Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-08 1.0.10-2
2014-12-21 1.0.10
2014-08-20 1.0.9-3
2014-08-11 1.0.9
Title: Tools Developed for Structured Sufficient Dimension Reduction
(sSDR)
Description: Performs structured OLS (sOLS) and structured SIR (sSIR).
Author: Yang Liu <zjubioly@gmail.com>, Francesca Chiaromonte, Bing Li
Maintainer: Yang Liu <zjubioly@gmail.com>
Diff between sSDR versions 1.1.0 dated 2016-01-14 and 1.2.0 dated 2016-03-26
DESCRIPTION | 8 - MD5 | 14 +- R/sSDR.R | 341 +++++++++++++++-------------------------------------- man/gOLS.Rd | 21 --- man/gOLS.comp.d.Rd | 7 - man/gSIR.Rd | 21 --- man/gSIR.comp.d.Rd | 7 - man/sOLS.comp.d.Rd | 8 - 8 files changed, 124 insertions(+), 303 deletions(-)
Title: Respondent-Driven Sampling
Description: Provides functionality for carrying out estimation
with data collected using Respondent-Driven Sampling. This includes
Heckathorn's RDS-I and RDS-II estimators as well as Gile's Sequential
Sampling estimator. The package is part of the "RDS Analyst" suite of
packages for the analysis of respondent-driven sampling data.
Author: Mark S. Handcock [aut, cre],
Krista J. Gile [aut],
Ian E. Fellows [aut],
W. Whipple Neely [aut]
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>
Diff between RDS versions 0.7-5 dated 2016-02-23 and 0.7-6 dated 2016-03-26
DESCRIPTION | 8 +++--- MD5 | 6 ++-- R/LRT.trend.R | 58 ++++++++++++++---------------------------------- R/rds.estimates.local.R | 5 ++-- 4 files changed, 28 insertions(+), 49 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
'citation("Rcpp")' for details on these last two.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey,
Qiang Kou, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 0.12.3 dated 2016-01-10 and 0.12.4 dated 2016-03-26
ChangeLog | 219 +++++++ DESCRIPTION | 8 MD5 | 264 ++++---- R/Attributes.R | 7 README.md | 2 build/Rcpp.pdf |binary build/vignette.rds |binary inst/NEWS.Rd | 38 + inst/doc/Rcpp-FAQ.R | 34 - inst/doc/Rcpp-FAQ.Rnw | 225 ++++++- inst/doc/Rcpp-FAQ.pdf |binary inst/doc/Rcpp-attributes.pdf |binary inst/doc/Rcpp-extending.pdf |binary inst/doc/Rcpp-introduction.pdf |binary inst/doc/Rcpp-modules.pdf |binary inst/doc/Rcpp-package.pdf |binary inst/doc/Rcpp-quickref.pdf |binary inst/doc/Rcpp-sugar.R | 2 inst/doc/Rcpp-sugar.Rnw | 10 inst/doc/Rcpp-sugar.pdf |binary inst/doc/Rcpp-unitTests.pdf |binary inst/doc/Rcpp.bib | 2 inst/examples/ConvolveBenchmarks/exampleRCode.r | 2 inst/examples/ConvolveBenchmarks/overhead.r | 16 inst/examples/FastLM/benchmark.r | 5 inst/examples/FastLM/benchmarkLongley.r | 2 inst/examples/FastLM/fastLMviaArmadillo.r | 2 inst/examples/FastLM/fastLMviaGSL.r | 2 inst/examples/FastLM/lmArmadillo.R | 10 inst/examples/FastLM/lmGSL.R | 10 inst/examples/Misc/fibonacci.r | 4 inst/examples/Misc/ifelseLooped.r | 2 inst/examples/Misc/newFib.r | 2 inst/examples/Misc/piBySimulation.r | 2 inst/examples/OpenMP/OpenMPandInline.r | 2 inst/examples/RcppInline/RObject.r | 2 inst/examples/RcppInline/RcppInlineExample.r | 2 inst/examples/RcppInline/RcppInlineWithLibsExamples.r | 70 +- inst/examples/RcppInline/RcppSimpleExample.r | 2 inst/examples/RcppInline/UncaughtExceptions.r | 2 inst/examples/RcppInline/external_pointer.r | 2 inst/examples/SugarPerformance/sugarBenchmarks.R | 2 inst/examples/functionCallback/newApiExample.r | 7 inst/include/Rcpp/Fast.h | 18 inst/include/Rcpp/Nullable.h | 21 inst/include/Rcpp/config.h | 6 inst/include/Rcpp/stats/beta.h | 4 inst/include/Rcpp/stats/binom.h | 4 inst/include/Rcpp/stats/cauchy.h | 30 inst/include/Rcpp/stats/chisq.h | 4 inst/include/Rcpp/stats/dpq/dpq.h | 527 ++++++++--------- inst/include/Rcpp/stats/exp.h | 73 +- inst/include/Rcpp/stats/f.h | 4 inst/include/Rcpp/stats/gamma.h | 25 inst/include/Rcpp/stats/geom.h | 4 inst/include/Rcpp/stats/hyper.h | 4 inst/include/Rcpp/stats/lnorm.h | 47 - inst/include/Rcpp/stats/logis.h | 73 +- inst/include/Rcpp/stats/nbeta.h | 4 inst/include/Rcpp/stats/nbinom.h | 4 inst/include/Rcpp/stats/nbinom_mu.h | 4 inst/include/Rcpp/stats/nchisq.h | 4 inst/include/Rcpp/stats/nf.h | 4 inst/include/Rcpp/stats/norm.h | 73 +- inst/include/Rcpp/stats/nt.h | 4 inst/include/Rcpp/stats/pois.h | 4 inst/include/Rcpp/stats/random/random.h | 558 +++++++++--------- inst/include/Rcpp/stats/random/rbeta.h | 25 inst/include/Rcpp/stats/random/rbinom.h | 23 inst/include/Rcpp/stats/random/rcauchy.h | 43 - inst/include/Rcpp/stats/random/rchisq.h | 27 inst/include/Rcpp/stats/random/rexp.h | 39 - inst/include/Rcpp/stats/random/rf.h | 76 +- inst/include/Rcpp/stats/random/rgamma.h | 25 inst/include/Rcpp/stats/random/rgeom.h | 27 inst/include/Rcpp/stats/random/rhyper.h | 24 inst/include/Rcpp/stats/random/rlnorm.h | 66 +- inst/include/Rcpp/stats/random/rlogis.h | 72 +- inst/include/Rcpp/stats/random/rnbinom.h | 32 - inst/include/Rcpp/stats/random/rnbinom_mu.h | 31 - inst/include/Rcpp/stats/random/rnchisq.h | 49 - inst/include/Rcpp/stats/random/rnorm.h | 89 +- inst/include/Rcpp/stats/random/rpois.h | 23 inst/include/Rcpp/stats/random/rsignrank.h | 22 inst/include/Rcpp/stats/random/rt.h | 39 - inst/include/Rcpp/stats/random/runif.h | 62 -- inst/include/Rcpp/stats/random/rweibull.h | 50 - inst/include/Rcpp/stats/random/rwilcox.h | 22 inst/include/Rcpp/stats/stats.h | 10 inst/include/Rcpp/stats/t.h | 4 inst/include/Rcpp/stats/unif.h | 40 - inst/include/Rcpp/stats/weibull.h | 41 - inst/include/Rcpp/sugar/functions/cbind.h |only inst/include/Rcpp/sugar/functions/functions.h | 4 inst/include/Rcpp/sugar/functions/median.h |only inst/include/Rcpp/vector/Subsetter.h | 18 inst/unitTests/cpp/Vector.cpp | 5 inst/unitTests/cpp/misc.cpp | 26 inst/unitTests/cpp/sugar.cpp | 309 +++++++++ inst/unitTests/runit.DataFrame.R | 2 inst/unitTests/runit.Date.R | 2 inst/unitTests/runit.Function.R | 2 inst/unitTests/runit.InternalFunction.R | 2 inst/unitTests/runit.InternalFunctionCPP11.R | 2 inst/unitTests/runit.Language.R | 2 inst/unitTests/runit.Matrix.R | 2 inst/unitTests/runit.Module.R | 2 inst/unitTests/runit.Module.client.package.R | 2 inst/unitTests/runit.RObject.R | 2 inst/unitTests/runit.Reference.R | 2 inst/unitTests/runit.S4.R | 2 inst/unitTests/runit.String.R | 2 inst/unitTests/runit.Vector.R | 11 inst/unitTests/runit.XPTr.R | 2 inst/unitTests/runit.as.R | 2 inst/unitTests/runit.attributes.R | 2 inst/unitTests/runit.binary.package.R | 2 inst/unitTests/runit.client.package.R | 2 inst/unitTests/runit.environments.R | 2 inst/unitTests/runit.misc.R | 21 inst/unitTests/runit.modref.R | 2 inst/unitTests/runit.na.R | 2 inst/unitTests/runit.rmath.R | 2 inst/unitTests/runit.stats.R | 2 inst/unitTests/runit.subset.R | 2 inst/unitTests/runit.sugar.R | 339 ++++++++++ inst/unitTests/runit.sugar.var.R | 2 inst/unitTests/runit.support.R | 2 inst/unitTests/runit.table.R | 2 inst/unitTests/runit.wrap.R | 2 inst/unitTests/runit.wstring.R | 2 vignettes/Rcpp-FAQ.Rnw | 225 ++++++- vignettes/Rcpp-sugar.Rnw | 10 vignettes/Rcpp.bib | 2 134 files changed, 2852 insertions(+), 1601 deletions(-)
Title: Manipulate and Play 'ProTracker' Modules
Description: 'ProTracker' is a popular music tracker to sequence
music on a Commodore Amiga machine. This package offers the
opportunity to import, export, manipulate an play 'ProTracker'
