Author: Ingo Feinerer
Title: Text Mining Package
Description: A framework for text mining applications within R.
Diff between tm versions 0.3-4.1 dated 2009-05-04 and 0.4 dated 2009-07-01
tm-0.3-4.1/tm/R/plaintextdoc.R |only tm-0.3-4.1/tm/R/resolve.R |only tm-0.3-4.1/tm/R/sparse.R |only tm-0.3-4.1/tm/R/textdoccol.R |only tm-0.3-4.1/tm/man/TermDocMatrix.Rd |only tm-0.3-4.1/tm/man/TextDocCol-class.Rd |only tm-0.3-4.1/tm/man/TextDocCol.Rd |only tm-0.3-4.1/tm/man/appendMeta.Rd |only tm-0.3-4.1/tm/man/loadDoc.Rd |only tm-0.3-4.1/tm/man/removeMeta.Rd |only tm-0.3-4.1/tm/man/tmUpdate.Rd |only tm-0.4/tm/DESCRIPTION | 12 - tm-0.4/tm/NAMESPACE | 49 ++---- tm-0.4/tm/R/aobjects.R | 106 +++++-------- tm-0.4/tm/R/chunks.R | 2 tm-0.4/tm/R/corpus.R |only tm-0.4/tm/R/distmeasure.R | 1 tm-0.4/tm/R/doc.R |only tm-0.4/tm/R/filter.R | 26 --- tm-0.4/tm/R/matrix.R | 44 ++++- tm-0.4/tm/R/meta.R | 54 ++++-- tm-0.4/tm/R/reader.R | 205 ++++++++++++++------------ tm-0.4/tm/R/source.R | 69 +++----- tm-0.4/tm/R/stopwords.R | 18 +- tm-0.4/tm/R/textrepo.R | 15 - tm-0.4/tm/R/transform.R | 107 ++++++------- tm-0.4/tm/R/weight.R | 29 --- tm-0.4/tm/data/acq.rda |binary tm-0.4/tm/data/crude.rda |binary tm-0.4/tm/inst/CITATION | 6 tm-0.4/tm/inst/NEWS | 24 +++ tm-0.4/tm/inst/doc/extensions.Rnw | 2 tm-0.4/tm/inst/doc/extensions.pdf |binary tm-0.4/tm/inst/doc/tm.Rnw | 162 ++++++++++---------- tm-0.4/tm/inst/doc/tm.pdf |binary tm-0.4/tm/man/Corpus-class.Rd |only tm-0.4/tm/man/IN-methods.Rd | 3 tm-0.4/tm/man/NewsgroupDocument-class.Rd | 28 ++- tm-0.4/tm/man/PCorpus-class.Rd |only tm-0.4/tm/man/PCorpus.Rd |only tm-0.4/tm/man/PlainTextDocument-class.Rd | 22 ++ tm-0.4/tm/man/StructuredTextDocument-class.Rd | 22 ++ tm-0.4/tm/man/TextRepository-class.Rd | 4 tm-0.4/tm/man/VCorpus-class.Rd |only tm-0.4/tm/man/VCorpus.Rd |only tm-0.4/tm/man/XMLTextDocument-class.Rd | 22 ++ tm-0.4/tm/man/acq.Rd | 5 tm-0.4/tm/man/appendElem.Rd | 11 - tm-0.4/tm/man/asPlain.Rd | 2 tm-0.4/tm/man/convertReut21578XMLPlain.Rd | 7 tm-0.4/tm/man/crude.Rd | 5 tm-0.4/tm/man/inspect.Rd | 6 tm-0.4/tm/man/materialize.Rd | 1 tm-0.4/tm/man/matrix.Rd |only tm-0.4/tm/man/meta.Rd | 1 tm-0.4/tm/man/prescindMeta.Rd | 33 ++-- tm-0.4/tm/man/readDOC.Rd | 4 tm-0.4/tm/man/readGmane.Rd | 4 tm-0.4/tm/man/readHTML.Rd | 5 tm-0.4/tm/man/readNewsgroup.Rd | 5 tm-0.4/tm/man/readPDF.Rd | 8 - tm-0.4/tm/man/readPlain.Rd | 9 - tm-0.4/tm/man/readRCV1.Rd | 4 tm-0.4/tm/man/readReut21578XML.Rd | 9 - tm-0.4/tm/man/readTabular.Rd | 6 tm-0.4/tm/man/readXML.Rd | 10 - tm-0.4/tm/man/removeSignature.Rd | 2 tm-0.4/tm/man/sFilter.Rd | 5 tm-0.4/tm/man/stopwords.Rd | 6 tm-0.4/tm/man/subset-methods.Rd | 26 +-- tm-0.4/tm/man/tmMap-methods.Rd | 11 - tm-0.4/tm/man/weightBin.Rd | 5 tm-0.4/tm/man/weightTf.Rd | 4 tm-0.4/tm/man/weightTfIdf.Rd | 5 74 files changed, 632 insertions(+), 599 deletions(-)
Author: D.J.J. Walvoort, D.J. Brus, and J.J. de Gruijter
Title: Spatial Coverage Sampling
Description: Spatial coverage sampling and random sampling from compact
geographical strata created by k-means.
