Title: Modelling with Sparse And Dense Matrices
Description: Modelling with sparse and dense 'Matrix' matrices, using
modular prediction and response module classes.
Author: Douglas Bates
Maintainer: Doug and Martin
Diff between MatrixModels versions 0.2-1 dated 2010-09-21 and 0.3-1 dated 2012-01-12
MatrixModels-0.2-1/MatrixModels/man/getCall.Rd |only MatrixModels-0.3-1/MatrixModels/ChangeLog | 33 +++++++++ MatrixModels-0.3-1/MatrixModels/DESCRIPTION | 12 +-- MatrixModels-0.3-1/MatrixModels/MD5 |only MatrixModels-0.3-1/MatrixModels/NAMESPACE | 12 +-- MatrixModels-0.3-1/MatrixModels/R/AllClass.R | 72 +++++++++++++++++++++ MatrixModels-0.3-1/MatrixModels/R/AllGeneric.R | 7 -- MatrixModels-0.3-1/MatrixModels/R/modelMatrix.R | 41 ----------- MatrixModels-0.3-1/MatrixModels/man/Model-class.Rd | 6 - MatrixModels-0.3-1/MatrixModels/tests/MModels.R |only 10 files changed, 120 insertions(+), 63 deletions(-)
Title: Reading M3 files
Description: This package contains functions to read in and manipulate
air quality model output from Models3-formatted files. This
format is used by the Community Multiscale Air Quaility (CMAQ)
model.
Author: Jenise Swall
Maintainer: Jenise Swall
Diff between M3 versions 0.1 dated 2011-06-20 and 0.2 dated 2012-01-12
DESCRIPTION | 12 +++++----- MD5 |only NAMESPACE |only R/combine.date.and.time.R | 22 +++++++++++-------- R/decipher.M3.date.R | 18 +++++++++------ R/decipher.M3.time.R | 30 ++++++++++++++----------- R/get.M3.var.R | 12 ++++++---- R/get.canmex.bds.R |only R/get.coord.for.dimension.R | 12 ++++++---- R/get.datetime.seq.R | 18 +++++++++------ R/get.grid.info.M3.R | 12 ++++++---- R/get.map.lines.M3.proj.R | 44 ++++++++++++++++++++++++++------------ R/get.matrix.all.grid.cell.ctrs.R | 12 ++++++---- R/get.proj.info.M3.R | 14 +++++++----- R/project.M3.1.to.M3.2.R | 12 ++++++---- R/project.M3.to.lonlat.R | 12 ++++++---- R/project.lonlat.to.M3.R | 10 ++++++-- R/var.subset.R | 14 +++++++----- man/get.M3.var.Rd | 2 - man/get.canmex.bds.Rd |only man/get.map.lines.M3.proj.Rd | 23 +++++++++++++------ 21 files changed, 179 insertions(+), 100 deletions(-)
Title: R interface to tslib (a time series library in c++)
Description: fast operations for time series objects
Author: Whit Armstrong
Maintainer: Whit Armstrong
Diff between fts versions 0.7.6 dated 2009-10-15 and 0.7.7 dated 2012-01-12
.gitignore | 2 DESCRIPTION | 6 - MD5 |only NAMESPACE | 8 +- R/fts.R | 72 +++++++++++++-------- man/as.fts.Rd | 1 man/frequency.convert.Rd | 8 ++ man/indicators.Rd | 6 + man/moving.Rd | 8 ++ man/pad.trim.Rd | 9 +- man/read.write.fts.Rd | 10 -- src/analog.h | 6 - src/interface.cpp | 30 +++++--- src/interface.h | 1 src/r.window.template.h | 2 src/tslib/test/test.cpp | 57 ++++++++++++++-- src/tslib/tslib/date.policies/date.partition.hpp | 39 ++++++----- src/tslib/tslib/range.specifier/rangeSpecifier.hpp | 42 ++---------- src/tslib/tslib/tseries.hpp | 71 ++++++++++++++++++-- test/fts.test.r | 2 20 files changed, 249 insertions(+), 131 deletions(-)
Title: R package for parsing and manipulating edit rules
Description: Facilitates reading and manipulating (multivariate) data
restrictions (edit rules) on numerical and categorical data.
Rules can be defined with common R syntax and parsed to an
internal (matrix-like format). Rules can be manipulated with
variable elimination and value substitution methods, allowing
for feasibility checks and more. Data can be tested against the
rules and erroneous fields can be found based on Fellegi and
Holt's generalized principle and rules can be visualized with
the igraph package.
Author: Edwin de Jonge, Mark van der Loo
Maintainer: Edwin de Jonge
Diff between editrules versions 2.0-1 dated 2011-12-08 and 2.0-3 dated 2012-01-12
editrules-2.0-1/editrules/R/localizeError_mip.R |only editrules-2.0-1/editrules/inst/doc/diamond.pdf |only editrules-2.0-1/editrules/inst/doc/editrules-categorical.aux |only editrules-2.0-1/editrules/inst/doc/editrules-categorical.bbl |only editrules-2.0-1/editrules/inst/doc/editrules-categorical.blg |only editrules-2.0-1/editrules/inst/doc/editrules-categorical.idx |only editrules-2.0-1/editrules/inst/doc/editrules-categorical.ilg |only editrules-2.0-1/editrules/inst/doc/editrules-categorical.ind |only editrules-2.0-1/editrules/inst/doc/editrules-categorical.loa |only editrules-2.0-1/editrules/inst/doc/editrules-categorical.log |only editrules-2.0-1/editrules/inst/doc/editrules-categorical.tex |only editrules-2.0-1/editrules/inst/doc/editrules-categorical.toc |only editrules-2.0-1/editrules/inst/doc/editrules-linear.aux |only editrules-2.0-1/editrules/inst/doc/editrules-linear.bbl |only editrules-2.0-1/editrules/inst/doc/editrules-linear.blg |only editrules-2.0-1/editrules/inst/doc/editrules-linear.idx |only editrules-2.0-1/editrules/inst/doc/editrules-linear.ilg |only editrules-2.0-1/editrules/inst/doc/editrules-linear.ind |only editrules-2.0-1/editrules/inst/doc/editrules-linear.loa |only editrules-2.0-1/editrules/inst/doc/editrules-linear.log |only editrules-2.0-1/editrules/inst/doc/editrules-linear.tex |only editrules-2.0-1/editrules/inst/doc/editrules-linear.toc |only editrules-2.0-1/editrules/inst/doc/twodiamond.pdf |only editrules-2.0-1/editrules/man/localizeError_mip.Rd |only editrules-2.0-3/editrules/DESCRIPTION | 45 editrules-2.0-3/editrules/MD5 | 375 - editrules-2.0-3/editrules/NAMESPACE | 206 editrules-2.0-3/editrules/NEWS | 359 - editrules-2.0-3/editrules/R/adjacency.R | 184 editrules-2.0-3/editrules/R/as.igraph.R | 122 editrules-2.0-3/editrules/R/as.matrix.R | 72 editrules-2.0-3/editrules/R/backtracker.R | 412 - editrules-2.0-3/editrules/R/blocks.R | 132 editrules-2.0-3/editrules/R/c.R |only editrules-2.0-3/editrules/R/cateditmatrix.R |only editrules-2.0-3/editrules/R/checkDatamodel.R |only editrules-2.0-3/editrules/R/checkRows.R | 154 editrules-2.0-3/editrules/R/contains.R | 114 editrules-2.0-3/editrules/R/duplicated.R | 46 editrules-2.0-3/editrules/R/echelon.R | 116 editrules-2.0-3/editrules/R/editarray.R | 521 - editrules-2.0-3/editrules/R/editarrayAttr.R | 100 editrules-2.0-3/editrules/R/editfile.R |only editrules-2.0-3/editrules/R/editmatrix.R | 543 - editrules-2.0-3/editrules/R/editmatrixAttr.R | 346 - editrules-2.0-3/editrules/R/editrules-data.R | 22 editrules-2.0-3/editrules/R/editset.R |only editrules-2.0-3/editrules/R/eliminate.R | 382 - editrules-2.0-3/editrules/R/errorLocalizer.R | 520 - editrules-2.0-3/editrules/R/errorLocation.R | 285 editrules-2.0-3/editrules/R/expandEdits.R |only editrules-2.0-3/editrules/R/fcf.R |only editrules-2.0-3/editrules/R/getVars.R | 67 editrules-2.0-3/editrules/R/is.R | 52 editrules-2.0-3/editrules/R/isFeasible.R | 72 editrules-2.0-3/editrules/R/isObviouslyInfeasible.R | 108 editrules-2.0-3/editrules/R/isObviouslyRedundant.R | 196 editrules-2.0-3/editrules/R/isSubset.R | 84 editrules-2.0-3/editrules/R/localizeErrors.R | 312 - editrules-2.0-3/editrules/R/localizeErrors_mip.R |only editrules-2.0-3/editrules/R/parseCat.R |only editrules-2.0-3/editrules/R/parseEdits.R | 284 editrules-2.0-3/editrules/R/parseMix.R |only editrules-2.0-3/editrules/R/parseNum.R |only editrules-2.0-3/editrules/R/pkg.R | 46 editrules-2.0-3/editrules/R/plot.editmatrix.R | 382 - editrules-2.0-3/editrules/R/plot_errorLocation.R | 288 - editrules-2.0-3/editrules/R/print.R | 124 editrules-2.0-3/editrules/R/reduce.R | 128 editrules-2.0-3/editrules/R/str.R | 54 editrules-2.0-3/editrules/R/subsetting.R | 72 editrules-2.0-3/editrules/R/substValue.R | 223 editrules-2.0-3/editrules/R/summary.R | 278 editrules-2.0-3/editrules/R/violatedEdits.R | 500 - editrules-2.0-3/editrules/inst/doc/.gitignore | 28 editrules-2.0-3/editrules/inst/doc/DeJongeVanderLoo2011-2.pdf |only editrules-2.0-3/editrules/inst/doc/Sweave.sty | 66 editrules-2.0-3/editrules/inst/doc/algorithm.sty | 200 editrules-2.0-3/editrules/inst/doc/algorithmic.sty | 464 - editrules-2.0-3/editrules/inst/doc/algorithmicx.sty | 1572 ++--- editrules-2.0-3/editrules/inst/doc/algpseudocode.sty | 184 editrules-2.0-3/editrules/inst/doc/buildVignette.bash | 32 editrules-2.0-3/editrules/inst/doc/editrules-categorical.Rnw | 2211 +++---- editrules-2.0-3/editrules/inst/doc/editrules-categorical.pdf |binary editrules-2.0-3/editrules/inst/doc/editrules-linear.Rnw | 2854 +++++----- editrules-2.0-3/editrules/inst/doc/editrules-linear.pdf |binary editrules-2.0-3/editrules/inst/doc/editrules.bib | 777 +- editrules-2.0-3/editrules/inst/doc/fig/tree.tex | 154 editrules-2.0-3/editrules/inst/doc/index.html | 4 editrules-2.0-3/editrules/inst/doc/pic.R | 294 - editrules-2.0-3/editrules/inst/doc/sweave.r | 12 editrules-2.0-3/editrules/inst/doc/tex/catedits.tex | 480 - editrules-2.0-3/editrules/inst/doc/tex/errorLocation.tex | 30 editrules-2.0-3/editrules/inst/doc/tex/smalltree.sty | 124 editrules-2.0-3/editrules/inst/doc/threeparttable.sty | 762 +- editrules-2.0-3/editrules/inst/tests/testBlocks.R | 66 editrules-2.0-3/editrules/inst/tests/testCheck.R | 90 editrules-2.0-3/editrules/inst/tests/testCheckDatamodel.R |only editrules-2.0-3/editrules/inst/tests/testEditRow.R | 54 editrules-2.0-3/editrules/inst/tests/testErrorLocalizer.R | 111 editrules-2.0-3/editrules/inst/tests/testFourierMotzkin.R | 84 editrules-2.0-3/editrules/inst/tests/testIsFeasible.R | 78 editrules-2.0-3/editrules/inst/tests/testIsObviouslyInfeasible.R | 38 editrules-2.0-3/editrules/inst/tests/testIsObviouslyRedundant.R | 48 editrules-2.0-3/editrules/inst/tests/testLocalizeErrors.R | 190 editrules-2.0-3/editrules/inst/tests/testParseEdits.R | 114 editrules-2.0-3/editrules/inst/tests/testSubstValue.R | 134 editrules-2.0-3/editrules/inst/tests/testViolatedEdits.R | 252 editrules-2.0-3/editrules/inst/tests/testc.R |only editrules-2.0-3/editrules/inst/tests/testdatamodel.R | 36 editrules-2.0-3/editrules/inst/tests/testechelon.R | 78 editrules-2.0-3/editrules/inst/tests/testeditarray.R | 86 editrules-2.0-3/editrules/inst/tests/testeditmatrix.R | 328 - editrules-2.0-3/editrules/inst/tests/testeditmatrixAttr.R | 96 editrules-2.0-3/editrules/inst/tests/testgetVars.R | 46 editrules-2.0-3/editrules/inst/tests/testlocalizeErrors_mip.R |only editrules-2.0-3/editrules/man/adddummies.Rd |only editrules-2.0-3/editrules/man/adjacency.Rd | 374 - editrules-2.0-3/editrules/man/as.character.cateditmatrix.Rd |only editrules-2.0-3/editrules/man/as.character.editarray.Rd | 60 editrules-2.0-3/editrules/man/as.character.editmatrix.Rd | 32 editrules-2.0-3/editrules/man/as.data.frame.editarray.Rd | 44 editrules-2.0-3/editrules/man/as.data.frame.editmatrix.Rd | 50 editrules-2.0-3/editrules/man/as.data.frame.violatedEdits.Rd | 30 editrules-2.0-3/editrules/man/as.editmatrix.Rd | 78 editrules-2.0-3/editrules/man/as.expression.editarray.Rd | 34 editrules-2.0-3/editrules/man/as.expression.editmatrix.Rd | 34 editrules-2.0-3/editrules/man/as.matrix.editarray.Rd | 42 editrules-2.0-3/editrules/man/as.matrix.editmatrix.Rd | 46 editrules-2.0-3/editrules/man/asLevels.Rd |only editrules-2.0-3/editrules/man/backtracker.Rd | 188 editrules-2.0-3/editrules/man/blocks.Rd | 100 editrules-2.0-3/editrules/man/buildELMatrix.Rd | 42 editrules-2.0-3/editrules/man/buildELMatrix.editmatrix.Rd |only editrules-2.0-3/editrules/man/c.editarray.Rd |only editrules-2.0-3/editrules/man/c.editmatrix.Rd |only editrules-2.0-3/editrules/man/cateditmatrix.Rd |only editrules-2.0-3/editrules/man/checkDatamodel.Rd |only editrules-2.0-3/editrules/man/checkRows.Rd | 158 editrules-2.0-3/editrules/man/contains.Rd | 80 editrules-2.0-3/editrules/man/contains.boolmat.Rd | 36 editrules-2.0-3/editrules/man/datamodel.Rd | 58 editrules-2.0-3/editrules/man/duplicated.editarray.Rd | 34 editrules-2.0-3/editrules/man/duplicated.editmatrix.Rd | 38 editrules-2.0-3/editrules/man/echelon.Rd | 60 editrules-2.0-3/editrules/man/editTypes.Rd | 26 editrules-2.0-3/editrules/man/editarray.Rd | 224 editrules-2.0-3/editrules/man/editfile.Rd |only editrules-2.0-3/editrules/man/editmatrix.Rd | 206 editrules-2.0-3/editrules/man/editrules-package.Rd | 126 editrules-2.0-3/editrules/man/editrules.Rd | 136 editrules-2.0-3/editrules/man/edits.Rd | 22 editrules-2.0-3/editrules/man/editset.Rd |only editrules-2.0-3/editrules/man/eliminate.Rd | 287 - editrules-2.0-3/editrules/man/errorLocalizer.Rd | 396 - editrules-2.0-3/editrules/man/errorLocation.Rd | 72 editrules-2.0-3/editrules/man/expandEdits.Rd |only editrules-2.0-3/editrules/man/fcf.Rd |only editrules-2.0-3/editrules/man/fcf.env.Rd |only editrules-2.0-3/editrules/man/getA.Rd | 110 editrules-2.0-3/editrules/man/getAb.Rd | 110 editrules-2.0-3/editrules/man/getArr.Rd | 34 editrules-2.0-3/editrules/man/getInd.Rd | 44 editrules-2.0-3/editrules/man/getOps.Rd | 110 editrules-2.0-3/editrules/man/getSep.Rd | 36 editrules-2.0-3/editrules/man/getVars.Rd | 76 editrules-2.0-3/editrules/man/getVars.cateditmatrix.Rd |only editrules-2.0-3/editrules/man/getVars.editarray.Rd | 22 editrules-2.0-3/editrules/man/getVars.editmatrix.Rd | 24 editrules-2.0-3/editrules/man/getb.Rd | 110 editrules-2.0-3/editrules/man/geth.Rd | 235 editrules-2.0-3/editrules/man/getlevels.Rd | 34 editrules-2.0-3/editrules/man/getnames.Rd | 34 editrules-2.0-3/editrules/man/ind2char.Rd | 62 editrules-2.0-3/editrules/man/indFromArray.Rd | 32 editrules-2.0-3/editrules/man/is.cateditmatrix.Rd |only editrules-2.0-3/editrules/man/is.editarray.Rd | 38 editrules-2.0-3/editrules/man/is.editmatrix.Rd | 38 editrules-2.0-3/editrules/man/isFeasible.Rd | 48 editrules-2.0-3/editrules/man/isNormalized.Rd | 110 editrules-2.0-3/editrules/man/isObviouslyInfeasible.Rd | 78 editrules-2.0-3/editrules/man/isObviouslyRedundant.Rd | 119 editrules-2.0-3/editrules/man/isRedundant.boolmat.Rd | 22 editrules-2.0-3/editrules/man/isSubset.Rd | 32 editrules-2.0-3/editrules/man/iter.backtracker.Rd | 50 editrules-2.0-3/editrules/man/listViolatedEdits.Rd | 80 editrules-2.0-3/editrules/man/localize.Rd | 66 editrules-2.0-3/editrules/man/localizeErrors.Rd | 321 - editrules-2.0-3/editrules/man/localize_mip_rec.Rd |only editrules-2.0-3/editrules/man/neweditarray.Rd | 32 editrules-2.0-3/editrules/man/neweditmatrix.Rd | 52 editrules-2.0-3/editrules/man/newerrorlocation.Rd | 50 editrules-2.0-3/editrules/man/normalize.Rd | 114 editrules-2.0-3/editrules/man/numcat.Rd |only editrules-2.0-3/editrules/man/parseCat.Rd | 48 editrules-2.0-3/editrules/man/parseCatEdit.Rd |only editrules-2.0-3/editrules/man/parseEdits.Rd | 44 editrules-2.0-3/editrules/man/parseMix.Rd |only editrules-2.0-3/editrules/man/parseNum.Rd | 32 editrules-2.0-3/editrules/man/plot.editmatrix.Rd | 430 - editrules-2.0-3/editrules/man/plot.errorLocation.Rd | 46 editrules-2.0-3/editrules/man/plot.violatedEdits.Rd | 36 editrules-2.0-3/editrules/man/print.Rd | 30 editrules-2.0-3/editrules/man/print.backtracker.Rd | 34 editrules-2.0-3/editrules/man/print.cateditmatrix.Rd |only editrules-2.0-3/editrules/man/print.editarray.Rd | 34 editrules-2.0-3/editrules/man/print.editmatrix.Rd | 34 editrules-2.0-3/editrules/man/print.editset.Rd |only editrules-2.0-3/editrules/man/print.violatedEdits.Rd | 30 editrules-2.0-3/editrules/man/reduce.Rd | 64 editrules-2.0-3/editrules/man/str.editarray.Rd | 30 editrules-2.0-3/editrules/man/str.editmatrix.Rd | 30 editrules-2.0-3/editrules/man/subsetting.Rd | 54 editrules-2.0-3/editrules/man/substValue.Rd | 106 editrules-2.0-3/editrules/man/summary.Rd | 414 - editrules-2.0-3/editrules/man/summary.violatedEdits.Rd | 40 editrules-2.0-3/editrules/man/toDataFrame.Rd | 36 editrules-2.0-3/editrules/man/violatedEdits.Rd | 228 editrules-2.0-3/editrules/t.R |only editrules-2.0-3/editrules/tests/test_all.R | 10 220 files changed, 13925 insertions(+), 13824 deletions(-)
Title: Core methods and classes used by aroma.* packages part of The
Aroma Framework
Description: This package contains core methods and classes used by
higher-level aroma.* packages part of the Aroma Project, e.g.
