescTools-0.99.10/DescTools/man/SaveAs.Rd |only
DescTools-0.99.10/DescTools/man/SiegelTukeyTest.Rd | 6
DescTools-0.99.10/DescTools/man/SpreadOut.Rd | 24 -
DescTools-0.99.10/DescTools/man/XLGetRange.Rd | 4
DescTools-0.99.10/DescTools/man/XLView.Rd | 6
DescTools-0.99.10/DescTools/man/ZeroIfNA.Rd | 2
DescTools-0.99.10/DescTools/man/fastPOSIXct.Rd |only
DescTools-0.99.10/DescTools/man/median.factor.Rd | 2
DescTools-0.99.10/DescTools/man/paste.Rd | 9
DescTools-0.99.10/DescTools/src/pan.f |only
DescTools-0.99.10/DescTools/src/tparse.c |only
DescTools-0.99.9/DescTools/man/Kappam.Rd |only
110 files changed, 1029 insertions(+), 572 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Diff between MASS versions 7.3-39 dated 2015-02-20 and 7.3-40 dated 2015-03-21
Description: Functions and datasets to support Venables and Ripley,
'Modern Applied Statistics with S' (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Kurt Hornik [trl] (partial port ca 1998),
Albrecht Gebhardt [trl] (partial port ca 1998),
David Firth [ctb]
Maintainer: Brian Ripley
DESCRIPTION | 12 ++++++------
MD5 | 6 +++---
R/lqs.R | 2 +-
tests/Examples/MASS-Ex.Rout.save | 18 +++++++-----------
4 files changed, 17 insertions(+), 21 deletions(-)
Title: Tools for Modeling Data with Functional Programming
Diff between lambda.tools versions 1.0.3 dated 2014-02-08 and 1.0.6 dated 2015-03-21
Description: Provides tools that manipulate and transform data using methods
and techniques consistent with functional programming. The idea is that
through the use of these tools, a program can be reasoned about insomuch
that the implementation can be proven to be equivalent to the mathematical
model.
Author: Brian Lee Yung Rowe
Maintainer: Brian Lee Yung Rowe
lambda.tools-1.0.3/lambda.tools/man/range.for.Rd |only
lambda.tools-1.0.6/lambda.tools/DESCRIPTION | 12 ++--
lambda.tools-1.0.6/lambda.tools/MD5 | 26 ++++-----
lambda.tools-1.0.6/lambda.tools/R/fold.R | 25 +++++---
lambda.tools-1.0.6/lambda.tools/R/lambda.tools-package.R | 4 -
lambda.tools-1.0.6/lambda.tools/R/map.R | 6 +-
lambda.tools-1.0.6/lambda.tools/R/ntry.R |only
lambda.tools-1.0.6/lambda.tools/R/transform.R | 8 +-
lambda.tools-1.0.6/lambda.tools/inst/tests/test_fold.R | 34 +++++++-----
lambda.tools-1.0.6/lambda.tools/inst/tests/test_rangefor.R | 8 +-
lambda.tools-1.0.6/lambda.tools/man/fold.Rd | 10 +--
lambda.tools-1.0.6/lambda.tools/man/foldblock.Rd | 2
lambda.tools-1.0.6/lambda.tools/man/lambda.tools-package.Rd | 4 -
lambda.tools-1.0.6/lambda.tools/man/mapblock.Rd | 2
lambda.tools-1.0.6/lambda.tools/man/ntry.Rd |only
lambda.tools-1.0.6/lambda.tools/man/range_for.Rd |only
16 files changed, 79 insertions(+), 62 deletions(-)
Title: A Logging Utility for R
Diff between futile.logger versions 1.3.7 dated 2014-01-23 and 1.4 dated 2015-03-21
Description: Provides a simple yet powerful logging utility. Based loosely on
log4j, futile.logger takes advantage of R idioms to make logging a
convenient and easy to use replacement for cat and print statements.
Author: Brian Lee Yung Rowe
Maintainer: Brian Lee Yung Rowe
futile.logger-1.3.7/futile.logger/inst |only
futile.logger-1.3.7/futile.logger/tests/doRUnit.Rold |only
futile.logger-1.3.7/futile.logger/tests/run_tests.R |only
futile.logger-1.4/futile.logger/DESCRIPTION | 13 +--
futile.logger-1.4/futile.logger/MD5 | 27 +++----
futile.logger-1.4/futile.logger/R/appender.R | 15 +++
futile.logger-1.4/futile.logger/R/futile.logger-package.R | 9 +-
futile.logger-1.4/futile.logger/R/layout.R | 42 +++++++++--
futile.logger-1.4/futile.logger/R/logger.R | 27 +++++--
futile.logger-1.4/futile.logger/README.md |only
futile.logger-1.4/futile.logger/man/flog.appender.Rd | 6 +
futile.logger-1.4/futile.logger/man/flog.layout.Rd | 15 +++
futile.logger-1.4/futile.logger/man/futile.logger-package.Rd | 12 +--
futile.logger-1.4/futile.logger/tests/testthat |only
futile.logger-1.4/futile.logger/tests/testthat.R |only
15 files changed, 127 insertions(+), 39 deletions(-)
Title: Computation of Bayes Factors for Common Designs
Diff between BayesFactor versions 0.9.11 dated 2015-03-16 and 0.9.11-1 dated 2015-03-21
Description: A suite of functions for computing
various Bayes factors for simple designs, including contingency tables,
one- and two-sample designs, one-way designs, general ANOVA designs, and
linear regression.
Author: Richard D. Morey [aut, cre],
Jeffrey N. Rouder [aut],
Tahira Jamil [ctb]
Maintainer: Richard D. Morey
DESCRIPTION | 10 -
MD5 | 24 +-
NEWS | 5
R/BayesFactorPCL-package.R | 2
build/vignette.rds |binary
inst/doc/compare_lme4.html | 72 +++----
inst/doc/manual.html | 261 ++++++++++++++--------------
inst/doc/odds_probs.html | 52 ++---
inst/doc/priors.html | 18 -
man/BayesFactor-package.Rd | 2
src/RcppExports.cpp | 418 +++++++++++++++++++--------------------------
src/jzs_marg_like.cpp | 2
src/logSummaryStats.cpp | 28 +--
13 files changed, 419 insertions(+), 475 deletions(-)