Diff between spcosa versions 0.1-3 dated 2009-05-17 and 0.1-4 dated 2009-07-01
spcosa-0.1-3/spcosa/tests/runTestSuite.Rout |only spcosa-0.1-4/spcosa/DESCRIPTION | 12 spcosa-0.1-4/spcosa/NEWS | 38 spcosa-0.1-4/spcosa/R/method_getCellSize-CompactStratification.R | 2 spcosa-0.1-4/spcosa/R/method_getNumberOfCells-CompactStratification.R | 2 spcosa-0.1-4/spcosa/R/method_setAs_CompactStratification-SpatialPixels.R | 2 spcosa-0.1-4/spcosa/R/method_setAs_CompactStratification-SpatialPixelsDataFrame.R | 8 spcosa-0.1-4/spcosa/R/method_spsample_CompactStratification-numeric-missing.R | 1 spcosa-0.1-4/spcosa/inst/doc/spcosa.pdf | 2077 ++++------ spcosa-0.1-4/spcosa/man/stratify-methods.Rd | 6 spcosa-0.1-4/spcosa/tests/unitTesting.html | 18 11 files changed, 1019 insertions(+), 1147 deletions(-)
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 dated 2009-06-26 and 0.1-1 dated 2009-07-01
DESCRIPTION | 10 +++++----- NAMESPACE | 24 ++++++++++++++++++++++++ R/matrix.R | 12 ++++++++++++ R/stm.R |only man/crossprod.Rd |only man/sums.Rd |only src |only tests |only 8 files changed, 41 insertions(+), 5 deletions(-)
Author: Delphine Charif and Jean R. Lobry and Anamaria Necsulea and
Leonor Palmeira and Simon Penel
Title: Biological Sequences Retrieval and Analysis
Description: Exploratory data analysis and data visualization for
biological sequence (DNA and protein) data. Include also
utilities for sequence data management under the ACNUC system.
Diff between seqinr versions 2.0-3 dated 2009-04-28 and 2.0-4 dated 2009-07-01
DESCRIPTION | 10 R/readBins.R | 9 R/readPanels.R | 7 inst/abif/Prototype_PowerPlex_EP01_Bins.txt |only inst/abif/Prototype_PowerPlex_EP01_Pa.txt |only inst/doc/seqinr_2_0-3.pdf | 8400 ++++++++++++++-------------- inst/doc/src/appendix/releasenotes.rnw | 28 man/readBins.Rd | 8 man/readPanels.Rd | 7 9 files changed, 4268 insertions(+), 4201 deletions(-)
Author: Julien Barnier
Diff between rgrs versions 0.2-10 dated 2009-06-09 and 0.2-11 dated 2009-07-01
Title: Functions to make R usage in social sciences easier (in french)
Description: This package provides functions for beginners and social
sciences students or researchers. Currently it includes
functions for cross-tabulation, weighting, results export, and
maps plotting. The documentation and help pages are written in
french.
DESCRIPTION | 10 +++++-----
R/copie.default.R | 10 ++++++----
data/hdv2003.rda |binary
3 files changed, 11 insertions(+), 9 deletions(-)
Author: Kurt Hornik and David Meyer
Title: Data Structures and Algorithms for Relations
Description: Data structures and algorithms for k-ary relations with
arbitrary domains, featuring relational algebra, predicate
functions, and fitters for consensus relations.
Diff between relations versions 0.5-1 dated 2009-02-20 and 0.5-2 dated 2009-07-01
relations-0.5-1/relations/R/sparse.R |only relations-0.5-2/relations/DESCRIPTION | 20 + relations-0.5-2/relations/NAMESPACE | 23 -- relations-0.5-2/relations/NEWS | 4 relations-0.5-2/relations/R/fitters.R | 6 relations-0.5-2/relations/R/mip.R | 44 ++-- relations-0.5-2/relations/R/relation.R | 5 relations-0.5-2/relations/inst/NEWS | 4 relations-0.5-2/relations/inst/doc/relations.pdf |binary relations-0.5-2/relations/inst/po/en@quot/LC_MESSAGES/R-relations.mo |binary relations-0.5-2/relations/po/R-en@quot.po | 105 ++++++---- relations-0.5-2/relations/po/R-relations.pot | 82 +++++-- 12 files changed, 178 insertions(+), 115 deletions(-)
Author: Karl W Broman
Diff between qtlbook versions 0.17-1 dated 2009-04-28 and 0.17-2 dated 2009-07-01
Title: Datasets for the R/qtl book
Description: Datasets for the book, A Guide to QTL Mapping with R/qtl
DESCRIPTION | 10 +++++-----
inst/CITATION |only
inst/STATUS.txt | 7 +++++++
man/ch3a.Rd | 5 +++++
man/ch3b.Rd | 5 +++++
man/ch3c.Rd | 5 +++++
6 files changed, 27 insertions(+), 5 deletions(-)
Author: Karl W Broman
Diff between qtl versions 1.11-12 dated 2009-03-29 and 1.12-26 dated 2009-07-01
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.