module files. Even though the file format could be considered
archaic, it still remains popular to this date. This package
intends to contribute to this popularity and therewith
keeping the legacy of 'ProTracker' and the Commodore Amiga
alive.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between ProTrackR versions 0.2.3 dated 2015-11-07 and 0.3.3 dated 2016-03-26
DESCRIPTION | 11 MD5 | 146 +++++----- NAMESPACE | 7 NEWS | 50 +++ R/02PTCell.r | 9 R/03PTTrack.r | 2 R/09playing_routines.r | 631 ++++++++++++++++++++++++++++++++++------------ R/10ModArchiveHelpers.r |only R/ProTrackR.r | 113 ++++---- man/PTBlock.Rd | 5 man/PTCell-class.Rd | 36 -- man/PTCell-method.Rd | 18 - man/PTModule-class.Rd | 43 --- man/PTPattern-class.Rd | 27 - man/PTPattern-method.Rd | 23 - man/PTSample-class.Rd | 51 --- man/PTSample-method.Rd | 48 --- man/PTTrack-class.Rd | 4 man/PTTrack-method.Rd | 8 man/ProTrackR.Rd | 113 ++++---- man/appendPattern.Rd | 67 ---- man/as.character.Rd | 27 - man/as.raw.Rd | 17 - man/clearSamples.Rd | 44 --- man/clearSong.Rd | 44 --- man/deletePattern.Rd | 68 ---- man/effect.Rd | 23 - man/fineTune.Rd | 49 --- man/funk_table.Rd | 2 man/loopLength.Rd | 59 ---- man/loopSample.Rd | 63 ---- man/loopStart.Rd | 59 ---- man/loopState.Rd | 60 ---- man/mod.intro.Rd | 2 man/modArchive.Rd |only man/modToWave.Rd | 44 --- man/moduleSize.Rd | 45 --- man/name.Rd | 61 ---- man/note.Rd | 69 ----- man/noteManipulation.Rd | 28 +- man/noteToPeriod.Rd | 50 --- man/nybble.Rd | 38 +- man/nybbleToSignedInt.Rd | 40 +- man/octave.Rd | 43 --- man/pasteBlock.Rd | 27 - man/patternLength.Rd | 66 ---- man/patternOrder.Rd | 67 +--- man/patternOrderLength.Rd | 69 +---- man/paula_clock.Rd | 2 man/periodToChar.Rd | 63 ---- man/period_table.Rd | 18 - man/playMod.Rd | 48 --- man/playSample.Rd | 63 ---- man/playWave.Rd | 9 man/playingtable.Rd | 43 --- man/plot.Rd | 2 man/print.Rd | 2 man/proTrackerVibrato.Rd | 2 man/rawToCharNull.Rd | 35 -- man/rawToSignedInt.Rd | 36 -- man/rawToUnsignedInt.Rd | 36 -- man/read.module.Rd | 51 --- man/read.sample.Rd | 61 ---- man/resample.Rd | 2 man/sampleLength.Rd | 51 --- man/sampleNumber.Rd | 22 - man/sampleRate.Rd | 62 +--- man/signedIntToNybble.Rd | 42 +-- man/signedIntToRaw.Rd | 36 -- man/trackerFlag.Rd | 42 --- man/unsignedIntToRaw.Rd | 36 -- man/volume.Rd | 49 --- man/waveform.Rd | 61 +--- man/write.module.Rd | 51 --- man/write.sample.Rd | 61 ---- 75 files changed, 1269 insertions(+), 2293 deletions(-)
Title: Weighted k-Nearest Neighbors
Description: Weighted k-Nearest Neighbors for Classification, Regression and Clustering.
Author: Klaus Schliep [aut, cre],
Klaus Hechenbichler [aut],
Antoine Lizee [ctb]
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>
Diff between kknn versions 1.3.0 dated 2015-07-09 and 1.3.1 dated 2016-03-26
DESCRIPTION | 20 ++++++++----- MD5 | 14 ++++----- NAMESPACE | 2 - NEWS | 14 ++++++++- R/kknn.R | 81 +++++++++++++++++++++++++++++++++++++++--------------- R/specClust.R | 4 +- README.md | 1 man/train.kknn.Rd | 5 ++- 8 files changed, 99 insertions(+), 42 deletions(-)
Title: Graphical Analysis of Structural Causal Models
Description: A port of the web-based software 'DAGitty', available at
<http://dagitty.net>, for analyzing structural causal models
(also known as directed acyclic graphs or DAGs).
This package computes covariate adjustment sets for estimating causal
effects, enumerates instrumental variables, derives testable
implications (d-separation and vanishing tetrads), generates equivalent
models, and includes a simple facility for data simulation.