aroma.affymetrix and aroma.cn. Its API should be considered to
be in alpha and beta versions, and is mostly of interest to
developers.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
Diff between aroma.core versions 2.3.2 dated 2011-11-15 and 2.4.1 dated 2012-01-12
aroma.core-2.3.2/aroma.core/R/serialize,patch.R |only aroma.core-2.4.1/aroma.core/DESCRIPTION | 12 aroma.core-2.4.1/aroma.core/MD5 | 69 ++-- aroma.core-2.4.1/aroma.core/R/009.setup.R | 27 - aroma.core-2.4.1/aroma.core/R/AromaCellCpgFile.R | 21 + aroma.core-2.4.1/aroma.core/R/AromaCellPositionFile.R | 20 + aroma.core-2.4.1/aroma.core/R/AromaCellSequenceFile.R | 5 aroma.core-2.4.1/aroma.core/R/AromaMicroarrayDataSetTuple.R | 9 aroma.core-2.4.1/aroma.core/R/AromaMicroarrayTabularBinaryFile.R | 16 aroma.core-2.4.1/aroma.core/R/AromaUcscGenomeTextFile.R |only aroma.core-2.4.1/aroma.core/R/AromaUflFile.R | 4 aroma.core-2.4.1/aroma.core/R/AromaUgpFile.R | 4 aroma.core-2.4.1/aroma.core/R/AromaUgpFile.plotCoverageMap.R |only aroma.core-2.4.1/aroma.core/R/AromaUnitFracBCnBinarySet.exportFracBDiffSet.R | 6 aroma.core-2.4.1/aroma.core/R/AromaUnitSignalBinarySet.writeDataFrame.R | 20 + aroma.core-2.4.1/aroma.core/R/AromaUnitTabularBinaryFile.R | 20 + aroma.core-2.4.1/aroma.core/R/AromaUnitTotalCnBinarySet.exportTotalCnRatioSet.R | 6 aroma.core-2.4.1/aroma.core/R/ChromosomeExplorer.R | 1 aroma.core-2.4.1/aroma.core/R/CopyNumberRegions.EXT.R | 8 aroma.core-2.4.1/aroma.core/R/RawGenomicSignals.OPS.R | 8 aroma.core-2.4.1/aroma.core/R/RawGenomicSignals.R | 23 + aroma.core-2.4.1/aroma.core/R/UnitAnnotationDataFile.R | 41 ++ aroma.core-2.4.1/aroma.core/R/colBinnedSmoothing.R | 169 ++++++++-- aroma.core-2.4.1/aroma.core/R/library.patch.R | 21 + aroma.core-2.4.1/aroma.core/incl/999.missingdocs.txt | 9 aroma.core-2.4.1/aroma.core/incl/colBinnedSmoothing.Rex | 60 +++ aroma.core-2.4.1/aroma.core/inst/NEWS | 53 +++ aroma.core-2.4.1/aroma.core/man/AromaGenomeTextFile.Rd | 4 aroma.core-2.4.1/aroma.core/man/AromaUnitTabularBinaryFile.Rd | 2 aroma.core-2.4.1/aroma.core/man/AromaUnitTotalCnBinaryFile.Rd | 2 aroma.core-2.4.1/aroma.core/man/AromaUnitTotalCnBinarySet.Rd | 1 aroma.core-2.4.1/aroma.core/man/AromaUnitTypesFile.Rd | 2 aroma.core-2.4.1/aroma.core/man/Non-documented_objects.Rd | 12 aroma.core-2.4.1/aroma.core/man/UnitNamesFile.Rd | 2 aroma.core-2.4.1/aroma.core/man/UnitTypesFile.Rd | 2 aroma.core-2.4.1/aroma.core/man/colBinnedSmoothing.matrix.Rd | 99 +++++ aroma.core-2.4.1/aroma.core/man/writeDataFrame.AromaUnitSignalBinarySet.Rd | 3 37 files changed, 621 insertions(+), 140 deletions(-)
Title: Copy-number analysis of large microarray data sets
Description: Package for analysis of copy-number estimates obtained
from various platforms.
Author: Henrik Bengtsson and Pierre Neuvial
Maintainer: Henrik Bengtsson
Diff between aroma.cn versions 0.9.3 dated 2011-11-15 and 1.0.0 dated 2012-01-12
DESCRIPTION | 17 ++--- MD5 | 44 +++++++------- R/PairedPSCBS.EXTS2.R | 11 ++- R/PairedPSCBS.calibrateC1C2.R | 79 ++++++++++++++++++-------- R/PairedPSCBS.deShearC1C2.R | 40 +++++++++---- R/TotalCnKernelSmoothing.R | 17 +++++ R/TotalCnSmoothing.R | 35 +++++------ incl/bootstrap.PairedPSCBS.Rex | 6 - incl/calibrateC1C2.PairedPSCBS.Rex | 4 - incl/callAllelicBalanceByBAFs.PairedPSCBS.Rex | 7 -- incl/callCopyNeutralRegions.PairedPSCBS.Rex | 7 -- incl/deShearC1C2.PairedPSCBS.Rex | 4 - incl/normalizeBAFsByRegions.PairedPSCBS.Rex | 4 - incl/orthogonalizeC1C2.PairedPSCBS.Rex | 4 - inst/NEWS | 17 +++++ man/TotalCnKernelSmoothing.Rd | 3 man/TotalCnSmoothing.Rd | 3 man/calibrateC1C2.PairedPSCBS.Rd | 9 +- man/callAllelicBalanceByBAFs.PairedPSCBS.Rd | 9 +- man/callCopyNeutralRegions.PairedPSCBS.Rd | 7 -- man/deShearC1C2.PairedPSCBS.Rd | 4 - man/normalizeBAFsByRegions.PairedPSCBS.Rd | 4 - man/testAllelicBalanceByBAFs.Rd | 7 -- 23 files changed, 212 insertions(+), 130 deletions(-)
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 the number of arrays that
can be analyzed. To install, do:
source("http://www.aroma-project.org/hbLite.R");
hbInstall("aroma.affymetrix").
Author: Henrik Bengtsson, James Bullard, Kasper Hansen, Pierre Neuvial,
Elizabeth Purdom, Mark Robinson, Ken Simpson
Maintainer: Henrik Bengtsson
Diff between aroma.affymetrix versions 2.3.0 dated 2011-11-02 and 2.4.0 dated 2012-01-12
aroma.affymetrix-2.3.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/test20070726c,10K,CN,segmentation.R |only aroma.affymetrix-2.4.0/aroma.affymetrix/DESCRIPTION | 33 aroma.affymetrix-2.4.0/aroma.affymetrix/MD5 | 103 +- aroma.affymetrix-2.4.0/aroma.affymetrix/R/AffymetrixCdfFile.R | 24 aroma.affymetrix-2.4.0/aroma.affymetrix/R/AffymetrixCdfFile.getUnitGroupNamesFromUgcMap.R | 11 aroma.affymetrix-2.4.0/aroma.affymetrix/R/AffymetrixCdfFile.groupUnitsByDimension.R | 56 + aroma.affymetrix-2.4.0/aroma.affymetrix/R/AffymetrixCelFile.R | 24 aroma.affymetrix-2.4.0/aroma.affymetrix/R/AffymetrixCelSet.justSNPRMA.R | 10 aroma.affymetrix-2.4.0/aroma.affymetrix/R/AffymetrixCsvFile.R | 12 aroma.affymetrix-2.4.0/aroma.affymetrix/R/AffymetrixCsvGenomeInformation.R | 15 aroma.affymetrix-2.4.0/aroma.affymetrix/R/AffymetrixNetAffxCsvFile.R | 9 aroma.affymetrix-2.4.0/aroma.affymetrix/R/AffymetrixProbeTabFile.R | 3 aroma.affymetrix-2.4.0/aroma.affymetrix/R/AffymetrixTsvFile.R | 14 aroma.affymetrix-2.4.0/aroma.affymetrix/R/AllelicCrosstalkCalibration.R | 8 aroma.affymetrix-2.4.0/aroma.affymetrix/R/AromaCellMatchScoreFile.R | 5 aroma.affymetrix-2.4.0/aroma.affymetrix/R/AromaChipTypeAnnotationFile.R | 40 aroma.affymetrix-2.4.0/aroma.affymetrix/R/AromaUgpFile.AFFX.R | 2 aroma.affymetrix-2.4.0/aroma.affymetrix/R/CrlmmModel.R | 62 - aroma.affymetrix-2.4.0/aroma.affymetrix/R/FirmaModel.R | 95 +- aroma.affymetrix-2.4.0/aroma.affymetrix/R/ProbeLevelModel.fit.R | 439 ++++++---- aroma.affymetrix-2.4.0/aroma.affymetrix/R/QuantileNormalization.R | 2 aroma.affymetrix-2.4.0/aroma.affymetrix/R/TransformReport.R | 6 aroma.affymetrix-2.4.0/aroma.affymetrix/R/doCRMA.R | 4 aroma.affymetrix-2.4.0/aroma.affymetrix/R/doFIRMA.R |only aroma.affymetrix-2.4.0/aroma.affymetrix/R/doGCRMA.R | 7 aroma.affymetrix-2.4.0/aroma.affymetrix/incl/999.missingdocs.txt | 8 aroma.affymetrix-2.4.0/aroma.affymetrix/inst/NEWS | 58 + aroma.affymetrix-2.4.0/aroma.affymetrix/inst/buildScripts/chipTypes/CytoScanHD_Array |only aroma.affymetrix-2.4.0/aroma.affymetrix/inst/buildScripts/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,ACS.R | 8 aroma.affymetrix-2.4.0/aroma.affymetrix/inst/buildScripts/chipTypes/MoGene-1_0-st-v1/.Rhistory |only aroma.affymetrix-2.4.0/aroma.affymetrix/inst/buildScripts/chipTypes/MoGene-1_0-st-v1/MoGene-1_0-st-v1,ACP.R |only aroma.affymetrix-2.4.0/aroma.affymetrix/inst/buildScripts/chipTypes/MoGene-1_0-st-v1/MoGene-1_0-st-v1,UGP.R |only aroma.affymetrix-2.4.0/aroma.affymetrix/inst/buildScripts/chipTypes/Sc03b_MF_v04 |only aroma.affymetrix-2.4.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping50K_Hind240,Xba240/test20081208,oligo,CRLMM.R | 2 aroma.affymetrix-2.4.0/aroma.affymetrix/inst/testScripts/system/chipTypes/CytoScanHD_Array |only aroma.affymetrix-2.4.