qtl-1.11-12/qtl/src/hmm_cc.c |only
qtl-1.11-12/qtl/src/hmm_cc.h |only
qtl-1.11-12/qtl/src/simulate_cc.c |only
qtl-1.11-12/qtl/src/simulate_cc.h |only
qtl-1.12-26/qtl/DESCRIPTION | 12
qtl-1.12-26/qtl/INDEX | 6
qtl-1.12-26/qtl/R/add.cim.covar.R | 13
qtl-1.12-26/qtl/R/add_threshold.R | 57 +++-
qtl-1.12-26/qtl/R/addqtl.R | 21 +
qtl-1.12-26/qtl/R/argmax.geno.R | 35 +-
qtl-1.12-26/qtl/R/arithscan.R | 31 +-
qtl-1.12-26/qtl/R/calc.genoprob.R | 59 +++-
qtl-1.12-26/qtl/R/calc.pairprob.R | 54 ++--
qtl-1.12-26/qtl/R/cim.R | 19 -
qtl-1.12-26/qtl/R/compareorder.R | 25 -
qtl-1.12-26/qtl/R/countXO.R | 49 ++-
qtl-1.12-26/qtl/R/discan.R | 13
qtl-1.12-26/qtl/R/effectplot.R | 13
qtl-1.12-26/qtl/R/effectscan.R | 13
qtl-1.12-26/qtl/R/errorlod.R | 21 -
qtl-1.12-26/qtl/R/est.map.R | 27 +-
qtl-1.12-26/qtl/R/est.rf.R | 31 +-
qtl-1.12-26/qtl/R/fitqtl.R | 16 -
qtl-1.12-26/qtl/R/fitstahl.R | 13
qtl-1.12-26/qtl/R/makeqtl.R | 13
qtl-1.12-26/qtl/R/map_construction.R | 13
qtl-1.12-26/qtl/R/plot.R | 27 +-
qtl-1.12-26/qtl/R/plot.scanone.R | 19 -
qtl-1.12-26/qtl/R/plot.scantwo.R | 22 -
qtl-1.12-26/qtl/R/plotModel.R | 13
qtl-1.12-26/qtl/R/plotperm.R | 13
qtl-1.12-26/qtl/R/qtlcart_io.R | 13
qtl-1.12-26/qtl/R/read.cross.R | 39 +-
qtl-1.12-26/qtl/R/read.cross.csv.R | 35 --
qtl-1.12-26/qtl/R/read.cross.csvs.R | 24 -
qtl-1.12-26/qtl/R/read.cross.gary.R | 13
qtl-1.12-26/qtl/R/read.cross.karl.R | 13
qtl-1.12-26/qtl/R/read.cross.mm.R | 13
qtl-1.12-26/qtl/R/read.cross.qtx.R | 13
qtl-1.12-26/qtl/R/readMWril.R |only
qtl-1.12-26/qtl/R/refineqtl.R | 13
qtl-1.12-26/qtl/R/replacemap.R | 20 -
qtl-1.12-26/qtl/R/ril48_reorg.R |only
qtl-1.12-26/qtl/R/ripple.R | 33 +-
qtl-1.12-26/qtl/R/scanone.R | 47 ++-
qtl-1.12-26/qtl/R/scanoneboot.R | 13
qtl-1.12-26/qtl/R/scanqtl.R | 13
qtl-1.12-26/qtl/R/scantwo.R | 74 +++--
qtl-1.12-26/qtl/R/sim.geno.R | 38 ++
qtl-1.12-26/qtl/R/sim_ril.R | 244 +++++++++++-------
qtl-1.12-26/qtl/R/simulate.R | 54 +++-
qtl-1.12-26/qtl/R/stepwiseqtl.R | 17 -
qtl-1.12-26/qtl/R/summary.cross.R | 60 ++--
qtl-1.12-26/qtl/R/summary.scanone.R | 47 ++-
qtl-1.12-26/qtl/R/summary.scantwo.R | 67 +++--
qtl-1.12-26/qtl/R/summary.scantwo.old.R | 13
qtl-1.12-26/qtl/R/tryallpositions.R | 27 +-
qtl-1.12-26/qtl/R/util.R | 301 +++++++++++++++++++++-
qtl-1.12-26/qtl/R/vbscan.R | 13
qtl-1.12-26/qtl/R/write.cross.R | 13
qtl-1.12-26/qtl/R/xchr.R | 13
qtl-1.12-26/qtl/R/zzz.R | 13
qtl-1.12-26/qtl/inst/BUGS.txt | 16 +
qtl-1.12-26/qtl/inst/CITATION |only
qtl-1.12-26/qtl/inst/LICENSE.txt | 10
qtl-1.12-26/qtl/inst/README.txt | 12
qtl-1.12-26/qtl/inst/STATUS.txt | 152 ++++++++++-