Author: Johannes Textor, Benito van der Zander
Maintainer: Johannes Textor <johannes.textor@gmx.de>
Diff between dagitty versions 0.1-9 dated 2016-03-22 and 0.1-10 dated 2016-03-26
DESCRIPTION | 15 ++++++++------- MD5 | 10 +++++----- R/dagitty.r | 8 ++++---- inst/doc/dagitty4semusers.html | 6 +++--- man/dagitty.Rd | 2 +- man/names.dagitty.Rd | 6 +++--- 6 files changed, 24 insertions(+), 23 deletions(-)
Title: Beta-Diversity of Species Interactions
Description: Measures of beta-diversity in networks, and easy visualization of why two networks are different.
Author: Timothee Poisot <tim@poisotlab.io>
Maintainer: Timothee Poisot <tim@poisotlab.io>
Diff between betalink versions 2.2.0 dated 2015-12-22 and 2.2.1 dated 2016-03-26
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS | 5 +++++ R/betalink.r | 8 ++++---- R/metaweb.r | 6 ++++++ 5 files changed, 24 insertions(+), 13 deletions(-)
Title: Mining Frequent Sequences
Description: Add-on for arules to handle and mine frequent sequences.
Provides interfaces to the C++ implementation of cSPADE by
Mohammed J. Zaki.
Author: Christian Buchta and Michael Hahsler, with contributions from
Daniel Diaz
Maintainer: Christian Buchta <christian.buchta@wu.ac.at>
Diff between arulesSequences versions 0.2-13 dated 2016-01-26 and 0.2-14 dated 2016-03-26
CHANGELOG | 6 DESCRIPTION | 8 - MD5 | 44 +++---- NAMESPACE | 6 R/02sequences.R | 9 + R/03rules.R | 2 R/05read_write.R | 12 - R/10timed.R | 21 +-- R/20support.R | 11 - R/30similarity.R | 93 ++++++++++---- data/zaki.rda |binary man/cspade.Rd | 2 man/match-methods.Rd | 1 man/read_baskets.Rd | 2 man/timedsequences-class.Rd | 5 src/ptree.c | 274 ++++++++++++++++++++++++++++++++++++++++++-- tests/arules.Rout.save | 2 tests/idlists.Rout.save | 2 tests/makebin.Rout.save | 2 tests/native.Rout.save | 2 tests/ptree.Rout.save | 2 tests/similarity.Rout.save | 2 tests/zaki.Rout.save | 2 23 files changed, 413 insertions(+), 97 deletions(-)
More information about arulesSequences at CRAN
Permanent link
Title: Treemap Visualization
Description: A treemap is a space-filling visualization of hierarchical
structures. This package offers great flexibility to draw treemaps.
Author: Martijn Tennekes
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between treemap versions 2.4 dated 2015-10-14 and 2.4-1 dated 2016-03-26
treemap-2.4-1/treemap/DESCRIPTION | 10 ++-- treemap-2.4-1/treemap/MD5 | 38 +++++++++--------- treemap-2.4-1/treemap/NAMESPACE | 12 ++++- treemap-2.4-1/treemap/NEWS | 4 + treemap-2.4-1/treemap/R/datasets.R | 15 ++++--- treemap-2.4-1/treemap/R/pkg.R | 9 ---- treemap-2.4-1/treemap/R/treecolors.R | 2 treemap-2.4-1/treemap/R/treemap.R | 23 +++++----- treemap-2.4-1/treemap/build/vignette.rds |binary treemap-2.4-1/treemap/data/GNI2014.rda |only treemap-2.4-1/treemap/man/GNI2014.Rd |only treemap-2.4-1/treemap/man/business.Rd | 4 - treemap-2.4-1/treemap/man/itreemap.Rd | 2 treemap-2.4-1/treemap/man/random.hierarchical.data.Rd | 2 treemap-2.4-1/treemap/man/tmPlot.Rd | 2 treemap-2.4-1/treemap/man/treecolors.Rd | 2 treemap-2.4-1/treemap/man/treegraph.Rd | 8 +-- treemap-2.4-1/treemap/man/treemap-package.Rd | 13 ------ treemap-2.4-1/treemap/man/treemap.Rd | 18 ++++---- treemap-2.4-1/treemap/man/treepalette.Rd | 4 - treemap-2.4/treemap/data/GNI2010.rda |only treemap-2.4/treemap/man/GNI2010.Rd |only 22 files changed, 83 insertions(+), 85 deletions(-)
More information about TotalCopheneticIndex at CRAN
Permanent link
Title: Collect Data Programmatically by POST Methods to Google Forms
Description: GET and POST data to Google Forms; more secure than having to
expose Google Sheets in order to POST data.