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/test20111111-doASCRMAv2.R |only aroma.affymetrix-2.4.0/aroma.affymetrix/inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/test20071031,Preprocessing.R | 27 aroma.affymetrix-2.4.0/aroma.affymetrix/inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/test20111110,doFIRMA.R |only aroma.affymetrix-2.4.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/test20070726c,10K,CN,segmentation,GLAD.R |only aroma.affymetrix-2.4.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/test20070820,10K,segmentation.R | 43 aroma.affymetrix-2.4.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/test20100421,10K,CDF,groupUnitsBy.R | 3 aroma.affymetrix-2.4.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Nsp,Sty/test20111111-doASCRMAv2,PSCBS.R |only aroma.affymetrix-2.4.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20100421,100K,CDF,groupUnitsBy.R | 3 aroma.affymetrix-2.4.0/aroma.affymetrix/man/AffymetrixCelSet.Rd | 1 aroma.affymetrix-2.4.0/aroma.affymetrix/man/AffymetrixProbeTabFile.Rd | 2 aroma.affymetrix-2.4.0/aroma.affymetrix/man/ChipEffectSet.Rd | 2 aroma.affymetrix-2.4.0/aroma.affymetrix/man/CnChipEffectSet.Rd | 2 aroma.affymetrix-2.4.0/aroma.affymetrix/man/ExonChipEffectSet.Rd | 2 aroma.affymetrix-2.4.0/aroma.affymetrix/man/FirmaSet.Rd | 2 aroma.affymetrix-2.4.0/aroma.affymetrix/man/Non-documented_objects.Rd | 7 aroma.affymetrix-2.4.0/aroma.affymetrix/man/ParameterCelSet.Rd | 2 aroma.affymetrix-2.4.0/aroma.affymetrix/man/QualityAssessmentSet.Rd | 2 aroma.affymetrix-2.4.0/aroma.affymetrix/man/ResidualSet.Rd | 2 aroma.affymetrix-2.4.0/aroma.affymetrix/man/SnpChipEffectSet.Rd | 2 aroma.affymetrix-2.4.0/aroma.affymetrix/man/WeightsSet.Rd | 2 aroma.affymetrix-2.4.0/aroma.affymetrix/man/doFIRMA.AffymetrixCelSet.Rd |only aroma.affymetrix-2.4.0/aroma.affymetrix/man/groupUnitsByDimension.AffymetrixCdfFile.Rd | 2 57 files changed, 829 insertions(+), 337 deletions(-)
More information about aroma.affymetrix at CRAN
Permanent link
Title: Tools for parsing and generating XML within R and S-Plus.
Description: This package provides many approaches for both reading and
creating XML (and HTML) documents (including DTDs), both local
and accessible via HTTP or FTP. It also offers access to an
XPath "interpreter".
Author: Duncan Temple Lang (duncan@wald.ucdavis.edu)
Maintainer: Duncan Temple Lang
Diff between XML versions 3.7-3 dated 2012-01-11 and 3.7-4 dated 2012-01-12
Changes | 4 ++++ DESCRIPTION | 6 +++--- INSTALL | 2 +- MD5 | 8 ++++---- R/saveXML.R | 2 +- 5 files changed, 13 insertions(+), 9 deletions(-)
Title: Functions to access vegetation databases (Turboveg) and prepare
data for analysis
Description: Handling of vegetation data sets from Turboveg. Taxonomic
harmonization of datasets with the help of the German
taxonomical standard list "GermanSL".
Author: Florian Jansen
Maintainer: Florian Jansen
Diff between vegdata versions 0.5.1 dated 2011-11-07 and 0.5.3 dated 2012-01-12
DESCRIPTION | 14 - MD5 | 27 +- NAMESPACE | 2 R/comb.species.r | 4 R/reShape.veg.r |only R/syntab.r | 127 ++++++----- R/tax.r | 479 ++++++++++++++++++++++----------------------- R/tv.refl.r | 42 +-- R/tv.write.r | 31 +- inst/doc/vegdata.pdf |binary inst/tvdata/Species/README | 4 man/tax.Rd | 11 - man/tv.write.Rd | 4 man/vegdata-internal.Rd | 39 +-- new |only 15 files changed, 399 insertions(+), 385 deletions(-)
Title: Detection of disease-associated SNP interactions in case-parent
trio data
Description: Testing SNPs and SNP interactions with a genotypic TDT.
This package furthermore contains functions for computing
pairwise values of LD measures and for identifying LD blocks,
as well as functions for setting up matched case pseudo-control
genotype data for case-parent trios in order to run trio logic
regreesion, to impute missing genotypes in trios, or to
simulate case-parent trios with disease risk dependent on SNP
interaction.
Author: Holger Schwender, Qing Li, Ingo Ruczinski
Maintainer: Holger Schwender
Diff between trio versions 1.2.9 dated 2011-10-14 and 1.4.12 dated 2012-01-12
trio-1.2.9/trio/R/compPermTDT2way.R |only trio-1.2.9/trio/inst/doc/figure1.eps |only trio-1.2.9/trio/inst/doc/figure1.png |only trio-1.2.9/trio/inst/doc/figure2.eps |only trio-1.2.9/trio/inst/doc/figure2.png |only trio-1.2.9/trio/inst/doc/figure3.eps |only trio-1.2.9/trio/inst/doc/figure3.png |only trio-1.2.9/trio/inst/plugin |only trio-1.2.9/trio/man/compPermTDT2way.Rd |only trio-1.2.9/trio/man/tdt2way.Rd |only trio-1.2.9/trio/man/trio.Rd |only trio-1.4.12/trio/DESCRIPTION | 13 trio-1.4.12/trio/MD5 | 79 ++-- trio-1.4.12/trio/NAMESPACE | 23 - trio-1.4.12/trio/R/allelicTDT.R |only trio-1.4.12/trio/R/colGxE.R | 251 +++++++++++- trio-1.4.12/trio/R/colGxEPerms.R | 10 trio-1.4.12/trio/R/colGxGperm.R |only trio-1.4.12/trio/R/lrControl.R |only trio-1.4.12/trio/R/tdt.R | 259 ++----------- trio-1.4.12/trio/R/trio.R | 3 trio-1.4.12/trio/R/trio.permTest.R | 33 - trio-1.4.12/trio/R/trioFS.R |only trio-1.4.12/trio/R/trioLR.R |only trio-1.4.12/trio/R/zzz.R |only trio-1.4.12/trio/inst/doc/figure1ld.eps |only trio-1.4.12/trio/inst/doc/figure1ld.png |only trio-1.4.12/trio/inst/doc/figure1lr.eps |only trio-1.4.12/trio/inst/doc/figure1lr.png |only trio-1.4.12/trio/inst/doc/figure2ld.eps |only trio-1.4.12/trio/inst/doc/figure2ld.png |only trio-1.4.12/trio/inst/doc/figure2lr.eps |only trio-1.4.12/trio/inst/doc/figure2lr.png |only trio-1.4.12/trio/inst/doc/figure3ld.eps |only trio-1.4.12/trio/inst/doc/figure3ld.png |only trio-1.4.12/trio/inst/doc/figure3lr.eps |only trio-1.4.12/trio/inst/doc/figure3lr.png |only trio-1.4.12/trio/inst/doc/trio.Rnw | 623 +++++++++++++++++++++----------- trio-1.4.12/trio/inst/doc/trio.pdf |binary trio-1.4.12/trio/man/allelicTDT.Rd |only trio-1.4.12/trio/man/colGxE.Rd | 60 ++- trio-1.4.12/trio/man/colGxGPerms.Rd |only trio-1.4.12/trio/man/findLDblocks.Rd | 12 trio-1.4.12/trio/man/getLD.Rd | 1 trio-1.4.12/trio/man/getMatPseudo.Rd |only trio-1.4.12/trio/man/lrControl.Rd |only trio-1.4.12/trio/man/plot.trioLR.Rd |only trio-1.4.12/trio/man/print.colGxE.Rd |only trio-1.4.12/trio/man/print.trioFS.Rd |only trio-1.4.12/trio/man/print.trioLR.Rd |only trio-1.4.12/trio/man/tdt.Rd | 9 trio-1.4.12/trio/man/tdtGxG.Rd |only trio-1.4.12/trio/man/trio.check.Rd | 19 trio-1.4.12/trio/man/trio.data.Rd | 5 trio-1.4.12/trio/man/trio.permTest.Rd | 43 -- trio-1.4.12/trio/man/trio.prepare.Rd |only trio-1.4.12/trio/man/trio.sim.Rd | 9 trio-1.4.12/trio/man/trioFS.Rd |only trio-1.4.12/trio/man/trioLR.Rd |only trio-1.4.12/trio/src |only 60 files changed, 860 insertions(+), 592 deletions(-)
Title: SPArse Matrix
Description: Set of function for sparse matrix algebra. Differences
with SparseM/Matrix are: (1) we only support (essentially) one
sparse matrix format, (2) based on transparent and simple
structure(s), (3) tailored for MCMC calculations within GMRF.