qtl-1.12-26/qtl/inst/TODO.txt | 32 +-
qtl-1.12-26/qtl/inst/docs/rqtltour.R | 2
qtl-1.12-26/qtl/inst/docs/rqtltour.pdf | 344 ++++++++++++--------------
qtl-1.12-26/qtl/inst/docs/rqtltour.tex | 6
qtl-1.12-26/qtl/man/add.threshold.Rd | 4
qtl-1.12-26/qtl/man/checkAlleles.Rd | 2
qtl-1.12-26/qtl/man/chrnames.Rd |only
qtl-1.12-26/qtl/man/clean.cross.Rd | 3
qtl-1.12-26/qtl/man/clean.scantwo.Rd | 13
qtl-1.12-26/qtl/man/compareorder.Rd | 2
qtl-1.12-26/qtl/man/findDupMarkers.Rd |only
qtl-1.12-26/qtl/man/geno.crosstab.Rd | 5
qtl-1.12-26/qtl/man/listeria.Rd | 2
qtl-1.12-26/qtl/man/max.scanone.Rd | 2
qtl-1.12-26/qtl/man/plot.rf.Rd | 5
qtl-1.12-26/qtl/man/plot.scanone.Rd | 2
qtl-1.12-26/qtl/man/qtl-internal.Rd | 30 +-
qtl-1.12-26/qtl/man/readMWril.Rd |only
qtl-1.12-26/qtl/man/ripple.Rd | 2
qtl-1.12-26/qtl/man/scanone.Rd | 7
qtl-1.12-26/qtl/man/scantwo.Rd | 14 -
qtl-1.12-26/qtl/man/sim.cross.Rd | 88 ++++++
qtl-1.12-26/qtl/man/simFounderSnps.Rd |only
qtl-1.12-26/qtl/man/subset.cross.Rd | 9
qtl-1.12-26/qtl/man/subset.map.Rd |only
qtl-1.12-26/qtl/man/summary.scanone.Rd | 6
qtl-1.12-26/qtl/man/summary.scantwo.Rd | 4
qtl-1.12-26/qtl/man/switch.order.Rd | 2
qtl-1.12-26/qtl/man/tryallpositions.Rd | 8
qtl-1.12-26/qtl/man/xaxisloc.scanone.Rd |only
qtl-1.12-26/qtl/src/countXO.c | 32 +-
qtl-1.12-26/qtl/src/countXO.h | 31 +-
qtl-1.12-26/qtl/src/discan.c | 13
qtl-1.12-26/qtl/src/discan.h | 13
qtl-1.12-26/qtl/src/discan_covar.c | 13
qtl-1.12-26/qtl/src/discan_covar.h | 13
qtl-1.12-26/qtl/src/effectscan.c | 13
qtl-1.12-26/qtl/src/effectscan.h | 13
qtl-1.12-26/qtl/src/findDupMarkers_notexact.c |only
qtl-1.12-26/qtl/src/findDupMarkers_notexact.h |only
qtl-1.12-26/qtl/src/fitqtl_hk.c | 13
qtl-1.12-26/qtl/src/fitqtl_hk.h | 13
qtl-1.12-26/qtl/src/fitqtl_imp.c | 13
qtl-1.12-26/qtl/src/fitqtl_imp.h | 13
qtl-1.12-26/qtl/src/forwsel.c | 13
qtl-1.12-26/qtl/src/forwsel.h | 13
qtl-1.12-26/qtl/src/hmm_4way.c | 23 -
qtl-1.12-26/qtl/src/hmm_4way.h | 13
qtl-1.12-26/qtl/src/hmm_bc.c | 19 -
qtl-1.12-26/qtl/src/hmm_bc.h | 13
qtl-1.12-26/qtl/src/hmm_bci.c | 13
qtl-1.12-26/qtl/src/hmm_bci.h | 13
qtl-1.12-26/qtl/src/hmm_f2.c | 23 -
qtl-1.12-26/qtl/src/hmm_f2.h | 15 -
qtl-1.12-26/qtl/src/hmm_f2i.c | 13
qtl-1.12-26/qtl/src/hmm_f2i.h | 13
qtl-1.12-26/qtl/src/hmm_main.c | 35 +-
qtl-1.12-26/qtl/src/hmm_main.h | 21 -
qtl-1.12-26/qtl/src/hmm_ri4self.c |only
qtl-1.12-26/qtl/src/hmm_ri4self.h |only
qtl-1.12-26/qtl/src/hmm_ri4sib.c |only
qtl-1.12-26/qtl/src/hmm_ri4sib.h |only
qtl-1.12-26/qtl/src/hmm_ri8self.c |only
qtl-1.12-26/qtl/src/hmm_ri8self.h |only