Author: Steve Simpson [aut, cre]
Maintainer: Steve Simpson <steven.troy.simpson@gmail.com>
Diff between googleformr versions 0.0.1 dated 2016-01-06 and 0.0.2 dated 2016-03-26
googleformr-0.0.1/googleformr/R/why_R_u_thankful.R |only googleformr-0.0.1/googleformr/man/why_R_u_thankful.Rd |only googleformr-0.0.2/googleformr/DESCRIPTION | 6 ++-- googleformr-0.0.2/googleformr/MD5 | 14 +++++----- googleformr-0.0.2/googleformr/NAMESPACE | 2 - googleformr-0.0.2/googleformr/R/gformr.R | 4 +- googleformr-0.0.2/googleformr/R/why_R_u_opensource.R |only googleformr-0.0.2/googleformr/README.md | 22 ++++++++-------- googleformr-0.0.2/googleformr/man/gformr.Rd | 2 - googleformr-0.0.2/googleformr/man/why_R_u_opensource.Rd |only 10 files changed, 25 insertions(+), 25 deletions(-)
Title: Tableplot, a Visualization of Large Datasets
Description: A tableplot is a visualisation of a (large)
dataset with a dozen of variables, both numeric and
categorical. Each column represents a variable and each
row bin is an aggregate of a certain number of records.
Numeric variables are visualized as bar charts, and
categorical variables as stacked bar charts. Missing
values are taken into account. Also supports large ffdf
datasets from the ff package.
Author: Martijn Tennekes and Edwin de Jonge
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between tabplot versions 1.1 dated 2014-02-24 and 1.3 dated 2016-03-26
tabplot-1.1/tabplot/vignettes/figure |only tabplot-1.3/tabplot/DESCRIPTION | 13 - tabplot-1.3/tabplot/MD5 | 114 ++++------ tabplot-1.3/tabplot/NAMESPACE | 29 ++ tabplot-1.3/tabplot/NEWS | 12 + tabplot-1.3/tabplot/R/bin_data.R | 11 tabplot-1.3/tabplot/R/columnTable.R | 11 tabplot-1.3/tabplot/R/coorNumCol.R | 52 +++- tabplot-1.3/tabplot/R/itableplot.R | 2 tabplot-1.3/tabplot/R/num2fac.R | 37 +-- tabplot-1.3/tabplot/R/pkg.R | 16 - tabplot-1.3/tabplot/R/plotCatCol.R | 11 tabplot-1.3/tabplot/R/plotNumCol.R | 148 +++++++++---- tabplot-1.3/tabplot/R/plot_tabplot.r | 61 +++-- tabplot-1.3/tabplot/R/save_loadPrepare.R |only tabplot-1.3/tabplot/R/scaleNumCol.R | 9 tabplot-1.3/tabplot/R/sysdata.rda |binary tabplot-1.3/tabplot/R/tablePalettes.R | 6 tabplot-1.3/tabplot/R/tablePrepare.R | 16 - tabplot-1.3/tabplot/R/tableSave.R | 113 +++++----- tabplot-1.3/tabplot/R/tableplot.R | 98 ++++++-- tabplot-1.3/tabplot/R/tableplot_checkCols.R | 10 tabplot-1.3/tabplot/R/tableplot_checkNumPals.R | 9 tabplot-1.3/tabplot/R/tableplot_checkPals.R | 2 tabplot-1.3/tabplot/R/tableplot_checkRevLeg.R |only tabplot-1.3/tabplot/R/tableplot_processCols.R |only tabplot-1.3/tabplot/R/tableplots_diff.R | 29 +- tabplot-1.3/tabplot/R/tabplot_object.R | 2 tabplot-1.3/tabplot/build/vignette.rds |binary tabplot-1.3/tabplot/inst/doc/tabplot-timings.R | 9 tabplot-1.3/tabplot/inst/doc/tabplot-timings.html | 139 ++++++------ tabplot-1.3/tabplot/inst/doc/tabplot-vignette.R | 20 - tabplot-1.3/tabplot/inst/doc/tabplot-vignette.Rmd | 10 tabplot-1.3/tabplot/inst/doc/tabplot-vignette.html | 198 +++++++++-------- tabplot-1.3/tabplot/inst/shinyapp/ui.R | 2 tabplot-1.3/tabplot/man/bin_data.Rd | 21 - tabplot-1.3/tabplot/man/bin_hcc_data.Rd | 9 tabplot-1.3/tabplot/man/datetime2fac.Rd | 19 - tabplot-1.3/tabplot/man/itableplot.Rd | 14 - tabplot-1.3/tabplot/man/loadPrepare.Rd |only tabplot-1.3/tabplot/man/num2fac.Rd | 42 +-- tabplot-1.3/tabplot/man/plot.tabplot.Rd | 58 ++--- tabplot-1.3/tabplot/man/print.tabplot.Rd | 6 tabplot-1.3/tabplot/man/savePrepare.Rd |only tabplot-1.3/tabplot/man/summary.tabplot.Rd | 9 tabplot-1.3/tabplot/man/tableChange.Rd | 44 +-- tabplot-1.3/tabplot/man/tablePalettes.Rd | 59 +---- tabplot-1.3/tabplot/man/tablePrepare.Rd | 38 +-- tabplot-1.3/tabplot/man/tableSave.Rd | 46 +--- tabplot-1.3/tabplot/man/tableplot.Rd | 237 ++++++--------------- tabplot-1.3/tabplot/man/tableplot_comparison.Rd | 17 - tabplot-1.3/tabplot/man/tabplot-object.Rd | 15 - tabplot-1.3/tabplot/man/tabplot-package.Rd | 44 +-- tabplot-1.3/tabplot/man/tabplot_compare-object.Rd | 8 tabplot-1.3/tabplot/vignettes/tabplot-vignette.Rmd | 10 55 files changed, 982 insertions(+), 903 deletions(-)
Title: Determine Optimal Clustering Algorithm and Number of Clusters
Description: Cluster analysis using statistical and biological
validation measures for both continuous and count data.