(4) S3 and S4 like-"compatible" ... and it is fast.
Author: Reinhard Furrer
Maintainer: Reinhard Furrer
Diff between spam versions 0.27-0 dated 2011-08-18 and 0.28-0 dated 2012-01-12
DESCRIPTION | 10 - MD5 | 231 +++++++++++++++--------------- NAMESPACE | 4 R/apply.R | 2 R/definitions.R | 17 +- R/diff.R | 2 R/dist.R | 2 R/foreign.R | 2 R/helper.R | 2 R/kronecker.R | 6 R/makeprec.R | 2 R/mle.R | 2 R/permutation.R | 2 R/plotting.R | 2 R/profile.R | 6 R/spam_solve.R | 10 - R/spamlist.R | 2 R/toepliz.R | 2 R/xybind.R | 9 - data/Oral.rda |binary data/UScounties.ndorder.rda |binary data/UScounties.storder.rda |binary data/USprecip.rda |binary data/germany.rda |binary demo/article-jss-example1.R | 2 demo/article-jss-example2.R | 2 demo/article-jss.R | 2 demo/cholesky.R | 2 demo/spam.R | 2 demo/timing.R | 2 inst/NEWS | 29 +++ man/Oral.Rd | 2 man/SPAM.Rd | 2 man/UScounties.Rd | 2 man/USprecip.Rd | 2 man/allequal.Rd | 20 ++ man/apply.Rd | 2 man/bandwidth.Rd | 2 man/bdiag.Rd | 2 man/chol.Rd | 8 - man/circulant.Rd | 2 man/cleanup.Rd |only man/complexity.Rd | 2 man/det.Rd | 2 man/diag.Rd | 2 man/dim.Rd | 4 man/display.Rd | 2 man/foreign.Rd | 2 man/germany.Rd | 2 man/history.spam.Rd | 2 man/image.Rd | 2 man/import.Rd | 2 man/isSymmetric.Rd | 11 - man/kronecker.Rd | 2 man/lu.tri.Rd | 2 man/makeprec.Rd | 2 man/math.Rd | 2 man/math2.Rd | 2 man/methods.Rd | 2 man/mle.Rd | 2 man/nearestdist.Rd | 2 man/operations.Rd | 2 man/options.Rd | 2 man/ordering.Rd | 2 man/permutation.Rd | 2 man/powerboost.Rd | 2 man/print.Rd | 2 man/rmvnorm.Rd | 2 man/solve.Rd | 6 man/spam-class.Rd | 2 man/spam.chol.NgPeyton-class.Rd | 2 man/spam.creation.Rd | 2 man/spam.internal.Rd | 2 man/summary.Rd | 2 man/todo.Rd | 2 man/toeplitz.Rd | 2 man/triplet.Rd | 2 man/version.Rd | 2 man/xybind.Rd | 2 src/cholmodified.f | 90 ----------- src/spamown.f | 9 - tests/demo_article-jss-example1.R | 2 tests/demo_article-jss-example1.Rout.save | 6 tests/demo_article-jss-example2.R | 2 tests/demo_article-jss-example2.Rout.save | 11 - tests/demo_article-jss.R | 2 tests/demo_article-jss.Rout.save | 6 tests/demo_cholesky.R | 2 tests/demo_cholesky.Rout.save | 6 tests/demo_spam.R | 2 tests/demo_spam.Rout.save | 6 tests/demo_timing.R | 2 tests/demo_timing.Rout.save | 6 tests/diff.R | 2 tests/diff.Rout.save | 6 tests/displays.R | 2 tests/displays.Rout.save | 6 tests/dist.R | 2 tests/dist.Rout.save | 6 tests/foreign.R | 2 tests/foreign.Rout.save | 4 tests/helper.R | 2 tests/helper.Rout.save | 6 tests/kronecker.R | 2 tests/kronecker.Rout.save | 6 tests/mle.R | 2 tests/mle.Rout.save | 6 tests/overall.R | 2 tests/overall.Rout.save | 6 tests/permutation.R | 2 tests/permutation.Rout.save | 6 tests/solve.R | 2 tests/solve.Rout.save | 6 tests/spamlist.R | 2 tests/spamlist.Rout.save | 6 tests/xybind.R | 2 tests/xybind.Rout.save | 6 117 files changed, 352 insertions(+), 383 deletions(-)
Title: Various programming utilities
Description: This package provides utility classes and methods useful
when programming in R and developing R packages.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
Diff between R.utils versions 1.9.7 dated 2011-12-22 and 1.9.9 dated 2012-01-12
DESCRIPTION | 11 ++++++----- MD5 | 10 +++++----- R/Verbose.R | 15 +++++++++++++-- R/evalWithTimeout.R | 10 ++++++++++ inst/NEWS | 11 +++++++++++ man/evalWithTimeout.Rd | 7 +++++++ 6 files changed, 52 insertions(+), 12 deletions(-)
Title: Dynamic generation of scientific reports
Description: An RSP document is a text-based document containing an
R-embedded template of the final document, e.g. "Today's date
is <%=Sys.Date()%>". An RSP document is preprocessed, parsed
and translated into an R script, which when sourced generates
the final document. This way it is possible to dynamically
generate reports in plain text, HTML, TeX etc, e.g.
"\includegraphics{<%=toPDF('Normal', { curve(dnorm, from=-5,
to=+5) })%>}". It can also be used to enhance other literate
programming languages such as Sweave, e.g.
"<
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
Diff between R.rsp versions 0.7.0 dated 2011-11-24 and 0.7.1 dated 2012-01-12
DESCRIPTION | 27 ++++++++++++++++++------ MD5 | 18 ++++++++-------- NAMESPACE | 6 +++++ R/rsp.R | 3 ++ inst/NEWS | 5 ++++ inst/doc/Dynamic_LaTeX_reports_with_RSP.pdf |binary inst/doc/Dynamic_LaTeX_reports_with_RSP.tex.rsp | 2 - inst/doc/NonSweaveVignettes.Rnw | 3 -- inst/doc/NonSweaveVignettes.pdf |binary inst/doc/NonSweaveVignettes.tex.rsp | 7 ++---- 10 files changed, 49 insertions(+), 22 deletions(-)
Title: Rook - a web server interface for R
Description: This package contains the Rook specification and
convenience software for building and running Rook
applications. To get started, be sure and read the 'Rook' help
file first.
Author: Jeffrey Horner
Maintainer: Jeffrey Horner
Diff between Rook versions 1.0-2 dated 2011-04-25 and 1.0-3 dated 2012-01-12
DESCRIPTION | 6 +++--- MD5 |only NAMESPACE | 1 + R/File.R | 2 +- R/Response.R | 3 +++ R/Rhttpd.R | 2 +- R/URLMap.R | 2 +- R/onLoad.R |only inst/exampleApps/RJSONIO.R |only inst/exampleApps/helloworldref.R | 2 +- inst/exampleApps/rnorm.R |only inst/servers |only man/Brewery-class.Rd | 4 ++-- man/Rhttpd-class.Rd | 11 +++++++---- man/RhttpdApp-class.Rd | 2 +- man/Rook-package.Rd | 5 +++-- man/Server.Rd |only 17 files changed, 24 insertions(+), 16 deletions(-)
Title: C++ classes to embed R in C++ applications
Description: C++ classes to embed R in C++ applications The RInside
packages makes it easier to have 'R inside' your C++
application by providing a few wrapper classes.
As R itself is embedded into your application, a shared library build
of R is required. This works on Linux, OS X and even on Windows
provided you use the same tools used to build R itself.
Numerous examples are provided in the three subdirectories the
examples/ directory of the installed package: standard, mpi
(for parallel computing) qt (showing how to embed RInside
inside a Qt application), and wt (showing how to build a
'web-application' using the Wt toolkit).
Doxygen-generated documentation of the C++ classes is available at the
RInside website as well.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel and Romain Francois
Diff between RInside versions 0.2.5 dated 2011-12-08 and 0.2.6 dated 2012-01-12
ChangeLog | 30 ++++ DESCRIPTION | 34 ++--- MD5 | 31 +++- cleanup | 5 inst/NEWS | 17 ++ inst/THANKS | 2 inst/examples/mpi/cmake |only inst/examples/qt/cmake |only inst/examples/qt/qtdensity.cpp |only inst/examples/qt/qtdensity.h |only inst/examples/qt/qtdensity.pro |only inst/examples/standard/Makefile.win | 42 +++--- inst/examples/standard/cmake |only inst/examples/standard/rinside_sample11.cpp |only inst/examples/wt/cmake |only inst/examples/wt/wtdensity.cpp |only inst/include/RInsideAutoloads.h | 3 inst/include/RInsideEnvVars.h | 7 - src/MemBuf.cpp | 7 - src/RInside.cpp | 180 ++++++++++++++-------------- src/setenv/setenv.c | 11 - 21 files changed, 210 insertions(+), 159 deletions(-)
Title: R/GNU Linear Programming Kit Interface
Description: R interface to the GNU Linear Programing Kit (GLPK version
4.45). GLPK is open source software for solving large-scale
linear programming (LP), mixed integer linear programming
(MILP) and other related problems.
Author: Kurt Hornik [aut], Stefan Theussl [aut, cre]
Maintainer: Stefan Theussl
Diff between Rglpk versions 0.3-6 dated 2011-12-30 and 0.3-7 dated 2012-01-12
DESCRIPTION | 18 +++++++------- MD5 | 8 +++--- R/filereader.R | 43 ++++++++++++++++++++++------------ man/Rglpk_read_file.Rd | 5 ++-- src/Rglpk_read_file.c | 61 +++++++++++++++++++++++++++++++++++++++++++++---- 5 files changed, 101 insertions(+), 34 deletions(-)
Title: Easy handling of and access to files organized in structured
directories
Description: A file set refers to a set of files located in one or more
directories on the file system. This package provides classes
and methods to locate, setup, subset, navigate and iterate
suchs sets. The API is designed such that these classes can be
subsetted to provide a richer API for special file formats.