qtl-1.12-26/qtl/src/hmm_ri8sib.c |only
qtl-1.12-26/qtl/src/hmm_ri8sib.h |only
qtl-1.12-26/qtl/src/info.c | 13
qtl-1.12-26/qtl/src/info.h | 13
qtl-1.12-26/qtl/src/lapackutil.c | 13
qtl-1.12-26/qtl/src/lapackutil.h | 13
qtl-1.12-26/qtl/src/ril48_reorg.c |only
qtl-1.12-26/qtl/src/ril48_reorg.h |only
qtl-1.12-26/qtl/src/ripple.c | 75 ++++-
qtl-1.12-26/qtl/src/ripple.h | 46 ++-
qtl-1.12-26/qtl/src/scanone_ehk.c | 13
qtl-1.12-26/qtl/src/scanone_ehk.h | 13
qtl-1.12-26/qtl/src/scanone_em.c | 13
qtl-1.12-26/qtl/src/scanone_em.h | 13
qtl-1.12-26/qtl/src/scanone_em_covar.c | 13
qtl-1.12-26/qtl/src/scanone_em_covar.h | 13
qtl-1.12-26/qtl/src/scanone_hk.c | 13
qtl-1.12-26/qtl/src/scanone_hk.h | 13
qtl-1.12-26/qtl/src/scanone_imp.c | 13
qtl-1.12-26/qtl/src/scanone_imp.h | 13
qtl-1.12-26/qtl/src/scanone_mr.c | 13
qtl-1.12-26/qtl/src/scanone_mr.h | 13
qtl-1.12-26/qtl/src/scanone_np.c | 13
qtl-1.12-26/qtl/src/scanone_np.h | 13
qtl-1.12-26/qtl/src/scantwo_binary_em.c | 13
qtl-1.12-26/qtl/src/scantwo_binary_em.h | 13
qtl-1.12-26/qtl/src/scantwo_em.c | 13
qtl-1.12-26/qtl/src/scantwo_em.h | 13
qtl-1.12-26/qtl/src/scantwo_hk.c | 13
qtl-1.12-26/qtl/src/scantwo_hk.h | 13
qtl-1.12-26/qtl/src/scantwo_imp.c | 13
qtl-1.12-26/qtl/src/scantwo_imp.h | 13
qtl-1.12-26/qtl/src/scantwo_mr.c | 13
qtl-1.12-26/qtl/src/scantwo_mr.h | 13
qtl-1.12-26/qtl/src/simulate.c | 13
qtl-1.12-26/qtl/src/simulate.h | 13
qtl-1.12-26/qtl/src/simulate_ril.c |only
qtl-1.12-26/qtl/src/simulate_ril.h |only
qtl-1.12-26/qtl/src/stahl_mf.c | 13
qtl-1.12-26/qtl/src/stahl_mf.h | 13
qtl-1.12-26/qtl/src/summary_scantwo.c | 13
qtl-1.12-26/qtl/src/summary_scantwo.h | 13
qtl-1.12-26/qtl/src/util.c | 75 ++++-
qtl-1.12-26/qtl/src/util.h | 45 ++-
qtl-1.12-26/qtl/src/vbscan.c | 13
qtl-1.12-26/qtl/src/vbscan.h | 13
qtl-1.12-26/qtl/tests/test_io.R | 13
qtl-1.12-26/qtl/tests/test_io.Rout.save | 29 +-
179 files changed, 2449 insertions(+), 1463 deletions(-)
Author: William Revelle
Diff between psych versions 1.0-74 dated 2009-06-26 and 1.0-75 dated 2009-07-01
Title: Procedures for Psychological, Psychometric, and Personality
Research
Description: A number of routines for personality, psychometrics and
experimental psychology. Functions are primarily for scale
construction using factor analysis, cluster analysis and
reliability analysis, although others provide basic descriptive
statistics. Functions for simulating particular item and test
structures are included. Several functions serve as a useful
front end for structural equation modeling. For more
information, see the personality-project.org/r webpage.