Author: Michael Sekula <michael.sekula@louisville.edu>,
Somnath Datta <somnath.datta@louisville.edu>,
and Susmita Datta <susmita.datta@louisville.edu>
Maintainer: Michael Sekula <michael.sekula@louisville.edu>
Diff between optCluster versions 1.0.1 dated 2015-10-19 and 1.1.0 dated 2016-03-26
DESCRIPTION | 8 +- MD5 | 12 +-- R/optCluster-Functions.R | 23 +++++-- man/arabid.Rd | 38 ++++++------ man/optCluster.Rd | 147 ++++++++++++++++++++++++++++++----------------- man/optHeatmap.Rd | 8 +- man/repRankAggreg.Rd | 39 +++++++++++- 7 files changed, 178 insertions(+), 97 deletions(-)
Title: Network Assisted Algorithm for Epigenetic Studies Using Mean and
Variance Combined Signals
Description: Package for a Network assisted algorithm for Epigenetic studies using mean and variance Combined signals: NEpiC. NEpiC combines both signals in mean and variance differences in methylation level between case and control groups searching for differentially methylated sub-networks (modules) using the protein-protein interaction network.
Author: Peifeng Ruan
Maintainer: Peifeng Ruan <pruan12@fudan.edu.cn>
Diff between NEpiC versions 1.0 dated 2015-11-26 and 1.0.1 dated 2016-03-26
DESCRIPTION | 10 +++++----- MD5 | 6 ++++-- NAMESPACE | 5 +++-- R/permutation.r |only man/permutation.Rd |only 5 files changed, 12 insertions(+), 9 deletions(-)
Title: Data Exploration with Information Theory (Weight-of-Evidence and
Information Value)
Description: Performs exploratory data analysis and variable screening for
binary classification models using weight-of-evidence (WOE) and information
value (IV). In order to make the package as efficient as possible, aggregations
are done in data.table and creation of WOE vectors can be distributed across
multiple cores. The package also supports exploration for uplift models (NWOE
and NIV).
Author: Larsen Kim [aut, cre]
Maintainer: Larsen Kim <kblarsen4@gmail.com>
Diff between Information versions 0.0.7 dated 2015-11-19 and 0.0.8 dated 2016-03-26
DESCRIPTION | 16 ++- MD5 | 45 ++++----- NAMESPACE | 2 NEWS.md |only R/Aggregate.R | 10 +- R/NWOE.R | 2 R/Penalty.R | 6 - R/WOE.R | 2 R/create_infotables.R | 4 build/vignette.rds |binary inst/doc/Information-vignette.html | 182 ++++++++++++++++++++----------------- man/Aggregate.Rd | 2 man/CheckInputs.Rd | 4 man/Information.Rd | 14 +- man/MultiPlot.Rd | 2 man/NWOE.Rd | 2 man/SinglePlot.Rd | 2 man/WOE.Rd | 2 man/create_infotables.Rd | 3 man/is.binary.Rd | 2 man/penalty.Rd | 2 man/plot_infotables.Rd | 5 - man/train.Rd | 2 man/valid.Rd | 2 24 files changed, 175 insertions(+), 138 deletions(-)
Title: 2D and 3D Hive Plots for R
Description: Creates and plots 2D and 3D hive plots. Hive plots are a unique method of displaying networks of many types in which node properties are mapped to axes using meaningful properties rather than being arbitrarily positioned. The hive plot concept was invented by Martin Krzywinski at the Genome Science Center (www.hiveplot.net/). Keywords: networks, food webs, linnet, systems biology, bioinformatics.
Author: Bryan A. Hanson [aut, cre],
Vesna Memisevic [ctb],
Jonathan Chung [ctb]
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between HiveR versions 0.2.46 dated 2016-01-25 and 0.2.55 dated 2016-03-26
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 6 ++++++ R/plotHive.R | 12 ++++++------ build/vignette.rds |binary inst/doc/HiveR.pdf |binary 6 files changed, 21 insertions(+), 15 deletions(-)
Title: Visualizing Hypothesis Tests in Multivariate Linear Models
Description: Provides HE plot and other functions for visualizing hypothesis tests in multivariate linear models.
HE plots represent sums-of-squares-and-products matrices for linear hypotheses and for error using ellipses
(in two dimensions) and ellipsoids (in three dimensions). The related "candisc" package provides visualizations
in a reduced-rank canonical discriminant space when there are more than a few response variables.
