Author: Ingo Feinerer, Kurt Hornik
Title: WordNet Interface
Description: An interface to WordNet using the Jawbone Java API to
WordNet. WordNet is an on-line lexical reference system
developed by the Cognitive Science Laboratory at Princeton
University. Its design is inspired by current psycholinguistic
theories of human lexical memory. English nouns, verbs,
adjectives and adverbs are organized into synonym sets, each
representing one underlying lexical concept. Different
relations link the synonym sets.
Diff between wordnet versions 0.1-4 dated 2009-06-25 and 0.1-5 dated 2009-09-10
wordnet-0.1-4/wordnet/inst/doc/wordnet.tex |only wordnet-0.1-5/wordnet/DESCRIPTION | 8 ++++---- wordnet-0.1-5/wordnet/inst/CITATION | 2 +- wordnet-0.1-5/wordnet/inst/doc/wordnet.pdf |binary 4 files changed, 5 insertions(+), 5 deletions(-)
Author: Compiled by Adrian Trapletti
Title: Time series analysis and computational finance
Description: Package for time series analysis and computational finance
Diff between tseries versions 0.10-19 dated 2009-08-31 and 0.10-20 dated 2009-09-10
ChangeLog | 6 ++++++ DESCRIPTION | 8 ++++---- inst/CITATION | 4 ++-- 3 files changed, 12 insertions(+), 6 deletions(-)
Author: Ingo Feinerer
Title: Text Mining Package
Description: A framework for text mining applications within R.
Diff between tm versions 0.4 dated 2009-07-01 and 0.5 dated 2009-09-10
tm-0.4/tm/R/AAA.R |only tm-0.4/tm/R/aobjects.R |only tm-0.4/tm/inst/texts/cars.csv |only tm-0.4/tm/inst/texts/gmane.comp.lang.r.general.mbox |only tm-0.4/tm/inst/texts/gmane.comp.lang.r.general.mbox.gz |only tm-0.4/tm/inst/texts/gmane.comp.lang.r.gr.rdf |only tm-0.4/tm/inst/texts/html |only tm-0.4/tm/inst/texts/newsgroup |only tm-0.4/tm/inst/texts/pdf |only tm-0.4/tm/inst/texts/rcv1 |only tm-0.4/tm/inst/texts/rcv1.xml |only tm-0.4/tm/inst/texts/reut21578 |only tm-0.4/tm/inst/texts/reut21578.xml |only tm-0.4/tm/inst/texts/reut21578.xml.gz |only tm-0.4/tm/man/Corpus-class.Rd |only tm-0.4/tm/man/DataframeSource-class.Rd |only tm-0.4/tm/man/Dictionary-class.Rd |only tm-0.4/tm/man/DirSource-class.Rd |only tm-0.4/tm/man/DublinCore-methods.Rd |only tm-0.4/tm/man/FunctionGenerator-class.Rd |only tm-0.4/tm/man/GmaneSource-class.Rd |only tm-0.4/tm/man/IN-methods.Rd |only tm-0.4/tm/man/MetaDataNode-class.Rd |only tm-0.4/tm/man/NewsgroupDocument-class.Rd |only tm-0.4/tm/man/PCorpus-class.Rd |only tm-0.4/tm/man/PlainTextDocument-class.Rd |only tm-0.4/tm/man/RCV1Document-class.Rd |only tm-0.4/tm/man/Reuters21578Document-class.Rd |only tm-0.4/tm/man/Source-class.Rd |only tm-0.4/tm/man/StructuredTextDocument-class.Rd |only tm-0.4/tm/man/TextDocument-class.Rd |only tm-0.4/tm/man/TextRepository-class.Rd |only tm-0.4/tm/man/URISource-class.Rd |only tm-0.4/tm/man/VCorpus-class.Rd |only tm-0.4/tm/man/VectorSource-class.Rd |only tm-0.4/tm/man/WeightFunction-class.Rd |only tm-0.4/tm/man/XMLSource-class.Rd |only tm-0.4/tm/man/XMLTextDocument-class.Rd |only tm-0.4/tm/man/activateCluster.Rd |only tm-0.4/tm/man/appendElem.Rd |only tm-0.4/tm/man/asPlain.Rd |only tm-0.4/tm/man/c-methods.Rd |only tm-0.4/tm/man/completeStems.Rd |only tm-0.4/tm/man/convertMboxEml.Rd |only tm-0.4/tm/man/convertRCV1Plain.Rd |only tm-0.4/tm/man/convertReut21578XMLPlain.Rd |only tm-0.4/tm/man/deactivateCluster.Rd |only tm-0.4/tm/man/dissimilarity-methods.Rd |only tm-0.4/tm/man/eoi-methods.Rd |only tm-0.4/tm/man/getElem-methods.Rd |only tm-0.4/tm/man/length-methods.Rd |only tm-0.4/tm/man/pGetElem-methods.Rd |only tm-0.4/tm/man/readHTML.Rd |only tm-0.4/tm/man/readNewsgroup.Rd |only tm-0.4/tm/man/removeCitation.Rd |only tm-0.4/tm/man/removeMultipart.Rd |only tm-0.4/tm/man/removeSignature.Rd |only tm-0.4/tm/man/replacePatterns.Rd |only tm-0.4/tm/man/show-methods.Rd |only tm-0.4/tm/man/stemDoc.Rd |only tm-0.4/tm/man/stepNext-methods.Rd |only tm-0.4/tm/man/subset-methods.Rd |only tm-0.4/tm/man/summary-methods.Rd |only tm-0.4/tm/man/tmFilter-methods.Rd |only tm-0.4/tm/man/tmIndex-methods.Rd |only tm-0.4/tm/man/tmIntersect.Rd |only tm-0.4/tm/man/tmMap-methods.Rd |only tm-0.4/tm/man/tmReduce.Rd |only tm-0.4/tm/man/tmTolower.Rd |only tm-0.4/tm/man/writeCorpus-methods.Rd |only tm-0.5/tm/DESCRIPTION | 13 tm-0.5/tm/NAMESPACE | 247 ++--- tm-0.5/tm/R/chunks.R | 2 tm-0.5/tm/R/cluster.R | 4 tm-0.5/tm/R/complete.R | 4 tm-0.5/tm/R/corpus.R | 737 +++++------------ tm-0.5/tm/R/dictionary.R | 7 tm-0.5/tm/R/doc.R | 82 + tm-0.5/tm/R/filter.R | 49 - tm-0.5/tm/R/fungen.R | 15 tm-0.5/tm/R/matrix.R | 67 - tm-0.5/tm/R/meta.R | 267 +++--- tm-0.5/tm/R/preprocess.R | 40 tm-0.5/tm/R/reader.R | 251 +---- tm-0.5/tm/R/source.R | 216 +--- tm-0.5/tm/R/textrepo.R | 64 - tm-0.5/tm/R/transform.R | 267 ++---- tm-0.5/tm/R/weight.R | 19 tm-0.5/tm/data/acq.rda |binary tm-0.5/tm/data/crude.rda |binary tm-0.5/tm/inst/CITATION | 10 tm-0.5/tm/inst/NEWS | 37 tm-0.5/tm/inst/doc/extensions.Rnw | 102 +- tm-0.5/tm/inst/doc/extensions.pdf |binary tm-0.5/tm/inst/doc/tm.Rnw | 164 +-- tm-0.5/tm/inst/doc/tm.pdf |binary tm-0.5/tm/inst/texts/loremipsum.txt |only tm-0.5/tm/inst/texts/rcv1_2330.xml |only tm-0.5/tm/inst/texts/reuters-21578.xml |only tm-0.5/tm/man/DataframeSource.Rd | 10 tm-0.5/tm/man/Dictionary.Rd | 5 