CHANGES | 6
DESCRIPTION | 8
R/fa.R | 1
R/omega.R | 2
R/principal.R | 2
R/print.psych.fa.R | 6
R/smc.R | 2
data/Harman.rda |only
inst/NEWS | 5
inst/doc/all.bib | 584 +-
inst/doc/overview.Rnw | 45
inst/doc/overview.pdf | 9090 ++++++++++++++++++++--------------------
inst/doc/psych_for_sem.Rnw | 29
inst/doc/psych_for_sem.pdf | 9988 ++++++++++++++++++++++-----------------------
man/00.psych-package.Rd | 12
man/Harman.Rd |only
man/ICLUST.Rd | 1
man/ICLUST.graph.Rd | 1
man/ICLUST.sort.Rd | 1
man/SD.Rd | 1
man/VSS.parallel.Rd | 1
man/VSS.plot.Rd | 1
man/VSS.scree.Rd | 6
man/bifactor.Rd | 1
man/circ.tests.Rd | 2
man/cluster.cor.Rd | 2
man/cluster.fit.Rd | 1
man/cluster.loadings.Rd | 1
man/count.pairwise.Rd | 1
man/describe.Rd | 1
man/describe.by.Rd | 1
man/eigen.loadings.Rd | 1
man/ellipses.Rd | 1
man/error.bars.Rd | 1
man/error.crosses.Rd | 1
man/fa.Rd | 2
man/fa.graph.Rd | 1
man/fa.parallel.Rd | 1
man/factor.congruence.Rd | 1
man/factor.fit.Rd | 1
man/factor.model.Rd | 1
man/factor.residuals.Rd | 1
man/factor.rotate.Rd | 1
man/factor2cluster.Rd | 1
man/geometric.mean.Rd | 1
man/harmonic.mean.Rd | 1
man/irt.item.diff.rasch.Rd | 1
man/irt.person.rasch.Rd | 1
man/mat.regress.Rd | 1
man/matrix.addition.Rd | 1
man/multi.hist.Rd | 1
man/omega.Rd | 3
man/omega.graph.Rd | 1
man/p.rep.Rd | 1
man/pairs.panels.Rd | 1
man/phi.demo.Rd | 1
man/phi2poly.Rd | 1
man/polar.Rd | 1
man/poly.mat.Rd | 5
man/polychor.matrix.Rd | 1
man/principal.Rd | 2
man/r.test.Rd | 1
man/read.clipboard.Rd | 1
man/schmid.Rd | 1
man/score.alpha.Rd | 1
man/score.items.Rd | 1
man/sim.VSS.Rd | 1
man/sim.congeneric.Rd | 1
man/sim.hierarchical.Rd | 1
man/sim.item.Rd | 1
man/simulation.circ.Rd | 1
man/table2matrix.Rd | 1
man/test.psych.Rd | 1
man/thurstone.Rd | 6
74 files changed, 10199 insertions(+), 9659 deletions(-)
Author: Karl W Broman
Diff between negenes versions 0.98-7 dated 2007-10-09 and 0.98-8 dated 2009-07-01
Title: Estimating the number of essential genes in a genome
Description: Estimating the number of essential genes in a genome on
the basis of data from a random transposon mutagenesis
experiment, through the use of a Gibbs sampler.
DESCRIPTION | 14 +++++++++-----
inst/CITATION |only
inst/STATUS.txt | 5 +++++
3 files changed, 14 insertions(+), 5 deletions(-)
Author: Chris Fraley and Adrian Raftery
Title: Model-Based Clustering / Normal Mixture Modeling
Description: Model-based clustering and normal mixture modeling
including Bayesian regularization
Diff between mclust versions 3.2.1 dated 2009-06-19 and 3.3.1 dated 2009-07-01
mclust-3.2.1/mclust/README |only mclust-3.3.1/mclust/CHANGELOG | 23 ++ mclust-3.3.1/mclust/DESCRIPTION | 6 mclust-3.3.1/mclust/R/mclust.R | 262 +++++++++++++++++++++--------- mclust-3.3.1/mclust/core |only mclust-3.3.1/mclust/man/Mclust.Rd | 14 + mclust-3.3.1/mclust/man/decomp2sigma.Rd | 6 mclust-3.3.1/mclust/man/defaultPrior.Rd | 12 - mclust-3.3.1/mclust/man/em.Rd | 12 - mclust-3.3.1/mclust/man/emE.Rd | 12 - mclust-3.3.1/mclust/man/mclustBIC.Rd | 17 + mclust-3.3.1/mclust/man/mclustVariance.Rd | 7 mclust-3.3.1/mclust/man/me.Rd | 17 + mclust-3.3.1/mclust/man/meE.Rd | 17 + mclust-3.3.1/mclust/man/priorControl.Rd | 12 - mclust-3.3.1/mclust/man/sigma2decomp.Rd | 8 mclust-3.3.1/mclust/man/unmap.Rd | 9 - 17 files changed, 307 insertions(+), 127 deletions(-)
Author: Toni Giorgino
Diff between dtw versions 1.12-5 dated 2009-01-07 and 1.13-1 dated 2009-07-01
Title: Dynamic Time Warping algorithms
Description: Comprehensive implementation of Dynamic Time Warping
algorithms in R. DTW finds the optimal (least cumulative
distance) mapping between two time series. All common DTW
variants are covered, including local and global constraints,
arbitrary timeseries lenghts, distance definitions, MVM, etc.
Package computes cumulative distance, warping functions, plots,
normalizations, etc.