Author: John Fox [aut], Michael Friendly [aut, cre], Georges Monette [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between heplots versions 1.0-16 dated 2015-07-12 and 1.1-0 dated 2016-03-26
DESCRIPTION | 18 MD5 | 156 ++- NAMESPACE | 56 - NEWS | 15 R/boxM.R |only R/colDevs.R |only R/covEllipses.R |only R/logdetCI.R |only R/pairs.mlm.R | 57 - R/plot.boxM.R |only build/vignette.rds |binary data/AddHealth.RData |only data/Adopted.RData |binary data/Bees.rda |binary data/FootHead.rda |binary data/Headache.RData |binary data/Hernior.RData |binary data/MockJury.RData |binary data/NLSY.RData |binary data/Oslo.RData |binary data/Plastic.rda |binary data/Pottery2.RData |binary data/Probe1.RData |binary data/Probe2.RData |binary data/RatWeight.RData |binary data/ReactTime.RData |binary data/Rohwer.rda |binary data/RootStock.rda |binary data/Sake.RData |binary data/Skulls.RData |binary data/SocGrades.RData |binary data/VocabGrowth.rda |binary data/WeightLoss.RData |binary data/schooldata.RData |binary inst/doc/HE-examples.R | 1096 +++++++++++++-------------- inst/doc/repeated.R | 1266 ++++++++++++++++---------------- man/AddHealth.Rd |only man/boxM.Rd |only man/colDevs.Rd |only man/covEllipses.Rd |only man/heplot-package.Rd | 9 man/logdetCI.Rd |only man/pairs.mlm.Rd | 6 man/plot.boxM.Rd |only vignettes/fig/plot-Ortho-fm1.pdf |binary vignettes/fig/plot-Ortho-fm3.pdf |binary vignettes/fig/plot-grades-can-class.pdf |binary vignettes/fig/plot-grades-can-gpa.pdf |binary vignettes/fig/plot-grades-can-sex.pdf |binary vignettes/fig/plot-grades-pairs.pdf |binary vignettes/fig/plot-hern-can-age.pdf |binary vignettes/fig/plot-hern-can-build.pdf |binary vignettes/fig/plot-hern-can-cardiac.pdf |binary vignettes/fig/plot-hern-can-pstat.pdf |binary vignettes/fig/plot-hern-pairs.pdf |binary vignettes/fig/plot-jury-can1.pdf |binary vignettes/fig/plot-jury-mod1-HE.pdf |binary vignettes/fig/plot-jury-mod1-pairs.pdf |binary vignettes/fig/plot-jury-mod2-HE.pdf |binary vignettes/fig/plot-jury-mod3-eff.pdf |binary vignettes/fig/plot-obk-HE1.pdf |binary vignettes/fig/plot-obk-HE2.pdf |binary vignettes/fig/plot-obk-HE3.pdf |binary vignettes/fig/plot-obk2-HE1.pdf |binary vignettes/fig/plot-obk2-HE2.pdf |binary vignettes/fig/plot-ortho-HE.pdf |binary vignettes/fig/plot-ortho-nonlin-HE.pdf |binary vignettes/fig/plot-ortho-xyplot1.pdf |binary vignettes/fig/plot-ortho-xyplot2.pdf |binary vignettes/fig/plot-plastic2.pdf |binary vignettes/fig/plot-rohwer-HE1.pdf |binary vignettes/fig/plot-rohwer-HE2.pdf |binary vignettes/fig/plot-rohwer-HE3.pdf |binary vignettes/fig/plot-rohwer-HE4.pdf |binary vignettes/fig/plot-skulls-HE-pairs.pdf |binary vignettes/fig/plot-skulls-bwplot.pdf |binary vignettes/fig/plot-skulls-can2.pdf |binary vignettes/fig/plot-skulls4.pdf |binary vignettes/fig/plot-voc1.pdf |binary vignettes/fig/plot-voc4.pdf |binary vignettes/fig/plot-voc8.pdf |binary vignettes/fig/plot-wl-HE1.pdf |binary vignettes/fig/plot-wl-HE2.pdf |binary vignettes/fig/plot-wl-HE3.pdf |binary vignettes/fig/plot-wl-means.pdf |binary 85 files changed, 1370 insertions(+), 1309 deletions(-)
Title: Expanding Ploidy and Allele-Frequency on Nested Subpopulations
Description: Expanding Ploidy and Allele Frequency on Nested Subpopulations (expands) characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data (http://www.ncbi.nlm.nih.gov/pubmed/24177718). The model detects coexisting genotypes by leveraging run-specific tradeoffs between depth of coverage and breadth of coverage. This package predicts the number of clonal expansions, the size of the resulting subpopulations in the tumor bulk, the mutations specific to each subpopulation, tumor purity and phylogeny. The main function runExPANdS() provides the complete functionality needed to predict coexisting subpopulations from single nucleotide variations (SNVs) and associated copy numbers. The robustness of subpopulation predictions increases with the number of mutations provided. It is recommended that at least 200 mutations are used as input to obtain stable results. Updates in version 1.7 include: (1) Higher subpopulation detection specificity, in particular for small subpopulations. (2) Higher accuracy for mutation assignment to subpopulations. (3) Whenever possible, SNVs are assigned not only to the subpopulation in which they first occurred, but also to descending subpopulations. (4) Two additional output files are created: subpopulation specific ploidy matrix and a summary file of all detected subpopulations, including information on the inferred ancestor and the closest descendant of each subpopulation. (5) New subpopulation plotting options (function plotSPs). (6) New phylogeny plotting option: user can choose between consensus and germline population to be included as control. (7) 50 simulated samples of various genetic complexities and noise levels included for user testing. Special thanks to Dr. Ryan Morin for his contributions that have led to higher accuracy measures during simulations for mutation assignment to subpopulations, as well as advanced visualization features of assigned mutations. Further documentation and FAQ available at http://dna-discovery.stanford.edu/software/expands.