tm-0.5/tm/man/DirSource.Rd | 20 tm-0.5/tm/man/FunctionGenerator.Rd | 16 tm-0.5/tm/man/GmaneSource.Rd | 15 tm-0.5/tm/man/PCorpus.Rd | 49 - tm-0.5/tm/man/PlainTextDocument.Rd |only tm-0.5/tm/man/RCV1Document.Rd |only tm-0.5/tm/man/Reuters21578Document.Rd |only tm-0.5/tm/man/ReutersSource.Rd | 31 tm-0.5/tm/man/Source.Rd |only tm-0.5/tm/man/TextDocument.Rd |only tm-0.5/tm/man/TextRepository.Rd | 20 tm-0.5/tm/man/URISource.Rd | 29 tm-0.5/tm/man/VCorpus.Rd | 55 - tm-0.5/tm/man/VectorSource.Rd | 23 tm-0.5/tm/man/WeightFunction.Rd | 19 tm-0.5/tm/man/XMLSource.Rd | 20 tm-0.5/tm/man/acq.Rd | 6 tm-0.5/tm/man/as.PlainTextDocument.Rd |only tm-0.5/tm/man/cluster.Rd |only tm-0.5/tm/man/combine.Rd |only tm-0.5/tm/man/convert_UTF_8.Rd |only tm-0.5/tm/man/crude.Rd | 6 tm-0.5/tm/man/dissimilarity.Rd |only tm-0.5/tm/man/findFreqTerms.Rd | 8 tm-0.5/tm/man/getFilters.Rd | 6 tm-0.5/tm/man/getReaders.Rd | 5 tm-0.5/tm/man/getSources.Rd | 5 tm-0.5/tm/man/getTransformations.Rd | 6 tm-0.5/tm/man/inspect.Rd | 4 tm-0.5/tm/man/makeChunks.Rd | 1 tm-0.5/tm/man/materialize.Rd | 6 tm-0.5/tm/man/matrix.Rd | 11 tm-0.5/tm/man/meta.Rd | 92 +- tm-0.5/tm/man/plot.Rd | 12 tm-0.5/tm/man/preprocessReut21578XML.Rd | 23 tm-0.5/tm/man/prescindMeta.Rd | 19 tm-0.5/tm/man/readDOC.Rd | 14 tm-0.5/tm/man/readGmane.Rd | 14 tm-0.5/tm/man/readPDF.Rd | 18 tm-0.5/tm/man/readPlain.Rd | 10 tm-0.5/tm/man/readRCV1.Rd | 15 tm-0.5/tm/man/readReut21578XML.Rd | 15 tm-0.5/tm/man/readTabular.Rd | 30 tm-0.5/tm/man/readXML.Rd | 38 tm-0.5/tm/man/removeNumbers.Rd | 26 tm-0.5/tm/man/removePunctuation.Rd | 25 tm-0.5/tm/man/removeSparseTerms.Rd | 9 tm-0.5/tm/man/removeWords.Rd | 27 tm-0.5/tm/man/sFilter.Rd | 15 tm-0.5/tm/man/searchFullText.Rd | 29 tm-0.5/tm/man/stemCompletion.Rd |only tm-0.5/tm/man/stemDocument.Rd |only tm-0.5/tm/man/stopwords.Rd | 10 tm-0.5/tm/man/stripWhitespace.Rd | 29 tm-0.5/tm/man/termFreq.Rd | 49 - tm-0.5/tm/man/tm_filter.Rd |only tm-0.5/tm/man/tm_intersect.Rd |only tm-0.5/tm/man/tm_map.Rd |only tm-0.5/tm/man/tm_reduce.Rd |only tm-0.5/tm/man/weightBin.Rd | 4 tm-0.5/tm/man/weightTf.Rd | 6 tm-0.5/tm/man/weightTfIdf.Rd | 6 tm-0.5/tm/man/writeCorpus.Rd |only tm-0.5/tm/src/lazyTmMap.c | 2 165 files changed, 1615 insertions(+), 1962 deletions(-)
More information about tm.plugin.mail at CRAN
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Author: Kurt Hornik, David Meyer, Christian Buchta
Title: Sparse Lightweight Arrays and Matrices
Description: Data structures and algorithms for sparse arrays and
matrices, based on index arrays and simple triplet
representations, respectively.
Diff between slam versions 0.1-4 dated 2009-08-26 and 0.1-5 dated 2009-09-10
DESCRIPTION | 8 ++++---- R/matrix.R | 22 ++++++++++++++++------ 2 files changed, 20 insertions(+), 10 deletions(-)
Author: Karl W Broman
Title: Tools for analyzing QTL experiments
Description: Analysis of experimental crosses to identify genes (called
quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Diff between qtl versions 1.12-26 dated 2009-07-01 and 1.13-7 dated 2009-09-10
DESCRIPTION | 8 +-- INDEX | 4 + R/addqtl.R | 28 +++++++++--- R/fitqtl.R | 103 ++++++++++++++++++++++++++++++++------------- R/makeqtl.R | 12 ++++- R/plot.R | 6 +- R/read.cross.mm.R | 8 +-- R/refineqtl.R | 11 +++- R/scanone.R | 62 +++++++++++++++++++++++++-- R/scanqtl.R | 11 +++- R/scantwo.R | 64 +++++++++++++++++++++++++++ R/summary.scantwo.R | 89 ++++++++++++++++++++++++++++++++++++++ R/util.R | 47 +++++++++++--------- inst/README.txt | 18 +++---- inst/STATUS.txt | 44 +++++++++++++++++++ inst/TODO.txt | 6 -- man/a.starting.point.Rd | 78 +++++++++++++++++----------------- man/add.cim.covar.Rd | 12 ++--- man/add.threshold.Rd | 24 +++++----- man/addcovarint.Rd | 12 ++--- man/addint.Rd | 12 ++--- man/addpair.Rd | 42 +++++++++--------- man/addqtl.Rd | 20 ++++---- man/addtoqtl.Rd | 12 ++--- man/argmax.geno.Rd | 6 +- man/arithscan.Rd | 6 +- man/arithscanperm.Rd | 8 +-- man/badorder.Rd | 6 +- man/bayesint.Rd | 14 +++--- man/bristle3.Rd | 8 +-- man/bristleX.Rd | 8 +-- man/c.cross.Rd | 4 - man/c.scanone.Rd | 14 +++--- man/c.scanoneperm.Rd | 12 ++--- man/c.scantwo.Rd |only man/c.scantwoperm.Rd | 12 ++--- man/calc.errorlod.Rd | 12 ++--- man/calc.genoprob.Rd | 8 +-- man/calc.penalties.Rd | 16 +++--- man/cbind.scanoneperm.Rd | 14 +++--- man/checkAlleles.Rd | 6 +- man/chrlen.Rd | 4 - man/chrnames.Rd | 4 - man/cim.Rd | 12 ++--- man/clean.cross.Rd | 10 ++-- man/clean.scantwo.Rd | 8 +-- man/comparecrosses.Rd | 6 +- man/comparegeno.Rd | 4 - man/compareorder.Rd | 6 +- man/condense.scantwo.Rd | 12 ++--- man/convert.scanone.Rd | 4 - man/convert.scantwo.Rd | 6 +- man/convert2sa.Rd | 4 - man/countXO.Rd | 4 - man/drop.markers.Rd | 8 +-- man/drop.nullmarkers.Rd | 8 +-- man/dropfromqtl.Rd | 10 ++-- man/effectplot.Rd | 4 - man/effectscan.Rd | 10 ++-- man/est.map.Rd | 6 +- man/est.rf.Rd | 6 +- man/fake.4way.Rd | 12 ++--- man/fake.bc.Rd | 12 ++--- man/fake.f2.Rd | 14 +++--- man/fill.geno.Rd | 18 +++---- man/find.flanking.Rd | 6 +- man/find.marker.Rd | 8 +-- man/find.markerpos.Rd | 6 +- man/find.pheno.Rd | 2 man/find.pseudomarker.Rd | 8 +-- man/findDupMarkers.Rd | 6 +- man/fitqtl.Rd | 16 +++--- man/fitstahl.Rd | 4 - man/formLinkageGroups.Rd | 6 +- man/geno.crosstab.Rd | 6 +- man/geno.image.Rd | 6 +- man/geno.table.Rd | 6 +- man/hyper.Rd | 8 +-- man/jittermap.Rd | 10 ++-- man/listeria.Rd | 8 +-- man/locateXO.Rd |only man/lodint.Rd | 12 ++--- man/makeqtl.Rd | 18 +++---- man/map10.Rd | 4 - man/markernames.Rd | 4 - man/max.scanone.Rd | 8 +-- man/max.scantwo.Rd | 12 ++--- man/movemarker.Rd | 6 +- man/nchr.Rd | 16 +++--- man/nind.Rd | 14 +++--- man/nmar.Rd | 16 +++--- man/nmissing.Rd | 6 +- man/nphe.Rd | 14 +++--- man/ntyped.Rd | 6 +- man/orderMarkers.Rd | 12 ++--- man/plot.cross.Rd | 12 ++--- man/plot.errorlod.Rd | 10 ++-- man/plot.geno.Rd | 10 ++-- man/plot.info.Rd | 12 ++--- man/plot.map.Rd | 2 man/plot.missing.Rd | 4 - man/plot.pheno.Rd | 6 +- man/plot.pxg.Rd | 8 +-- man/plot.qtl.Rd | 8 +-- man/plot.rf.Rd | 6 +- man/plot.scanone.Rd | 10 ++-- man/plot.scanoneboot.Rd | 8 +-- man/plot.scanoneperm.Rd | 8 +-- man/plot.scantwo.Rd | 18 +++---- man/plot.scantwoperm.Rd | 8 +-- man/plotLodProfile.Rd | 8 +-- man/plotModel.Rd | 4 - man/pull.geno.Rd | 4 - man/pull.map.Rd | 4 - man/pull.pheno.Rd | 4 - man/qtl-internal.Rd | 4 - man/qtlversion.Rd | 1 man/read.cross.Rd | 18 ++++--- man/readMWril.Rd | 6 +- man/refineqtl.Rd | 18 +++---- man/reorderqtl.Rd | 8 +-- man/replace.map.Rd | 4 - man/replacemap.scanone.Rd | 8 +-- man/replacemap.scantwo.Rd | 8 +-- man/replaceqtl.Rd | 14 +++--- man/ripple.Rd | 8 +-- man/scanone.Rd | 20 ++++---- man/scanoneboot.Rd | 14 +++--- man/scanqtl.Rd | 6 +- man/scantwo.Rd | 32 ++++++------- man/sim.cross.Rd | 14 +++--- man/sim.geno.Rd | 6 +- man/sim.map.Rd | 4 - man/simFounderSnps.Rd | 2 man/stepwiseqtl.Rd | 24 +++++----- man/strip.partials.Rd | 4 - man/subset.cross.Rd | 4 - man/subset.map.Rd | 2 man/subset.scanone.Rd | 8 +-- man/subset.scanoneperm.Rd | 12 ++--- man/subset.scantwo.Rd | 8 +-- man/subset.scantwoperm.Rd | 11 ++-- man/summary.cross.Rd | 14 +++--- man/summary.fitqtl.Rd | 8 +-- man/summary.map.Rd | 6 +- man/summary.qtl.Rd | 4 - man/summary.ripple.Rd | 8 +-- man/summary.scanone.Rd | 20 ++++---- man/summary.scanoneboot.Rd | 8 +-- man/summary.scanoneperm.Rd | 14 +++--- man/summary.scantwo.Rd | 16 +++--- man/summary.scantwo.old.Rd | 14 +++--- man/summary.scantwoperm.Rd | 10 ++-- man/switch.order.Rd | 10 ++-- man/top.errorlod.Rd | 4 - man/totmar.Rd | 16 +++--- man/tryallpositions.Rd | 12 ++--- man/write.cross.Rd | 6 +- man/xaxisloc.scanone.Rd | 18 +++---- 159 files changed, 1134 insertions(+), 809 deletions(-)
Author: S original by Bill Venables
Title: A collection of functions to implement a class for univariate
polynomial manipulations
Description: A collection of functions to implement a class for
univariate polynomial manipulations.
Diff between polynom versions 1.3-5 dated 2009-02-05 and 1.3-6 dated 2009-09-10
ChangeLog | 4 ++++ DESCRIPTION | 18 ++++++++++-------- inst/CITATION | 6 +++--- man/poly.orth.Rd | 2 +- 4 files changed, 18 insertions(+), 12 deletions(-)
Author: S original by Bill Venables
Title: Plot the Australian coastline and states
Description: Functions for plotting Australia's coastline and state
boundaries.
Diff between oz versions 1.0-17 dated 2009-02-05 and 1.0-18 dated 2009-09-10
ChangeLog | 6 ++++++ DESCRIPTION | 14 ++++++++------ inst/CITATION | 4 ++-- man/oz-states.Rd | 2 +- 4 files changed, 17 insertions(+), 9 deletions(-)
Author: Fridolin Wild
Title: Latent Semantic Analysis
Description: The basic idea of latent semantic analysis (LSA) is, that
text do have a higher order (=latent semantic) structure which,
however, is obscured by word usage (e.g. through the use of
synonyms or polysemy). By using conceptual indices that are
derived statistically via a truncated singular value
decomposition (a two-mode factor analysis) over a given
document-term matrix, this variability problem can be overcome.
Diff between lsa versions 0.63 dated 2009-08-21 and 0.63-1 dated 2009-09-10
DESCRIPTION | 8 ++++---- R/textmatrix.R | 12 ++++++------ tests/lsa-tests.R | 7 +++---- 3 files changed, 13 insertions(+), 14 deletions(-)
Author: Terry Therneau
Title: Functions for handling dates
Description: Functions for handling dates.
Diff between date versions 1.2-27 dated 2009-02-05 and 1.2-28 dated 2009-09-10
ChangeLog | 6 ++++++ DESCRIPTION | 13 ++++++++----- inst/CITATION | 8 ++++---- 3 files changed, 18 insertions(+), 9 deletions(-)
Author: Kurt Hornik, with contributions from Walter Boehm
Title: Cluster ensembles
Description: CLUster Ensembles
Diff between clue versions 0.3-30 dated 2009-08-31 and 0.3-31 dated 2009-09-10
DESCRIPTION | 8 ++++---- inst/CITATION | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-)
Author: S original by David James
Title: Chronological objects which can handle dates and times
Description: Chronological objects which can handle dates and times
Diff between chron versions 2.3-30 dated 2009-02-18 and 2.3-31 dated 2009-09-10
ChangeLog | 6 ++++++ DESCRIPTION | 12 +++++++----- inst/CITATION | 4 ++-- man/chron.Rd | 2 +- 4 files changed, 16 insertions(+), 8 deletions(-)
Author: Nicolas Turenne
Title: svcR package
Description: svcR implements a support vector machine technique for
clustering It includes choice between three kinds of kernel.