Moreover, a specific name format is defined such that filenames
and directories can be considered to have fullnames which
consists of a name followed by comma-separated tags. This adds
additional flexibility to identify file sets and individual
files. NOTE: This package's API should be considered to be in
an beta stage. Its main purpose is currently to support the
aroma.* packages, where it is one of the main core components;
if you decide to build on top of this package, please contact
the author first.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
Diff between R.filesets versions 1.1.3 dated 2011-11-02 and 1.1.4 dated 2012-01-12
DESCRIPTION | 27 +++++++--- MD5 | 26 ++++----- R/GenericDataFile.R | 79 ++++++++++++++++++++++-------- R/GenericDataFileSet.R | 6 +- R/GenericTabularFile.R | 3 - R/TabularTextFile.R | 3 - inst/NEWS | 5 + man/getDefaultFullName.GenericDataFile.Rd | 2 man/getExtension.GenericDataFile.Rd | 2 man/getFileSize.GenericDataFile.Rd | 1 man/getFileType.GenericDataFile.Rd | 3 - man/getFilename.GenericDataFile.Rd | 2 man/getPath.GenericDataFile.Rd | 2 man/getPathname.GenericDataFile.Rd | 2 14 files changed, 112 insertions(+), 51 deletions(-)
Title: Record Linkage in R
Description: Provides functions for linking and deduplicating data
sets. Methods based on a stochastical approach are implemented
as well as classification algorithms from the machine learning
domain.
Author: Andreas Borg
Maintainer: Murat Sariyar
Diff between RecordLinkage versions 0.3-5 dated 2011-09-12 and 0.4-1 dated 2012-01-12
RecordLinkage-0.3-5/RecordLinkage/man/delete.NULLs.Rd |only RecordLinkage-0.4-1/RecordLinkage/DESCRIPTION | 12 RecordLinkage-0.4-1/RecordLinkage/MD5 | 124 +-- RecordLinkage-0.4-1/RecordLinkage/NAMESPACE | 1 RecordLinkage-0.4-1/RecordLinkage/NEWS | 8 RecordLinkage-0.4-1/RecordLinkage/R/RLBigData-classes.r | 183 +++- RecordLinkage-0.4-1/RecordLinkage/R/RLResult-class.r | 81 - RecordLinkage-0.4-1/RecordLinkage/R/classifySupv-methods.r | 63 - RecordLinkage-0.4-1/RecordLinkage/R/compare.r | 2 RecordLinkage-0.4-1/RecordLinkage/R/em-methods.r | 146 --- RecordLinkage-0.4-1/RecordLinkage/R/em.r | 254 ++++-- RecordLinkage-0.4-1/RecordLinkage/R/epilink-methods.r | 174 ---- RecordLinkage-0.4-1/RecordLinkage/R/evt.r | 209 ++++- RecordLinkage-0.4-1/RecordLinkage/R/genSamples.r | 113 ++ RecordLinkage-0.4-1/RecordLinkage/R/getPairs-methods.r | 278 +++++- RecordLinkage-0.4-1/RecordLinkage/R/getPairs.r | 107 +- RecordLinkage-0.4-1/RecordLinkage/R/internals.r | 162 +-- RecordLinkage-0.4-1/RecordLinkage/R/serialization.r | 133 +-- RecordLinkage-0.4-1/RecordLinkage/R/stochastic.r | 249 ++---- RecordLinkage-0.4-1/RecordLinkage/R/summary.r | 192 +++- RecordLinkage-0.4-1/RecordLinkage/R/tools.r | 159 ++- RecordLinkage-0.4-1/RecordLinkage/data/RLdata10000.rda |binary RecordLinkage-0.4-1/RecordLinkage/data/RLdata500.rda |binary RecordLinkage-0.4-1/RecordLinkage/inst/doc/BigData.pdf |binary RecordLinkage-0.4-1/RecordLinkage/inst/doc/BigData.rnw | 63 - RecordLinkage-0.4-1/RecordLinkage/inst/doc/EVT.pdf |binary RecordLinkage-0.4-1/RecordLinkage/inst/doc/Supervised.pdf |binary RecordLinkage-0.4-1/RecordLinkage/inst/doc/WeightBased.pdf |binary RecordLinkage-0.4-1/RecordLinkage/inst/unitTests/runit.RLBigDataDedup.r | 79 - RecordLinkage-0.4-1/RecordLinkage/inst/unitTests/runit.RLBigDataLinkage.r | 99 +- RecordLinkage-0.4-1/RecordLinkage/inst/unitTests/runit.classify.r | 66 - RecordLinkage-0.4-1/RecordLinkage/inst/unitTests/runit.em.r | 319 ++++--- RecordLinkage-0.4-1/RecordLinkage/inst/unitTests/runit.epilink.r | 66 - RecordLinkage-0.4-1/RecordLinkage/inst/unitTests/runit.getErrorMeasures.r | 19 RecordLinkage-0.4-1/RecordLinkage/inst/unitTests/runit.getPairs-methods.r | 13 RecordLinkage-0.4-1/RecordLinkage/inst/unitTests/runit.getPairs.r | 5 RecordLinkage-0.4-1/RecordLinkage/inst/unitTests/runit.getTable.r | 24 RecordLinkage-0.4-1/RecordLinkage/inst/unitTests/runit.serialization.r | 99 -- RecordLinkage-0.4-1/RecordLinkage/inst/unitTests/runit.stochastic.r | 66 - RecordLinkage-0.4-1/RecordLinkage/inst/unitTests/runit.tools.r | 144 +++ RecordLinkage-0.4-1/RecordLinkage/inst/unitTests/runit.various.r | 2 RecordLinkage-0.4-1/RecordLinkage/man/RLResult-class.Rd | 13 RecordLinkage-0.4-1/RecordLinkage/man/RecLinkData-class.rd | 11 RecordLinkage-0.4-1/RecordLinkage/man/clone.Rd | 49 - RecordLinkage-0.4-1/RecordLinkage/man/deleteNULLs.Rd |only RecordLinkage-0.4-1/RecordLinkage/man/editMatch.Rd | 9 RecordLinkage-0.4-1/RecordLinkage/man/emWeights.Rd | 28 RecordLinkage-0.4-1/RecordLinkage/man/epiClassify.Rd | 8 RecordLinkage-0.4-1/RecordLinkage/man/epiWeights.Rd | 20 RecordLinkage-0.4-1/RecordLinkage/man/ff_vector-class.Rd |only RecordLinkage-0.4-1/RecordLinkage/man/ffdf-class.rd |only RecordLinkage-0.4-1/RecordLinkage/man/getExpectedSize.Rd | 12 RecordLinkage-0.4-1/RecordLinkage/man/getMinimalTrain.Rd | 15 RecordLinkage-0.4-1/RecordLinkage/man/getPairs-methods.rd | 15 RecordLinkage-0.4-1/RecordLinkage/man/getParetoThreshold.Rd | 9 RecordLinkage-0.4-1/RecordLinkage/man/internals.Rd | 32 RecordLinkage-0.4-1/RecordLinkage/man/mrl.Rd | 2 RecordLinkage-0.4-1/RecordLinkage/man/optimalThreshold.Rd | 22 RecordLinkage-0.4-1/RecordLinkage/man/show.Rd | 2 RecordLinkage-0.4-1/RecordLinkage/man/subset.Rd | 5 RecordLinkage-0.4-1/RecordLinkage/man/summary.RLBigData.rd | 18 RecordLinkage-0.4-1/RecordLinkage/man/summary.rd | 8 RecordLinkage-0.4-1/RecordLinkage/src/phonet.c | 410 +++++----- RecordLinkage-0.4-1/RecordLinkage/vignettes |only 64 files changed, 2370 insertions(+), 2032 deletions(-)
Title: Reads mass spectrometry data in mzXML format.
Description: Functions for reading mass spectrometry data in mzXML
format.
Author: Sebastian Gibb, Jarek Tuszynski
Maintainer: Sebastian Gibb
Diff between readMzXmlData versions 2.0 dated 2011-10-04 and 2.0.1 dated 2012-01-12
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 3 +++ R/parseMzXml.R | 6 +++--- man/readMzXmlData-package.Rd | 4 ++-- 5 files changed, 16 insertions(+), 13 deletions(-)
Title: Statistical inference for partially observed Markov processes
Description: Inference methods for partially-observed Markov processes
Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner,
Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael
Lavine, Daniel C. Reuman
Maintainer: Aaron A. King
Diff between pomp versions 0.40-1 dated 2012-01-10 and 0.40-2 dated 2012-01-12
DESCRIPTION | 8 ++++---- MD5 | 34 ++++++++++++++++++---------------- data/blowflies.rda |binary data/dacca.rda |binary data/euler.sir.rda |binary data/gillespie.sir.rda |binary data/gompertz.rda |binary data/ou2.rda |binary data/ricker.rda |binary data/rw2.rda |binary data/verhulst.rda |binary inst/ChangeLog | 6 ++++++ inst/NEWS | 4 ++++ inst/doc/advanced_topics_in_pomp.pdf |binary inst/doc/intro_to_pomp.pdf |binary inst/doc/manual.pdf |binary src/euler.c | 8 ++------ tests/steps.R |only tests/steps.Rout.save |only 19 files changed, 34 insertions(+), 26 deletions(-)
Title: A Package for Running jags from R
Description: Using this package to call jags from R.
Author: Yu-Sung Su
Maintainer: Yu-Sung Su
Diff between R2jags versions 0.02-17 dated 2011-07-27 and 0.03-02 dated 2012-01-12
CHANGELOG | 8 +++ DESCRIPTION | 14 ++--- MD5 |only R/jags.R | 135 ++++++++++++++++++++++++++++++++----------------------- R/jags2.R | 6 +- R/jagsParallel.R |only man/jags.Rd | 12 ++++ 7 files changed, 110 insertions(+), 65 deletions(-)
Title: Multiple comparisons using normal approximation
Description: Multiple contrast tests and simultaneous confidence
intervals based on normal approximation. With implementations
for binomial proportions in a 2xk setting (risk difference and
odds ratio), poly-3-adjusted tumour rates, biodiversity indices
(multinomial data) and expected values under lognormal
assumption. Approximative power calculation for multiple
contrast tests of binomial and Gaussian data.