Author: Noemi Andor
Maintainer: Noemi Andor <expands.r@gmail.com>
Diff between expands versions 1.6.1 dated 2015-12-03 and 1.7 dated 2016-03-26
expands-1.6.1/expands/java/expands.jar |only expands-1.7/expands/DESCRIPTION | 14 - expands-1.7/expands/MD5 | 47 +-- expands-1.7/expands/NAMESPACE | 2 expands-1.7/expands/R/addColumn.R | 20 - expands-1.7/expands/R/assignMutations.R | 186 +++++++++++--- expands-1.7/expands/R/assignQuantityToMutation.R | 166 ++++++------ expands-1.7/expands/R/buildPhylo.R | 121 ++++++--- expands-1.7/expands/R/cellfrequency_pdf.R | 164 ++++++------ expands-1.7/expands/R/clusterCellFrequencies.R | 53 +-- expands-1.7/expands/R/computeCellFrequencyDistributions.R | 1 expands-1.7/expands/R/plotSPs.R | 85 +++++- expands-1.7/expands/R/runExPANdS.R | 93 +++++-- expands-1.7/expands/data/simulation.rda |only expands-1.7/expands/inst/doc/expands.Rnw | 8 expands-1.7/expands/inst/doc/expands.pdf |binary expands-1.7/expands/inst/java/expands.jar |binary expands-1.7/expands/java/Common.java |only expands-1.7/expands/java/ExPANdS.java |only expands-1.7/expands/man/assignMutations.Rd | 17 - expands-1.7/expands/man/assignQuantityToSP.Rd | 2 expands-1.7/expands/man/buildMultiSamplePhylo.Rd | 2 expands-1.7/expands/man/buildPhylo.Rd | 7 expands-1.7/expands/man/plotSPs.Rd | 23 + expands-1.7/expands/man/runExPANdS.Rd | 8 expands-1.7/expands/man/simulation.Rd |only expands-1.7/expands/vignettes/expands.Rnw | 8 27 files changed, 681 insertions(+), 346 deletions(-)
Title: Calculation of Thermal Comfort Indices
Description: Functions to calculate various common and less common thermal comfort indices.
Author: Marcel Schweiker [aut, cre] and Sophia Mueller [aut] and Michael Kleber [ctr] and Boris Kingma [ctr] and Masanori Shukuya [ctr]
Maintainer: Marcel Schweiker <marcel.schweiker@kit.edu>
Diff between comf versions 0.1.1 dated 2016-03-06 and 0.1.2 dated 2016-03-26
comf-0.1.1/comf/man/calcMeanBias.Rd |only comf-0.1.2/comf/DESCRIPTION | 9 ++++---- comf-0.1.2/comf/MD5 | 36 +++++++++++++++++--------------- comf-0.1.2/comf/NAMESPACE | 2 - comf-0.1.2/comf/NEWS |only comf-0.1.2/comf/R/ComfortIndices.r | 6 ++--- comf-0.1.2/comf/R/dfField.R |only comf-0.1.2/comf/R/fct2Node.r | 19 ++++++++-------- comf-0.1.2/comf/R/fctHBxStSt.r | 2 - comf-0.1.2/comf/R/fctHelp.r | 11 ++++++--- comf-0.1.2/comf/R/fctOther.r | 4 +++ comf-0.1.2/comf/data |only comf-0.1.2/comf/man/calc2Node.Rd | 8 ++++--- comf-0.1.2/comf/man/calcBias.Rd |only comf-0.1.2/comf/man/calcComfInd.Rd | 2 - comf-0.1.2/comf/man/calcHbExSteady.Rd | 10 ++++---- comf-0.1.2/comf/man/calcHbExUnsteady.Rd | 2 - comf-0.1.2/comf/man/calcPMVPPD.Rd | 2 + comf-0.1.2/comf/man/calcTAdapt.Rd | 6 ++++- comf-0.1.2/comf/man/calcdTNZ.Rd | 2 - comf-0.1.2/comf/man/comf-package.Rd | 12 +++++----- comf-0.1.2/comf/man/dfField.Rd |only 22 files changed, 76 insertions(+), 57 deletions(-)