Original cluster labeling and export of clusters. Format of
data require 3 files: matrix, attributes, variables.
Diff between svcR versions 1.4.2 dated 2009-05-06 and 1.6.1 dated 2009-09-10
svcR-1.4.2/svcR/data/iris_att.txt |only svcR-1.4.2/svcR/data/iris_mat.txt |only svcR-1.4.2/svcR/data/iris_var.txt |only svcR-1.4.2/svcR/man/findModelCluster-class.Rd |only svcR-1.4.2/svcR/man/findModelCluster.Rd |only svcR-1.4.2/svcR/man/iris_att.Rd |only svcR-1.4.2/svcR/man/iris_mat.Rd |only svcR-1.4.2/svcR/man/iris_var.Rd |only svcR-1.6.1/svcR/DESCRIPTION | 8 svcR-1.6.1/svcR/NAMESPACE | 20 +- svcR-1.6.1/svcR/R/classes.R | 91 ++++++++-- svcR-1.6.1/svcR/R/display.R | 128 ++++++++++++-- svcR-1.6.1/svcR/R/eval.R | 16 - svcR-1.6.1/svcR/R/labelling.R | 20 +- svcR-1.6.1/svcR/R/model.R | 12 - svcR-1.6.1/svcR/R/svcR.R | 228 +++++++++++++++----------- svcR-1.6.1/svcR/data/term_att.txt |only svcR-1.6.1/svcR/data/term_mat.txt |only svcR-1.6.1/svcR/data/term_var.txt |only svcR-1.6.1/svcR/man/ClusterEval-class.Rd | 2 svcR-1.6.1/svcR/man/ClusterEval.Rd | 26 +- svcR-1.6.1/svcR/man/Display.Rd | 49 ++++- svcR-1.6.1/svcR/man/Labelling-class.Rd | 14 - svcR-1.6.1/svcR/man/Labelling.Rd | 34 +-- svcR-1.6.1/svcR/man/ModelSV-class.Rd | 7 svcR-1.6.1/svcR/man/ModelSV.Rd | 14 - svcR-1.6.1/svcR/man/findSvcModel-class.Rd |only svcR-1.6.1/svcR/man/findSvcModel.Rd |only svcR-1.6.1/svcR/man/kernelMatrix-class.Rd | 4 svcR-1.6.1/svcR/man/kernelMatrix.Rd | 10 - svcR-1.6.1/svcR/man/term_att.Rd |only svcR-1.6.1/svcR/man/term_mat.Rd |only svcR-1.6.1/svcR/man/term_var.Rd |only svcR-1.6.1/svcR/src/svcR.c | 2 34 files changed, 462 insertions(+), 223 deletions(-)
Author: Torsten Hothorn, Frank Bretz and Peter Westfall with
contributions by Richard M. Heiberger and Andre
Schuetzenmeister
Title: Simultaneous Inference in General Parametric Models
Description: Simultaneous tests and confidence intervals for general
linear hypotheses in parametric models, including linear,
generalized linear, linear mixed effects, and survival models.
Diff between multcomp versions 1.1-1 dated 2009-07-18 and 1.1-2 dated 2009-09-10
multcomp-1.1-1/multcomp/inst/doc/generalsiminf.bbl |only multcomp-1.1-1/multcomp/inst/doc/generalsiminf.blg |only multcomp-1.1-2/multcomp/DESCRIPTION | 10 multcomp-1.1-2/multcomp/NEWS | 9 multcomp-1.1-2/multcomp/R/glht.R | 14 multcomp-1.1-2/multcomp/R/helpers.R | 11 multcomp-1.1-2/multcomp/R/mcp.R | 162 + multcomp-1.1-2/multcomp/R/plot.R | 9 multcomp-1.1-2/multcomp/inst/CHANGES | 9 multcomp-1.1-2/multcomp/inst/doc/chfls1.pdf |binary multcomp-1.1-2/multcomp/inst/doc/generalsiminf.pdf | 1020 +++++------ multcomp-1.1-2/multcomp/inst/doc/multcomp-examples.pdf |binary multcomp-1.1-2/multcomp/man/glht.Rd | 6 multcomp-1.1-2/multcomp/man/methods.Rd | 3 multcomp-1.1-2/multcomp/man/modelparm.Rd | 4 multcomp-1.1-2/multcomp/tests/Examples/multcomp-Ex.Rout.save | 7 16 files changed, 733 insertions(+), 531 deletions(-)
Author: Andrea Peters and Torsten Hothorn
Title: Improved Predictors
Description: Improved predictive models by indirect classification and
bagging for classification, regression and survival problems as
well as resampling based estimators of prediction error.
Diff between ipred versions 0.8-7 dated 2009-03-28 and 0.8-8 dated 2009-09-10
CHANGES | 6 +++++- DESCRIPTION | 8 ++++---- inst/doc/ipred-examples.pdf |binary man/bagging.Rd | 2 +- 4 files changed, 10 insertions(+), 6 deletions(-)
Author: Michael J. Kane and John W. Emerson
Title: Manage massive matrices in R using C++, with support for shared
memory and memory-mapped files.
Description: Use C++ to create, store, access, and manipulate massive
matrices. Matrices may optionally be allocated to shared
memory and/or may use memory-mapped files.
Diff between bigmemory versions 3.10 dated 2009-07-18 and 3.11 dated 2009-09-10
bigmemory-3.10/bigmemory/configure.Rout |only bigmemory-3.10/bigmemory/src/BigMatrix.h |only bigmemory-3.10/bigmemory/src/BigMatrixAccessor.hpp |only bigmemory-3.10/bigmemory/src/BigMemoryDefines.h |only bigmemory-3.10/bigmemory/src/BigMemoryMutex.cpp |only bigmemory-3.10/bigmemory/src/BigMemoryMutex.h |only bigmemory-3.10/bigmemory/src/CUserMutex.cpp |only bigmemory-3.10/bigmemory/src/Cbigmemory.cpp |only bigmemory-3.10/bigmemory/src/CbigmemoryLib.cpp |only bigmemory-3.10/bigmemory/src/Makevars.darwin |only bigmemory-3.10/bigmemory/src/Makevars.linux |only bigmemory-3.10/bigmemory/src/Makevars.win |only bigmemory-3.10/bigmemory/src/SharedCounter.h |only bigmemory-3.10/bigmemory/src/TODO.txt |only bigmemory-3.10/bigmemory/src/bigmemoryutils.cpp |only bigmemory-3.10/bigmemory/src/isna.hpp |only bigmemory-3.10/bigmemory/src/tab2space.pl |only bigmemory-3.10/bigmemory/src/util.h |only bigmemory-3.11/bigmemory/DESCRIPTION | 8 bigmemory-3.11/bigmemory/cleanup | 1 bigmemory-3.11/bigmemory/configure.R | 19 + bigmemory-3.11/bigmemory/configure.win |only bigmemory-3.11/bigmemory/include/BigMatrix.h |only bigmemory-3.11/bigmemory/include/BigMatrixAccessor.hpp |only bigmemory-3.11/bigmemory/include/SharedCounter.h |only bigmemory-3.11/bigmemory/include/bigmemoryDefines.h |only bigmemory-3.11/bigmemory/include/bigmemoryMutex.h |only bigmemory-3.11/bigmemory/include/isna.hpp |only bigmemory-3.11/bigmemory/include/util.h |only bigmemory-3.11/bigmemory/man/big.matrix.Rd | 32 +-- bigmemory-3.11/bigmemory/man/biglm.big.matrix.Rd | 7 bigmemory-3.11/bigmemory/man/bigmemory-package.Rd | 29 +- bigmemory-3.11/bigmemory/man/rw.mutex.Rd | 6 bigmemory-3.11/bigmemory/man/write.big.matrix.Rd | 12 - bigmemory-3.11/bigmemory/src/BigMatrix.cpp | 178 ++++------------- bigmemory-3.11/bigmemory/src/SharedCounter.cpp | 8 bigmemory-3.11/bigmemory/src/UserMutex.cpp |only bigmemory-3.11/bigmemory/src/bigmemory.cpp |only bigmemory-3.11/bigmemory/src/bigmemoryLib.cpp |only bigmemory-3.11/bigmemory/src/bigmemoryMutex.cpp |only bigmemory-3.11/bigmemory/src/bigmemoryUtils.cpp |only bigmemory-3.11/bigmemory/src/util.cpp | 8 42 files changed, 126 insertions(+), 182 deletions(-)
Author: Henrik Bengtsson
Title: Support package for aroma.affymetrix et al.