Author: Frank Schaarschmidt, Daniel Gerhard, Martin Sill
Maintainer: Frank Schaarschmidt
Diff between MCPAN versions 1.1-13 dated 2011-11-02 and 1.1-14 dated 2012-01-12
DESCRIPTION | 19 +++++++++-------- MD5 | 11 +++++----- NAMESPACE |only R/mosaicShannonSimpson.R | 48 +------------------------------------------- man/MCPAN-package.Rd | 4 +-- man/lnrci.Rd | 6 +++-- man/mosaicplot.Shannonci.Rd | 13 +++++------ 7 files changed, 30 insertions(+), 71 deletions(-)
Title: Maximum Likelihood Estimation
Description: Tools for Maximum Likelihood Estimation
Author: Ott Toomet
Maintainer: Arne Henningsen
Diff between maxLik versions 1.0-2 dated 2011-10-17 and 1.1-0 dated 2012-01-12
DESCRIPTION | 10 MD5 | 44 NAMESPACE | 1 NEWS | 12 R/maxCG.R |only R/maxLik.R | 2 R/maxOptim.R | 3 R/nParam.R | 3 R/stdEr.maxLik.R |only R/summary.maxLik.R | 14 R/vcov.maxLik.R | 6 man/maxBFGS.Rd | 10 tests/BFGSR.R | 1 tests/BFGSR.Rout.save | 47 tests/constraints.R | 1 tests/constraints.Rout.save | 690 +-- tests/examples.Rout.save | 2 tests/finalHessian.Rout.save | 4 tests/fitExpDist.R | 16 tests/fitExpDist.Rout.save | 607 +-- tests/fitNormalDist.R | 3 tests/fitNormalDist.Rout.save | 8462 +++++++++++++++++++++--------------------- tests/methods.R | 1 tests/methods.Rout.save | 2 24 files changed, 5039 insertions(+), 4902 deletions(-)
Title: Draw Geographical Maps
Description: Display of maps. Projection code and larger maps are in
separate packages (mapproj and mapdata).
Author: Original S code by Richard A. Becker and Allan R. Wilks. R
version by Ray Brownrigg
Maintainer: Ray Brownrigg
Diff between maps versions 2.2-3 dated 2011-12-13 and 2.2-4 dated 2012-01-12
DESCRIPTION | 14 +++++++------- MD5 | 12 ++++++------ src/county.gon | 4 +++- src/county.gonstats | 2 +- src/county.line | 20 ++++++++++++++------ src/county.linestats | 2 +- src/county.name | 3 ++- 7 files changed, 34 insertions(+), 23 deletions(-)
Title: GeneticStudio packages for R.
Description: This package was created to support population genetics
and landscape genetic courses I teach at Virginia Commonwealth
University. This package contains classes and functions for
the spatial analysis of marker data to include structure
statistics, analyses based upon allele frequencies, and the
Population Graphs network analysis of spatial conditional
genetic covariance.
Author: Rodney J. Dyer
Maintainer: Rodney J. Dyer
Diff between gstudio versions 0.5 dated 2011-12-31 and 0.6 dated 2012-01-12
gstudio-0.5/gstudio/inst/docs/AlleleFrequencies.pdf |only gstudio-0.5/gstudio/inst/docs/DataImport.pdf |only gstudio-0.5/gstudio/inst/docs/GeneticDistance.pdf |only gstudio-0.5/gstudio/inst/docs/GeneticDiversity.pdf |only gstudio-0.5/gstudio/inst/docs/GeneticStructure.pdf |only gstudio-0.5/gstudio/inst/docs/ParentOffspringData.pdf |only gstudio-0.5/gstudio/inst/docs/PopulationGraphs.pdf |only gstudio-0.6/gstudio/.tm_properties |only gstudio-0.6/gstudio/ChangeLog | 3 gstudio-0.6/gstudio/DESCRIPTION | 23 +-- gstudio-0.6/gstudio/MD5 | 65 ++++++-- gstudio-0.6/gstudio/inst/docs/AlleleFrequencies.Rnw | 55 ++----- gstudio-0.6/gstudio/inst/docs/DataImport.Rnw | 54 +------ gstudio-0.6/gstudio/inst/docs/GStudioMapping.Rnw | 28 +-- gstudio-0.6/gstudio/inst/docs/GeneticDistance.Rnw | 81 +++-------- gstudio-0.6/gstudio/inst/docs/GeneticDiversity.Rnw | 36 ---- gstudio-0.6/gstudio/inst/docs/GeneticStructure.Rnw | 42 +---- gstudio-0.6/gstudio/inst/docs/ParentOffspringData.Rnw | 47 +----- gstudio-0.6/gstudio/inst/docs/PopulationGraphs.Rnw | 35 ---- gstudio-0.6/gstudio/inst/docs/Rplots.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-019.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-021.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-023.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-024.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-025.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-058.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-059.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-060.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-061.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-062.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-063.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-064.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-065.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-066.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-067.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-068.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-069.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-070.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-071.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-072.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-073.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-074.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-075.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-araptus_he.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-sonora_ind_dist.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-sonora_strata_dist.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio-spiderplot.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio.Rnw |only gstudio-0.6/gstudio/inst/docs/gstudio.aux |only gstudio-0.6/gstudio/inst/docs/gstudio.log |only gstudio-0.6/gstudio/inst/docs/gstudio.pdf |only gstudio-0.6/gstudio/inst/docs/gstudio.tex |only gstudio-0.6/gstudio/inst/docs/gstudio.toc |only gstudio-0.6/gstudio/man/araptus_attenuatus.Rd | 2 gstudio-0.6/gstudio/man/cornus_florida.Rd | 2 55 files changed, 160 insertions(+), 313 deletions(-)
Title: Integration of base and grid graphics
Description: Integration of base and grid graphics
Author: Paul Murrell
Maintainer: Paul Murrell
Diff between gridBase versions 0.4-3 dated 2006-04-24 and 0.4-4 dated 2012-01-12
gridBase-0.4-3/gridBase/inst/doc/Rplots.ps |only gridBase-0.4-3/gridBase/inst/doc/gridBase-005.pdf |only gridBase-0.4-3/gridBase/inst/doc/gridBase-009.pdf |only gridBase-0.4-3/gridBase/inst/doc/gridBase-013.pdf |only gridBase-0.4-3/gridBase/inst/doc/gridBase-complex.pdf |only gridBase-0.4-3/gridBase/inst/doc/gridBase-multiplot.pdf |only gridBase-0.4-3/gridBase/inst/doc/gridBase.aux |only gridBase-0.4-3/gridBase/inst/doc/gridBase.log |only gridBase-0.4-3/gridBase/inst/doc/gridBase.tex |only gridBase-0.4-4/gridBase/DESCRIPTION | 6 ++++-- gridBase-0.4-4/gridBase/MD5 |only gridBase-0.4-4/gridBase/inst/doc/gridBase-004.pdf |binary gridBase-0.4-4/gridBase/inst/doc/gridBase-007.pdf |binary gridBase-0.4-4/gridBase/inst/doc/gridBase-010.pdf |binary gridBase-0.4-4/gridBase/inst/doc/gridBase-011.pdf |binary gridBase-0.4-4/gridBase/inst/doc/gridBase-012.pdf |binary gridBase-0.4-4/gridBase/inst/doc/gridBase-014.pdf |binary gridBase-0.4-4/gridBase/inst/doc/gridBase-015.pdf |binary gridBase-0.4-4/gridBase/inst/doc/gridBase-022.pdf |binary gridBase-0.4-4/gridBase/inst/doc/gridBase.pdf |binary 20 files changed, 4 insertions(+), 2 deletions(-)
Title: A package for Graphical Markov Models
Description: Functions for analyzing and fitting Graphical Markov
models
Author: Giovanni M. Marchetti, Mathias Drton, Kayvan Sadeghi
Maintainer: Giovanni M. Marchetti
Diff between ggm versions 1.99-1 dated 2011-12-11 and 1.99-2 dated 2012-01-12
DESCRIPTION | 11 ++++++----- MD5 | 16 ++++++++-------- R/functions.R | 9 ++++----- data/anger.rda |binary data/glucose.rda |binary data/marks.rda |binary data/stress.rda |binary data/surdata.rda |binary inst/doc/mixed-graphs.pdf |binary 9 files changed, 18 insertions(+), 18 deletions(-)
Title: Interactive exploratory spatial data analysis
Description: GeoXp is a tool for researchers in spatial statistics,
spatial econometrics, geography, ecology etc allowing to link
dynamically statistical plots with elementary maps. This
coupling consists in the fact that the selection of a zone on
the map results in the automatic highlighting of the
corresponding points on the statistical graph or reversely the
selection of a portion of the graph results in the automatic
highlighting of the corresponding points on the map. GeoXp
includes tools from different areas of spatial statistics
including geostatistics as well as spatial econometrics and
point processes. Besides elementary plots like boxplots,
histograms or simple scatterplos, GeoXp also couples with maps
Moran scatterplots, variogram cloud, Lorentz Curves,...In order
to make the most of the multidimensionality of the data, GeoXp
includes some dimension reduction techniques such as PCA.