DESCRIPTION | 25 +++++++++++++----------
NAMESPACE |only
R/dtw.R | 13 +++++++++++-
R/globalCostMatrix.R | 4 +--
R/plot.dtw.R | 7 +++---
R/window.R | 6 +----
R/zzz.R | 16 +++++----------
inst/ChangeLog | 6 +++++
inst/TODO | 46 ++++++++++----------------------------------
inst/dtw.bib | 49 +++++++++++++++++++++++++++++++++++++++++++++++
man/dtw-package.Rd | 8 +++----
man/dtw.Rd | 2 +
man/dtwPlot.Rd | 13 +++++++-----
man/stepPattern.Rd | 6 ++---
tests/dtw_test.R | 21 ++++++++++++++++----
tests/dtw_test.Rout.save | 25 ++++++++++++++++++-----
16 files changed, 159 insertions(+), 88 deletions(-)
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer and Allan Engelhardt
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification
and regression models
Diff between caret versions 4.18 dated 2009-06-18 and 4.19 dated 2009-07-01
DESCRIPTION | 8 R/createModel.R | 185 +++++++++- R/misc.R | 2 R/predict.train.R | 2 R/predictionFunction.R | 1 R/train.default.R | 25 - inst/CHANGES | 11 inst/doc/caretMisc.pdf | 782 ++++++++++++++++++++++---------------------- inst/doc/caretSelection.pdf | 637 +++++++++++++++++------------------ inst/doc/caretTrain.pdf |binary inst/doc/caretVarImp.pdf |binary man/train.Rd | 4 12 files changed, 911 insertions(+), 746 deletions(-)
Author: Tomas William Fitzgerald
Title: Robust spline interpolation for dual color array comparative
genomic hybridisation data
Description: Spline fitting and interpolation
Diff between aCGH.Spline versions 1.0 dated 2009-06-24 and 2.1 dated 2009-07-01
DESCRIPTION | 10 +++++----- R/GenomePlot.R | 1 + R/Jspline.R | 7 ++++--- R/SetJ.R | 1 + R/WriteGFF.R | 2 +- R/fe.write.R | 3 ++- 6 files changed, 14 insertions(+), 10 deletions(-)
Author: Adrian Dusa
Diff between QCA versions 0.5-3 dated 2009-03-28 and 0.5-4 dated 2009-07-01
Title: Qualitative Comparative Analysis
Description: Performs the Quine-McCluskey algorithm for Qualitative
Comparative Analysis, as described in Ragin, Charles C. 1987
"The Comparative Method. Moving beyond qualitative and
quantitative strategies", Berkeley: University of California
Press. In the classical approach it currently handles about 15
conditions and one outcome, but since version 0.4-5 the package
has an enhanced, faster function that obtains the same exact
solutions with a substantially lower memory consumption, and it
handles even more causal conditions. The next versions of this
algorithm will be oriented towards multi-value and fuzzy-set
functions. Also, in the near future the current functions will
deal with missing values in the data
DESCRIPTION | 10 +++++-----
R/eqmcc.R | 18 +++++++++---------
R/qmcc.R | 23 ++++++++++++-----------
R/verifyQCA.R | 2 +-
R/writePrimeimp.R | 6 +++---
inst/CHANGES | 6 +++++-
man/QCA.package.Rd | 4 ++--
7 files changed, 37 insertions(+), 32 deletions(-)
Author: Martin Schlather
Diff between RandomFields versions 1.3.39 dated 2009-06-29 and 1.3.40 dated 2009-07-01
Title: Simulation and Analysis of Random Fields
Description: Simulation of Gaussian and extreme value random fields;
conditional simulation; kriging
DESCRIPTION | 6 +++---
src/auxiliary.cc | 6 +++---
2 files changed, 6 insertions(+), 6 deletions(-)
Author: Kurt Hornik, with contributions from Christian Buchta, Torsten
Hothorn, Alexandros Karatzoglou, David Meyer, and Achim Zeileis
Title: R/Weka interface
Description: An R interface to Weka (Version 3.6.1). Weka is a
collection of machine learning algorithms for data mining tasks
written in Java, containing tools for data pre-processing,
classification, regression, clustering, association rules, and
visualization. Both the R interface and Weka itself are
contained in the RWeka package. For more information on Weka
see http://www.cs.waikato.ac.nz/~ml/weka/.
Diff between RWeka versions 0.3-19 dated 2009-06-09 and 0.3-20 dated 2009-07-01
CHANGELOG | 6 +++++- DESCRIPTION | 10 +++++----- R/classifiers.R | 20 +++++++++++++------- R/onLoad.R | 10 ++-------- R/readers.R | 38 +++++++++++++++++++------------------- inst/java/RWeka.jar |binary inst/java/weka.jar |binary java/Makefile | 20 ++++++++++++++++++++ 8 files changed, 64 insertions(+), 40 deletions(-)
Author: Jose L. Izquierdo
Diff between Metabonomic versions 3.1.3.3 dated 2009-05-12 and 3.2 dated 2009-07-01
Title: GUI for Metabonomic Analysis
Description: Graphical User Interface for the Metabonomic Analysis
(Baseline, Normalization, Peak Detection, PCA, PLS, Nearest
Neigbourgt, Neural Network) developed to make easy this data
analysis.