Description: This package is a private support package for
aroma.affymetrix et al. The methods and classes of this
package are independent of platform. Its API is in alpha and
beta stage.
Diff between aroma.core versions 1.1.2 dated 2009-06-16 and 1.2.0 dated 2009-09-10
DESCRIPTION | 23 - R/009.setup.R | 6 R/AromaPlatform.R | 6 R/AromaPlatformInterface.R | 151 +++++++++ R/AromaTabularBinaryFile.R | 4 R/AromaTransform.R | 2 R/AromaUnitChromosomeTabularBinaryFile.R | 8 R/AromaUnitFracBCnBinarySet.R | 5 R/AromaUnitSignalBinaryFile.R | 20 - R/AromaUnitTabularBinaryFile.R | 25 + R/AromaUnitTotalCnBinarySet.R | 5 R/AromaUnitTypesFile.R |only R/Interface.R | 23 + R/RawGenomicSignals.R | 31 + R/RawGenomicSignals.segmentByCBS.R | 4 R/RawGenomicSignals.segmentByGLAD.R | 10 R/RawGenomicSignals.segmentByHaarSeg.R | 4 R/RawSequenceReads.EXTRAS.R |only R/RawSequenceReads.R |only R/SegmentedGenomicSignalsInterface.COLS.R |only R/SegmentedGenomicSignalsInterface.R | 156 +++++++--- R/UnitAnnotationDataFile.R |only R/UnitNamesFile.R | 115 ------- R/UnitTypesFile.R |only R/fitGenotypeCone.matrix.R | 2 R/fitMultiDimensionalCone.matrix.R | 2 R/matrixBlockPolish.matrix.R | 2 R/private.patchSmoothScatter.R |only R/serialize,patch.R | 2 incl/999.missingdocs.txt | 25 + incl/RawGenomicSignals.SEG.Rex | 13 inst/NEWS | 52 +++ inst/testScripts/system/RawGenomicSignals/test20090628,binSmoothing.Rex |only inst/testScripts/system/RawGenomicSignals/test20090628,binSmoothingByState.Rex |only man/AromaCellTabularBinaryFile.Rd | 4 man/AromaMicroarrayDataFile.Rd | 2 man/AromaMicroarrayDataSet.Rd | 2 man/AromaMicroarrayDataSetTuple.Rd | 2 man/AromaMicroarrayTabularBinaryFile.Rd | 4 man/AromaPlatform.Rd | 4 man/AromaTabularBinaryFile.Rd | 4 man/AromaTabularBinarySet.Rd | 2 man/AromaTransform.Rd | 2 man/AromaUnitCallFile.Rd | 6 man/AromaUnitCallSet.Rd | 2 man/AromaUnitFracBCnBinaryFile.Rd | 6 man/AromaUnitFracBCnBinarySet.Rd | 2 man/AromaUnitGenotypeCallFile.Rd | 6 man/AromaUnitGenotypeCallSet.Rd | 2 man/AromaUnitSignalBinaryFile.Rd | 7 man/AromaUnitSignalBinarySet.Rd | 2 man/AromaUnitTabularBinaryFile.Rd | 5 man/AromaUnitTotalCnBinaryFile.Rd | 6 man/AromaUnitTotalCnBinarySet.Rd | 2 man/AromaUnitTypesFile.Rd |only man/Explorer.Rd | 2 man/Interface.Rd | 2 man/Non-documented_objects.Rd | 40 ++ man/RawAlleleBFractions.Rd | 4 man/RawCopyNumbers.Rd | 4 man/RawGenomicSignals.Rd | 7 man/RawMirroredAlleleBFractions.Rd | 4 man/RawSequenceReads.Rd |only man/SegmentedAlleleBFractions.Rd | 6 man/SegmentedCopyNumbers.Rd | 6 man/SegmentedGenomicSignalsInterface.Rd | 2 man/UnitAnnotationDataFile.Rd |only man/UnitNamesFile.Rd | 17 - man/UnitTypesFile.Rd |only man/allocate.AromaTabularBinaryFile.Rd | 2 man/aroma.core-package.Rd | 2 man/matrixBlockPolish.matrix.Rd | 2 man/segmentByCBS.RawGenomicSignals.Rd | 17 - man/segmentByGLAD.RawGenomicSignals.Rd | 6 man/segmentByHaarSeg.RawGenomicSignals.Rd | 4 75 files changed, 623 insertions(+), 272 deletions(-)
Author: Holger Froehlich
Title: Computation of functional similarities between GO terms and gene
products; GO enrichement analysis
Description: This package implements several functions useful for
computing similarities between GO terms and gene products based
on their GO annotation. Moreover it allows for computing a GO
enrichment analysis
Diff between GOSim versions 1.1.5.4 dated 2008-12-04 and 1.2 dated 2009-09-10
GOSim-1.1.5.4/GOSim/data/ICsBPflyall.rda |only GOSim-1.1.5.4/GOSim/data/ICsBPmalariaall.rda |only GOSim-1.1.5.4/GOSim/data/ICsBPmouseall.rda |only GOSim-1.1.5.4/GOSim/data/ICsBPratall.rda |only GOSim-1.1.5.4/GOSim/data/ICsBPyeastall.rda |only GOSim-1.1.5.4/GOSim/data/ICsCCflyall.rda |only GOSim-1.1.5.4/GOSim/data/ICsCCmalariaall.rda |only GOSim-1.1.5.4/GOSim/data/ICsCCmouseall.rda |only GOSim-1.1.5.4/GOSim/data/ICsCCratall.rda |only GOSim-1.1.5.4/GOSim/data/ICsCCyeastall.rda |only GOSim-1.1.5.4/GOSim/data/ICsMFflyall.rda |only GOSim-1.1.5.4/GOSim/data/ICsMFmalariaall.rda |only GOSim-1.1.5.4/GOSim/data/ICsMFmouseall.rda |only GOSim-1.1.5.4/GOSim/data/ICsMFratall.rda |only GOSim-1.1.5.4/GOSim/data/ICsMFyeastall.rda |only GOSim-1.2/GOSim/.project |only GOSim-1.2/GOSim/DESCRIPTION | 26 GOSim-1.2/GOSim/NAMESPACE | 5 GOSim-1.2/GOSim/R/geneSimilarity.R | 2 GOSim-1.2/GOSim/R/general.R | 22 GOSim-1.2/GOSim/R/normalize.kernel.R | 24 GOSim-1.2/GOSim/R/pca.R | 12 GOSim-1.2/GOSim/R/termSimilarity.R | 29 GOSim-1.2/GOSim/data/ICsBPhumanall.rda |binary GOSim-1.2/GOSim/data/ICsCChumanall.rda |binary GOSim-1.2/GOSim/data/ICsMFhumanall.rda |binary GOSim-1.2/GOSim/inst/doc/GOSim.Rnw | 12 GOSim-1.2/GOSim/inst/doc/GOSim.pdf | 2634 +++---- GOSim-1.2/GOSim/inst/doc/references.bib | 8349 +++++++++++------------ GOSim-1.2/GOSim/man/IC.Rd | 4 GOSim-1.2/GOSim/man/calc.diffusion.kernel.Rd | 2 GOSim-1.2/GOSim/man/getGeneFeaturesPrototypes.Rd | 7 GOSim-1.2/GOSim/man/getGeneSim.Rd | 4 GOSim-1.2/GOSim/man/getGeneSimPrototypes.Rd | 4 GOSim-1.2/GOSim/man/getTermSim.Rd | 15 GOSim-1.2/GOSim/man/selectPrototypes.Rd | 28 GOSim-1.2/GOSim/man/setEvidenceLevel.Rd | 11 GOSim-1.2/GOSim/man/setOntology.Rd | 2 38 files changed, 5628 insertions(+), 5564 deletions(-)
Author: A.I. McLeod and Changjiang Xu
Title: Best Subset GLM
Description: Best subset glm using AIC, BIC, EBIC, BICq or
Cross-Validation. For the normal case, the 'leaps' is used.