Author: Yves Aragon, Thibault Laurent, Lauriane Robidou, Anne
Ruiz-Gazen, Christine Thomas-Agnan
Maintainer: Thibault Laurent
Diff between GeoXp versions 1.5.0 dated 2010-05-01 and 1.5.2 dated 2012-01-12
GeoXp-1.5.0/GeoXp/inst/doc/fig2d.ps |only GeoXp-1.5.2/GeoXp/DESCRIPTION | 10 +++--- GeoXp-1.5.2/GeoXp/GeoXp-Ex.R |only GeoXp-1.5.2/GeoXp/MD5 |only GeoXp-1.5.2/GeoXp/NAMESPACE |only GeoXp-1.5.2/GeoXp/R/angleplotmap.R | 20 ++++++------ GeoXp-1.5.2/GeoXp/R/barnbmap.r | 11 ++++-- GeoXp-1.5.2/GeoXp/R/boxplotmap.R | 25 +++++++-------- GeoXp-1.5.2/GeoXp/R/carte.R | 6 ++- GeoXp-1.5.2/GeoXp/R/densitymap.R | 24 +++++++------- GeoXp-1.5.2/GeoXp/R/driftmap.R | 24 +++++++------- GeoXp-1.5.2/GeoXp/R/ginimap.R | 23 +++++++------- GeoXp-1.5.2/GeoXp/R/histnbmap.r | 31 +++++++++--------- GeoXp-1.5.2/GeoXp/R/histomap.R | 21 ++++++------ GeoXp-1.5.2/GeoXp/R/moranplotmap.R | 36 ++++++++++++---------- GeoXp-1.5.2/GeoXp/R/neighbourmap.R | 24 +++++++------- GeoXp-1.5.2/GeoXp/R/variocloudmap.R | 26 ++++++++------- GeoXp-1.5.2/GeoXp/inst/doc/Thumbs.db |binary GeoXp-1.5.2/GeoXp/inst/doc/fig2d.log |only GeoXp-1.5.2/GeoXp/inst/doc/presentation_geoxp.pdf |binary GeoXp-1.5.2/GeoXp/inst/doc/presentation_geoxp.rnw | 1 GeoXp-1.5.2/GeoXp/man/GeoXp-package.Rd | 6 +-- GeoXp-1.5.2/GeoXp/man/angleplotmap.Rd | 2 - GeoXp-1.5.2/GeoXp/man/barmap.Rd | 2 - GeoXp-1.5.2/GeoXp/man/barnbmap.rd | 2 - GeoXp-1.5.2/GeoXp/man/boxplotmap.Rd | 2 - GeoXp-1.5.2/GeoXp/man/carte.Rd | 2 - GeoXp-1.5.2/GeoXp/man/choix.bubble.Rd | 2 - GeoXp-1.5.2/GeoXp/man/choix.couleur.Rd | 2 - GeoXp-1.5.2/GeoXp/man/choixvarfunc.Rd | 2 - GeoXp-1.5.2/GeoXp/man/clustermap.Rd | 2 - GeoXp-1.5.2/GeoXp/man/dbledensitymap.Rd | 2 - GeoXp-1.5.2/GeoXp/man/dblehistomap.Rd | 2 - GeoXp-1.5.2/GeoXp/man/densitymap.Rd | 2 - GeoXp-1.5.2/GeoXp/man/driftmap.Rd | 2 - GeoXp-1.5.2/GeoXp/man/genpca.Rd | 2 - GeoXp-1.5.2/GeoXp/man/gini.Rd | 2 - GeoXp-1.5.2/GeoXp/man/ginimap.Rd | 2 - GeoXp-1.5.2/GeoXp/man/graphique.Rd | 2 - GeoXp-1.5.2/GeoXp/man/histnbmap.rd | 2 - GeoXp-1.5.2/GeoXp/man/histobarmap.Rd | 2 - GeoXp-1.5.2/GeoXp/man/histomap.Rd | 2 - GeoXp-1.5.2/GeoXp/man/makeneighborsw.Rd | 2 - GeoXp-1.5.2/GeoXp/man/misolationmap.rd | 2 - GeoXp-1.5.2/GeoXp/man/moranplotmap.Rd | 2 - GeoXp-1.5.2/GeoXp/man/mvariocloudmap.rd | 2 - GeoXp-1.5.2/GeoXp/man/neighbourmap.Rd | 2 - GeoXp-1.5.2/GeoXp/man/nonormmoran.Rd | 2 - GeoXp-1.5.2/GeoXp/man/normw.Rd | 2 - GeoXp-1.5.2/GeoXp/man/pcamap.Rd | 2 - GeoXp-1.5.2/GeoXp/man/plot3dmap.rd | 2 - GeoXp-1.5.2/GeoXp/man/polyboxplotmap.Rd | 2 - GeoXp-1.5.2/GeoXp/man/rotation.Rd | 2 - GeoXp-1.5.2/GeoXp/man/scattermap.Rd | 2 - GeoXp-1.5.2/GeoXp/man/selectgraph.Rd | 2 - GeoXp-1.5.2/GeoXp/man/selectmap.Rd | 2 - GeoXp-1.5.2/GeoXp/man/selectstat.Rd | 2 - GeoXp-1.5.2/GeoXp/man/slider1.Rd | 2 - GeoXp-1.5.2/GeoXp/man/spdf2list.Rd | 2 - GeoXp-1.5.2/GeoXp/man/variocloudmap.Rd | 2 - 60 files changed, 192 insertions(+), 172 deletions(-)
Title: Flexible Mixture Modeling
Description: FlexMix implements a general framework for finite mixtures
of regression models using the EM algorithm. FlexMix provides
the E-step and all data handling, while the M-step can be
supplied by the user to easily define new models. Existing
drivers implement mixtures of standard linear models,
generalized linear models and model-based clustering.
Author: Friedrich Leisch and Bettina Gruen
Maintainer: Bettina Gruen
Diff between flexmix versions 2.3-5 dated 2011-04-24 and 2.3-6 dated 2012-01-12
flexmix-2.3-5/flexmix/COPYING |only flexmix-2.3-5/flexmix/inst/doc/jss.bst |only flexmix-2.3-5/flexmix/inst/doc/jss.cls |only flexmix-2.3-6/flexmix/DESCRIPTION | 10 - flexmix-2.3-6/flexmix/LICENSE |only flexmix-2.3-6/flexmix/MD5 |only flexmix-2.3-6/flexmix/NAMESPACE | 1 flexmix-2.3-6/flexmix/NEWS | 22 ++++ flexmix-2.3-6/flexmix/R/boot.R | 90 +++++++++------- flexmix-2.3-6/flexmix/R/concomitant.R | 5 flexmix-2.3-6/flexmix/R/flexmix.R | 20 ++- flexmix-2.3-6/flexmix/R/flxdist.R | 4 flexmix-2.3-6/flexmix/R/lmm.R | 81 +++++++++++--- flexmix-2.3-6/flexmix/R/plot-FLXboot.R | 21 ++- flexmix-2.3-6/flexmix/R/refit.R | 3 flexmix-2.3-6/flexmix/R/rflexmix.R | 2 flexmix-2.3-6/flexmix/R/stepFlexmix.R | 10 + flexmix-2.3-6/flexmix/data/Mehta.RData |binary flexmix-2.3-6/flexmix/inst/CITATION | 10 - flexmix-2.3-6/flexmix/inst/NEWS | 22 ++++ flexmix-2.3-6/flexmix/inst/doc/bootstrapping.Rnw | 93 +++++++++++++++-- flexmix-2.3-6/flexmix/inst/doc/bootstrapping.pdf |binary flexmix-2.3-6/flexmix/inst/doc/flexmix-intro.Rnw | 16 +- flexmix-2.3-6/flexmix/inst/doc/flexmix-intro.pdf |binary flexmix-2.3-6/flexmix/inst/doc/flexmix.bib | 79 +++++++------- flexmix-2.3-6/flexmix/inst/doc/mixture-regressions.Rnw | 30 ++--- flexmix-2.3-6/flexmix/inst/doc/mixture-regressions.pdf |binary flexmix-2.3-6/flexmix/inst/doc/mixture.bib | 19 ++- flexmix-2.3-6/flexmix/inst/doc/regression-examples.Rnw | 82 +++++++------- flexmix-2.3-6/flexmix/inst/doc/regression-examples.pdf |binary flexmix-2.3-6/flexmix/man/FLXMRlmer.Rd | 8 - flexmix-2.3-6/flexmix/man/FLXMRmgcv.Rd | 1 flexmix-2.3-6/flexmix/man/Mehta.Rd | 4 flexmix-2.3-6/flexmix/man/betablocker.Rd | 4 flexmix-2.3-6/flexmix/vignettes |only 35 files changed, 427 insertions(+), 210 deletions(-)
Title: Plots Coefficients from Fitted Models
Description: Plots the coefficients from a model object
Author: Jared P. Lander
Maintainer:
Diff between coefplot versions 1.1.4 dated 2012-01-04 and 1.1.5 dated 2012-01-12
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/utilities.r | 6 +++--- README | 2 ++ 4 files changed, 11 insertions(+), 9 deletions(-)
Title: Analogue and weighted averaging methods for palaeoecology
Description: Fits Modern Analogue Technique and Weighted Averaging
transfer function models for prediction of environmental data
from species data, and related methods used in palaeoecology.
Author: Gavin L. Simpson, Jari Oksanen
Maintainer: Gavin L. Simpson
Diff between analogue versions 0.7-0 dated 2011-05-26 and 0.8-0 dated 2012-01-12
DESCRIPTION | 15 +- MD5 |only NAMESPACE |only R/Stratiplot.R | 17 +-- R/ccaFit.R |only R/chooseTaxa.R | 2 R/crossval.R |only R/distance.R | 63 ++++++++--- R/distance2.R |only R/gradientDist.R |only R/internal.R | 31 +++-- R/mat.R | 32 +++--- R/panel.Stratiplot.R | 3 R/pcr.R |only R/plot.gradientDist.R |only R/predict.wa.R | 3 R/print.performance.R | 15 +- R/rdaFit.R |only R/tolerance.R | 4 R/varExpl.R |only R/weightedCor.R |only R/zzz.R | 9 + data/Biome.rda |binary data/Climate.rda |binary data/ImbrieKipp.rda |binary data/Location.rda |binary data/Pollen.rda |binary data/Salinity.rda |binary data/SumSST.rda |binary data/V12.122.rda |binary data/WinSST.rda |binary data/abernethy.rda |binary data/rlgh.rda |binary data/swapdiat.rda |binary data/swappH.rda |binary inst/ChangeLog | 85 ++++++++++++++++ inst/doc/analogue_methods.pdf |binary man/analogue-internal.Rd | 2 man/crossval.Rd |only man/gradientDist.Rd |only man/mat.Rd | 36 ++++++ man/optima.Rd | 7 - man/panel.Stratiplot.Rd | 7 + man/pcr.Rd |only man/varExpl.Rd |only man/weightedCor.Rd |only src/distx.c | 68 +++++++++--- src/distxy.c | 222 +++++++++++++++++++++++++++++++++++++----- tests |only 49 files changed, 504 insertions(+), 117 deletions(-)