Metabonomic-3.1.3.3/Metabonomic/R/Met.Baseline.R |only
Metabonomic-3.1.3.3/Metabonomic/R/Met.LDA.multi.R |only
Metabonomic-3.1.3.3/Metabonomic/R/Met.LDA.multi2.R |only
Metabonomic-3.1.3.3/Metabonomic/R/Met.PLS2.multi.R |only
Metabonomic-3.1.3.3/Metabonomic/R/Met.PLS2.multi2.R |only
Metabonomic-3.1.3.3/Metabonomic/R/Met.PLS3D.R |only
Metabonomic-3.1.3.3/Metabonomic/man/Met.Baseline.Rd |only
Metabonomic-3.1.3.3/Metabonomic/man/Met.LDA.multi.Rd |only
Metabonomic-3.1.3.3/Metabonomic/man/Met.LDA.multi2.Rd |only
Metabonomic-3.1.3.3/Metabonomic/man/Met.PLS2.multi.Rd |only
Metabonomic-3.1.3.3/Metabonomic/man/Met.PLS2.multi2.Rd |only
Metabonomic-3.1.3.3/Metabonomic/man/Met.PLS3D.Rd |only
Metabonomic-3.2/Metabonomic/DESCRIPTION | 10
Metabonomic-3.2/Metabonomic/R/Import.data.R | 36
Metabonomic-3.2/Metabonomic/R/Met.KNN.R | 168 -
Metabonomic-3.2/Metabonomic/R/Met.LDA.R | 611 ++--
Metabonomic-3.2/Metabonomic/R/Met.Load.Data.R | 2
Metabonomic-3.2/Metabonomic/R/Met.NN1.R | 165 -
Metabonomic-3.2/Metabonomic/R/Met.NN2.R | 239 -
Metabonomic-3.2/Metabonomic/R/Met.PLS1.R | 109
Metabonomic-3.2/Metabonomic/R/Met.PLS2.R | 2223 ++++-------------
Metabonomic-3.2/Metabonomic/R/Met.Selection.R | 319 --
Metabonomic-3.2/Metabonomic/R/Phase.correction.R | 376 +-
Metabonomic-3.2/Metabonomic/inst |only
24 files changed, 1435 insertions(+), 2823 deletions(-)
Author: Andrew D. Martin
Diff between MCMCpack versions 0.9-6 dated 2009-02-17 and 1.0-1 dated 2009-07-01
Title: Markov chain Monte Carlo (MCMC) Package
Description: This package contains functions to perform Bayesian
inference using posterior simulation for a number of
statistical models. Most simulation is done in compiled C++
written in the Scythe Statistical Library Version 1.0.2. All
models return coda mcmc objects that can then be summarized
using the coda package. MCMCpack also contains some useful
utility functions, including some additional density functions
and pseudo-random number generators for statistical
distributions, a general purpose Metropolis sampling algorithm,
and tools for visualization.
DESCRIPTION | 32 +++++++++++++++++---------------
HISTORY | 1 +
NAMESPACE | 1 +
R/MCMCdynamicIRT1d-b.R |only
R/MCMCdynamicIRT1d.R |only
data/Rehnquist.rda |only
man/MCMCdynamicIRT1d.Rd |only
man/MCMCirtKd.Rd | 2 +-
man/Rehnquist.Rd |only
src/MCMCdynamicIRT1d-b.cc |only
src/MCMCdynamicIRT1d.cc |only
11 files changed, 20 insertions(+), 16 deletions(-)
Author: Klaus Nordhausen, Jean-Francois Cardoso, Hannu Oja, Esa Ollila
Title: JADE and ICA performance criteria
Description: The package ports JF Cardoso's JADE algorithm as well as
his function for joint diagonalization. There are also several
criteria for performance evaluation of ICA algorithms.
Diff between JADE versions 1.0-2 dated 2009-04-22 and 1.0-3 dated 2009-07-01
DESCRIPTION | 8 ++++---- R/JADE.R | 10 ++++++++-- inst/CHANGES | 5 +++++ man/ComonGAP.Rd | 2 +- man/JADE-package.Rd | 4 ++-- man/JADE.Rd | 14 ++++++++++++++ man/rjd.Rd | 3 ++- 7 files changed, 36 insertions(+), 10 deletions(-)
Author: Hadley Wickham
Diff between DescribeDisplay versions 0.2.0 dated 2009-05-15 and 0.2.1 dated 2009-07-01
More information about DescribeDisplay at CRAN
Title: R interface to DescribeDisplay (GGobi plugin)
Description: Produce publication quality graphics from output of
GGobi's describe display plugin
DESCRIPTION | 6 +++---
NAMESPACE |only
R/data.r | 16 +++++++++++-----
R/ggplot-barchart.r | 12 +++++++-----
R/ggplot-parcoords.r | 3 +++
R/ggplot-scatmat.r | 1 +
R/ggplot-timeseries.r | 6 +++++-
R/ggplot.r | 5 ++++-
man/addbrush.Rd | 4 +---
man/ddpanelGrob.Rd | 4 +---
man/ggplot.ddplot.Rd | 3 +--
man/ggplot.parcoords.Rd | 3 +--
man/plot.dd.Rd | 3 +--
man/plot.ddplot.Rd | 4 +---
14 files changed, 40 insertions(+), 30 deletions(-)
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