Otherwise, a slower exhaustive search. The 'xtable' package is
needed for vignette 'SimExperimentBICq.Rnw' accompanying this
package.
Diff between bestglm versions 0.10 dated 2009-08-27 and 0.13 dated 2009-09-10
bestglm-0.10/bestglm/inst/BICqSimulation.R |only bestglm-0.10/bestglm/inst/SimBICq.R |only bestglm-0.10/bestglm/inst/SimBICqRmpi.R |only bestglm-0.10/bestglm/inst/doc/SimExperimentBICq.dvi |only bestglm-0.10/bestglm/inst/doc/bestglm-plotCVHTF-repeat.ps |only bestglm-0.10/bestglm/inst/doc/bestglm.dvi |only bestglm-0.10/bestglm/inst/tb1.dat |only bestglm-0.10/bestglm/inst/tb2.dat |only bestglm-0.10/bestglm/inst/tb3.dat |only bestglm-0.10/bestglm/inst/tb4.dat |only bestglm-0.13/bestglm/DESCRIPTION | 8 bestglm-0.13/bestglm/inst/doc/Rplots.pdf | 4 bestglm-0.13/bestglm/inst/doc/SimExperimentBICq.Rnw | 9 bestglm-0.13/bestglm/inst/doc/SimExperimentBICq.pdf | 1033 +- bestglm-0.13/bestglm/inst/doc/bestglm.Rnw | 146 bestglm-0.13/bestglm/inst/doc/bestglm.bib | 11 bestglm-0.13/bestglm/inst/doc/bestglm.pdf | 6344 ++++++-------- bestglm-0.13/bestglm/man/bestglm-package.Rd | 150 bestglm-0.13/bestglm/man/bestglm.Rd | 482 - 19 files changed, 3982 insertions(+), 4205 deletions(-)
Author: Henrik Bengtsson
Title: Analysis of large Affymetrix microarray data sets
Description: This package implements classes for files and sets of
files for various Affymetrix file formats, e.g.
AffymetrixCdfFile, AffymetrixCelFile, and AffymetrixCelSet.
These are designed to be memory efficient but still being fast.
The idea is to keep all data on file and only read data into
memory when needed. Clever caching mechanisms are used to
minimize the overhead of data IO. All of the above is hidden
in the package API and for the developer (and the end user),
the data is queried as if it lives in memory. With this design
it is only the diskspace that limits what number of arrays can
be analyzed.
Diff between aroma.affymetrix versions 1.1.1 dated 2009-06-29 and 1.2.0 dated 2009-09-10
DESCRIPTION | 26 ++-- R/999.package.R | 54 +------- R/AbstractProbeSequenceNormalization.R | 24 +++ R/AdditiveCovariatesNormalization.R | 6 R/AffymetrixCdfFile.R | 21 ++- R/AffymetrixCdfFile.getAlleleProbePairs.R | 1 R/AffymetrixCdfFile.getAlleleProbePairs3.R | 1 R/AffymetrixCdfFile.getSubsetOfCellIndices.R | 2 R/AffymetrixCdfFile.getSubsetOfUnits.R | 2 R/AffymetrixCdfFile.getUnitGroupCellMap.R | 2 R/AffymetrixCelFile.BG.R | 2 R/AffymetrixCelFile.PLOT.R | 24 --- R/AffymetrixCelFile.R | 8 + R/AffymetrixCelSet.BG.R | 11 + R/AffymetrixCelSet.R | 64 +++------- R/AffymetrixCelSet.convertToUnique.R | 3 R/AffymetrixCelSetTuple.R | 8 + R/AffymetrixCnChpFile.R | 8 + R/AffymetrixCnChpSet.R | 45 +------ R/AffymetrixCsvGenomeInformation.R | 7 - R/AffymetrixFile.R | 4 R/AffymetrixFileSet.R | 2 R/AffymetrixPlatform.R | 6 R/AffymetrixProbeTabFile.R | 8 - R/AffymetrixTabularFile.R | 8 - R/AffymetrixTsvFile.R | 8 - R/AllelicCrosstalkCalibration.R | 13 -- R/AromaChipTypeAnnotationFile.R | 7 - R/AromaUnitTabularBinaryFile.AFFX.R | 2 R/ArrayExplorer.R | 6 R/ChipEffectFile.R | 2 R/ChromosomalModel.R | 7 + R/CnagCfhFile.R | 9 - R/CnagCfhSet.R | 53 ++------ R/CopyNumberSegmentationModel.plot.R | 12 + R/DChipCdfBinFile.R | 2 R/DChipDcpFile.R | 2 R/DChipDcpSet.R | 52 +------- R/DChipGenomeInformation.R | 7 - R/DChipSnpInformation.R | 7 - R/FirmaModel.R | 11 - R/FragmentEquivalentClassNormalization.R | 9 - R/FragmentLengthNormalization.R | 6 R/GcContentNormalization2.plotCovariateEffects.R | 4 R/GenomeInformation.R | 18 ++ R/Model.R | 1 R/MultiArrayUnitModel.R | 1 R/ParameterCelFile.R | 2 R/ProbeLevelModel.fit.R | 2 R/QualityAssessmentModel.R | 10 + R/ReseqCrosstalkCalibration.R | 6 R/ScaleNormalization.R | 9 - R/ScaleNormalization3.R | 3 R/SingleArrayUnitModel.R | 1 R/SnpInformation.R | 9 - R/TransformReport.R | 7 + R/UflSnpInformation.R | 8 - R/UgpGenomeInformation.R | 7 - R/UnitTypeScaleNormalization.R | 3 R/doCRMA.R | 4 R/plotBoxplotStats.list.R | 4 R/readCfhHeader.R | 14 +- R/readCfhUnits.R | 4 R/readCfnHeader.R | 10 - R/readCfnUnits.R | 6 incl/999.missingdocs.txt | 15 ++ inst/CITATION | 37 +++++ inst/NEWS | 53 +++++++- inst/testScripts/replication/chipTypes/Hs_PromPR_v02/test20081209,MatNormalization,MAT.R | 32 ++++- inst/testScripts/system/chipTypes/Cytogenetics_Array |only inst/testScripts/system/chipTypes/GenomeWideSNP_6/test20080730,6.0,BPN,alleleSpecific.R | 6 inst/testScripts/system/chipTypes/GenomeWideSNP_6/test20080827,6.0,CRMAv2.R | 2 inst/testScripts/system/chipTypes/GenomeWideSNP_6/test20090901,6.0,CRMAv2,ASCN,TumorBoost.R |only inst/testScripts/system/chipTypes/Mapping10K_Xba142/test20080510,10K,CN,alleleSpecific.R | 2 inst/testScripts/system/chipTypes/Mapping10K_Xba142/test20090813,10K,SN.R |only inst/testScripts/system/chipTypes/Mapping250K_Nsp,Sty/test20090117,250K,TumorNormal,ASCN,pairy.R | 4 inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20080730,100K,BPN,alleleSpecific.R | 6 inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20080819,100K,BPNz,alleleSpecific.R | 6 man/AbstractProbeSequenceNormalization.Rd | 2 man/AdditiveCovariatesNormalization.Rd | 2 man/AffineCnPlm.Rd | 2 man/AffinePlm.Rd | 2 man/AffineSnpPlm.Rd | 2 man/AffymetrixCdfFile.Rd | 30 +++- man/AffymetrixCelFile.Rd | 5 man/AffymetrixCelSet.Rd | 6 man/AffymetrixCelSetReporter.Rd | 2 man/AffymetrixCelSetTuple.Rd | 2 man/AffymetrixCnChpSet.Rd | 4 man/AffymetrixFile.Rd | 8 - man/AffymetrixFileSet.Rd | 6 man/AffymetrixFileSetReporter.Rd | 2 man/AffymetrixProbeTabFile.Rd | 5 man/AlleleSummation.Rd | 2 man/AllelicCrosstalkCalibration.Rd | 2 man/AromaChipTypeAnnotationFile.Rd | 4 man/ArrayExplorer.Rd | 2 man/AvgCnPlm.Rd | 2 man/AvgPlm.Rd | 2 man/AvgSnpPlm.Rd | 2 man/BackgroundCorrection.Rd | 2 man/BaseCountNormalization.Rd | 2 man/BasePositionNormalization.Rd | 2 man/CbsModel.Rd | 2 man/ChipEffectFile.Rd | 6 man/ChipEffectGroupMerge.Rd | 2 man/ChipEffectSet.Rd | 6 man/ChipEffectTransform.Rd | 2 man/ChromosomalModel.Rd | 2 man/ChromosomeExplorer.Rd | 2 man/CnChipEffectFile.Rd | 6 man/CnChipEffectSet.Rd | 6 man/CnProbeAffinityFile.Rd | 6 man/CnagCfhFile.Rd | 4 man/CnagCfhSet.Rd | 2 man/CopyNumberChromosomalModel.Rd | 2 man/CopyNumberSegmentationModel.Rd | 2 man/CrlmmParametersFile.Rd | 6 man/CrlmmParametersSet.Rd | 2 man/DChipCdfBinFile.Rd | 17 +- man/DChipDcpFile.Rd | 6 man/DChipDcpSet.Rd | 5 man/DChipGenomeInformation.Rd | 5 man/DChipQuantileNormalization.Rd | 2 man/DChipSnpInformation.Rd | 5 man/ExonChipEffectFile.Rd | 6 man/ExonChipEffectSet.Rd | 6 man/ExonProbeAffinityFile.Rd | 6 man/ExonRmaPlm.Rd | 2 man/FirmaFile.Rd | 6 man/FirmaModel.Rd | 2 man/FirmaSet.Rd | 6 man/FragmentEquivalentClassNormalization.Rd | 5 man/FragmentLengthNormalization.Rd | 2 man/GcContentNormalization.Rd | 2 man/GcContentNormalization2.Rd | 2 man/GcRmaBackgroundCorrection.Rd | 2 man/GenericReporter.Rd | 2 man/GenomeInformation.Rd | 6 man/GladModel.Rd | 2 man/HaarSegModel.Rd | 2 man/HetLogAddCnPlm.Rd | 2 man/HetLogAddPlm.Rd | 2 man/HetLogAddSnpPlm.Rd | 2 man/LimmaBackgroundCorrection.Rd | 2 man/LinearModelProbeSequenceNormalization.Rd | 2 man/MatNormalization.Rd | 2 man/MatSmoothing.Rd | 2 man/MbeiCnPlm.Rd | 2 man/MbeiPlm.Rd | 2 man/MbeiSnpPlm.Rd | 2 man/Model.Rd | 2 man/MultiArrayUnitModel.Rd | 2 man/Non-documented_objects.Rd | 12 + man/NormExpBackgroundCorrection.Rd | 2 man/OpticalBackgroundCorrection.Rd | 2 man/ParameterCelFile.Rd | 8 - man/ParameterCelSet.Rd | 6 man/ProbeAffinityFile.Rd | 6 man/ProbeLevelModel.Rd | 2 man/ProbeLevelTransform.Rd | 2 man/ProbeLevelTransform3.Rd | 2 man/QualityAssessmentFile.Rd | 6 man/QualityAssessmentModel.Rd | 2 man/QualityAssessmentSet.Rd | 6 man/QuantileNormalization.Rd | 2 man/RawCopyNumberModel.Rd | 2 man/ReseqCrosstalkCalibration.Rd | 2 man/ResidualFile.Rd | 6 man/ResidualSet.Rd | 6 man/RmaBackgroundCorrection.Rd | 2 man/RmaCnPlm.Rd | 2 man/RmaPlm.Rd | 2 man/RmaSnpPlm.Rd | 2 man/ScaleNormalization.Rd | 5 man/ScaleNormalization3.Rd | 5 man/SingleArrayUnitModel.Rd | 2 man/SmoothMultiarrayModel.Rd | 2 man/SmoothRmaModel.Rd | 2 man/SnpChipEffectFile.Rd | 6 man/SnpChipEffectGroupMerge.Rd | 2 man/SnpChipEffectSet.Rd | 6 man/SnpInformation.Rd | 5 man/SnpProbeAffinityFile.Rd | 6 man/SpatialReporter.Rd | 2 man/TransformReport.Rd | 3 man/UgpGenomeInformation.Rd | 5 man/UnitModel.Rd | 2 man/UnitTypeScaleNormalization.Rd | 5 man/WeightsFile.Rd | 6 man/WeightsSet.Rd | 6 man/allocateFromCdf.AromaUnitTabularBinaryFile.Rd | 2 man/aroma.affymetrix-package.Rd | 54 +------- man/convert.AffymetrixCdfFile.Rd | 2 man/findByChipType.AffymetrixCdfFile.Rd | 1 man/fit.FirmaModel.Rd | 7 - man/fit.ProbeLevelModel.Rd | 2 man/fromFile.AffymetrixCdfFile.Rd | 1 man/getAlleleProbePairs.AffymetrixCdfFile.Rd | 1 man/getAlleleProbePairs3.AffymetrixCdfFile.Rd | 1 man/getCdf.Model.Rd | 1 man/getUnitTypes.AffymetrixCdfFile.Rd | 1 man/getWeights.QualityAssessmentModel.Rd | 10 + man/image270.AffymetrixCelFile.Rd | 3 man/plotBoxplotStats.list.Rd | 4 man/readUnits.CnagCfhFile.Rd | 1 man/readUnits.MultiArrayUnitModel.Rd | 1 man/readUnits.SingleArrayUnitModel.Rd | 1 man/smoothScatterMvsA.AffymetrixCelFile.Rd | 2 209 files changed, 715 insertions(+), 673 deletions(-)
More information about aroma.affymetrix at CRAN
Permanent link
Author: Henrik Bengtsson
Title: Various programming utilities
Description: This package provides utility classes and methods useful
when programming in R and developing R packages.
Diff between R.utils versions 1.1.7 dated 2009-06-08 and 1.2.0 dated 2009-09-10
R.utils-1.1.7/R.utils/R/beta |only R.utils-1.1.7/R.utils/R/devel |only R.utils-1.2.0/R.utils/DESCRIPTION | 10 +-- R.utils-1.2.0/R.utils/R/Arguments.R | 13 +++- R.utils-1.2.0/R.utils/R/Settings.R | 7 +- R.utils-1.2.0/R.utils/R/Sys.setenv.patch.R | 2 R.utils-1.2.0/R.utils/R/callHooks.R | 2 R.utils-1.2.0/R.utils/R/copyFile.R | 2 R.utils-1.2.0/R.utils/R/countLines.R | 2 R.utils-1.2.0/R.utils/R/deviceUtils.R | 10 +-- R.utils-1.2.0/R.utils/R/dimNA.R |only R.utils-1.2.0/R.utils/R/fileAccess.R | 2 R.utils-1.2.0/R.utils/R/getParent.R | 53 ++++++++++++------- R.utils-1.2.0/R.utils/R/isPackageLoaded.R | 5 - R.utils-1.2.0/R.utils/R/patchCode.R | 2 R.utils-1.2.0/R.utils/R/readWindowsShortcut.R | 22 +++---- R.utils-1.2.0/R.utils/R/toCamelCase.R | 2 R.utils-1.2.0/R.utils/R/touchFile.R | 2 R.utils-1.2.0/R.utils/R/writeBinFragments.R | 3 - R.utils-1.2.0/R.utils/incl/displayCode.Rex | 4 - R.utils-1.2.0/R.utils/inst/NEWS | 16 +++++ R.utils-1.2.0/R.utils/man/Arguments.Rd | 2 R.utils-1.2.0/R.utils/man/Assert.Rd | 2 R.utils-1.2.0/R.utils/man/FileProgressBar.Rd | 2 R.utils-1.2.0/R.utils/man/Java.Rd | 2 R.utils-1.2.0/R.utils/man/LComments.Rd | 2 R.utils-1.2.0/R.utils/man/MultiVerbose.Rd | 2 R.utils-1.2.0/R.utils/man/NullVerbose.Rd | 2 R.utils-1.2.0/R.utils/man/Options.Rd | 2 R.utils-1.2.0/R.utils/man/ProgressBar.Rd | 2 R.utils-1.2.0/R.utils/man/Settings.Rd | 2 R.utils-1.2.0/R.utils/man/SmartComments.Rd | 2 R.utils-1.2.0/R.utils/man/Sys.setenv.Rd |only R.utils-1.2.0/R.utils/man/System.Rd | 2 R.utils-1.2.0/R.utils/man/TextStatusBar.Rd | 2 R.utils-1.2.0/R.utils/man/VComments.Rd | 2 R.utils-1.2.0/R.utils/man/Verbose.Rd | 2 R.utils-1.2.0/R.utils/man/callHooks.Rd | 1 R.utils-1.2.0/R.utils/man/callHooks.function.Rd | 1 R.utils-1.2.0/R.utils/man/copyFile.Rd | 2 R.utils-1.2.0/R.utils/man/devList.Rd | 2 R.utils-1.2.0/R.utils/man/devOff.Rd | 4 - R.utils-1.2.0/R.utils/man/devSet.Rd | 4 - R.utils-1.2.0/R.utils/man/dimNALT_-.Rd |only R.utils-1.2.0/R.utils/man/displayCode.Rd | 4 - R.utils-1.2.0/R.utils/man/getCharacters.Arguments.Rd | 6 +- R.utils-1.2.0/R.utils/man/isPackageLoaded.Rd | 5 - R.utils-1.2.0/R.utils/man/loadAnywhere.Settings.Rd | 2 R.utils-1.2.0/R.utils/man/patchCode.Rd | 2 R.utils-1.2.0/R.utils/man/promptAndSave.Settings.Rd | 3 - R.utils-1.2.0/R.utils/man/saveAnywhere.Settings.Rd | 2 R.utils-1.2.0/R.utils/man/toCamelCase.Rd | 2 R.utils-1.2.0/R.utils/man/writeBinFragments.Rd | 3 - 53 files changed, 132 insertions(+), 100 deletions(-)
Author: Henrik Bengtsson
Title: R object-oriented programming with or without references
Description: Methods and classes for object-oriented programming in R
with or without references. Large effort has been made on
making definition of methods as simple as possible with a
minimum of maintenance for package developers. The package has
been developed since 2001 and is now considered very stable.
This is a cross-platform package implemented in pure R that
defines standard S3 classes without any tricks.
Diff between R.oo versions 1.4.8 dated 2009-06-08 and 1.5.0 dated 2009-09-10
DESCRIPTION | 10 +- R/050.Object.R | 95 +++++++++++++++++++++++++- R/999.NonDocumentedObjects.R | 1 R/BasicObject.R | 8 -- R/Class.misc.R | 2 R/Exception.R | 12 +-- R/Package.R | 8 +- R/Rdoc.R | 3 R/classRepresentation.misc.R | 11 --- R/getName.environment.R | 2 R/throw.default.R | 2 inst/NEWS | 8 ++ man/Class.Rd | 2 man/Exception.Rd | 4 - man/InternalErrorException.Rd | 2 man/Non-documented_objects.Rd | 1 man/Object.Rd | 1 man/Package.Rd | 2 man/R.oo-package.Rd | 2 man/RccViolationException.Rd | 2 man/Rdoc.Rd | 2 man/RdocException.Rd | 2 man/declaration.Rdoc.Rd | 1 man/equals.BasicObject.Rd | 2 man/getContents.Package.Rd | 2 man/getFields.BasicObject.Rd | 2 man/getInternalAddress.Object.Rd | 2 man/getKnownSubclasses.classRepresentation.Rd | 4 - man/getLastException.Exception.Rd | 2 man/getName.environment.Rd | 2 man/getPosition.Package.Rd | 2 man/getRdDeclaration.Class.Rd | 1 man/getRdHierarchy.Class.Rd | 1 man/getStackTrace.Exception.Rd | 4 - man/getSuperclasses.classRepresentation.Rd | 4 - man/hasField.BasicObject.Rd | 2 man/hierarchy.Rdoc.Rd | 1 man/isLoaded.Package.Rd | 2 man/methodsInheritedFrom.Rdoc.Rd | 1 man/objectSize.BasicObject.Rd | 2 man/objectSize.Object.Rd | 2 man/printStackTrace.Exception.Rd | 2 man/registerFinalizer.Object.Rd |only man/throw.Exception.Rd | 2 man/throw.Rd | 2 man/update.Package.Rd | 2 46 files changed, 148 insertions(+), 81 deletions(-)