Title: Modelling with Sparse And Dense Matrices
Diff between MatrixModels versions 0.2-1 dated 2010-09-21 and 0.3-1 dated 2012-01-12
Description: Modelling with sparse and dense 'Matrix' matrices, using
modular prediction and response module classes.
Author: Douglas Bates
Maintainer: Doug and Martin
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
Diff between M3 versions 0.1 dated 2011-06-20 and 0.2 dated 2012-01-12
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
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++)
Diff between fts versions 0.7.6 dated 2009-10-15 and 0.7.7 dated 2012-01-12
Description: fast operations for time series objects
Author: Whit Armstrong
Maintainer: Whit Armstrong
.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
Diff between editrules versions 2.0-1 dated 2011-12-08 and 2.0-3 dated 2012-01-12
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
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
Diff between aroma.core versions 2.3.2 dated 2011-11-15 and 2.4.1 dated 2012-01-12
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
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
Diff between aroma.cn versions 0.9.3 dated 2011-11-15 and 1.0.0 dated 2012-01-12
Description: Package for analysis of copy-number estimates obtained
from various platforms.
Author: Henrik Bengtsson and Pierre Neuvial
Maintainer: Henrik Bengtsson
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
Diff between aroma.affymetrix versions 2.3.0 dated 2011-11-02 and 2.4.0 dated 2012-01-12
More information about aroma.affymetrix at CRAN
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
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(-)
Permanent link
Title: Tools for parsing and generating XML within R and S-Plus.
Diff between XML versions 3.7-3 dated 2012-01-11 and 3.7-4 dated 2012-01-12
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
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
Diff between vegdata versions 0.5.1 dated 2011-11-07 and 0.5.3 dated 2012-01-12
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
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
Diff between trio versions 1.2.9 dated 2011-10-14 and 1.4.12 dated 2012-01-12
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
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
Diff between spam versions 0.27-0 dated 2011-08-18 and 0.28-0 dated 2012-01-12
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
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
Diff between R.utils versions 1.9.7 dated 2011-12-22 and 1.9.9 dated 2012-01-12
Description: This package provides utility classes and methods useful
when programming in R and developing R packages.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
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
Diff between R.rsp versions 0.7.0 dated 2011-11-24 and 0.7.1 dated 2012-01-12
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
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
Diff between Rook versions 1.0-2 dated 2011-04-25 and 1.0-3 dated 2012-01-12
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
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
Diff between RInside versions 0.2.5 dated 2011-12-08 and 0.2.6 dated 2012-01-12
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
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
Diff between Rglpk versions 0.3-6 dated 2011-12-30 and 0.3-7 dated 2012-01-12
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
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
Diff between R.filesets versions 1.1.3 dated 2011-11-02 and 1.1.4 dated 2012-01-12
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
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
Diff between RecordLinkage versions 0.3-5 dated 2011-09-12 and 0.4-1 dated 2012-01-12
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
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.
Diff between readMzXmlData versions 2.0 dated 2011-10-04 and 2.0.1 dated 2012-01-12
Description: Functions for reading mass spectrometry data in mzXML
format.
Author: Sebastian Gibb, Jarek Tuszynski
Maintainer: Sebastian Gibb
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
Diff between pomp versions 0.40-1 dated 2012-01-10 and 0.40-2 dated 2012-01-12
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
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
Diff between R2jags versions 0.02-17 dated 2011-07-27 and 0.03-02 dated 2012-01-12
Description: Using this package to call jags from R.
Author: Yu-Sung Su
Maintainer: Yu-Sung Su
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
Diff between MCPAN versions 1.1-13 dated 2011-11-02 and 1.1-14 dated 2012-01-12
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
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
Diff between maxLik versions 1.0-2 dated 2011-10-17 and 1.1-0 dated 2012-01-12
Description: Tools for Maximum Likelihood Estimation
Author: Ott Toomet
Maintainer: Arne Henningsen
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
Diff between maps versions 2.2-3 dated 2011-12-13 and 2.2-4 dated 2012-01-12
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
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.
Diff between gstudio versions 0.5 dated 2011-12-31 and 0.6 dated 2012-01-12
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
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
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gstudio-0.6/gstudio/inst/docs/gstudio-066.pdf |only
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gstudio-0.6/gstudio/inst/docs/gstudio-069.pdf |only
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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
Diff between gridBase versions 0.4-3 dated 2006-04-24 and 0.4-4 dated 2012-01-12
Description: Integration of base and grid graphics
Author: Paul Murrell
Maintainer: Paul Murrell
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
Diff between ggm versions 1.99-1 dated 2011-12-11 and 1.99-2 dated 2012-01-12
Description: Functions for analyzing and fitting Graphical Markov
models
Author: Giovanni M. Marchetti, Mathias Drton, Kayvan Sadeghi
Maintainer: Giovanni M. Marchetti
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
Diff between GeoXp versions 1.5.0 dated 2010-05-01 and 1.5.2 dated 2012-01-12
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
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 -
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GeoXp-1.5.2/GeoXp/man/plot3dmap.rd | 2 -
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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
Diff between flexmix versions 2.3-5 dated 2011-04-24 and 2.3-6 dated 2012-01-12
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
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
Diff between coefplot versions 1.1.4 dated 2012-01-04 and 1.1.5 dated 2012-01-12
Description: Plots the coefficients from a model object
Author: Jared P. Lander
Maintainer:
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
Diff between analogue versions 0.7-0 dated 2011-05-26 and 0.8-0 dated 2012-01-12
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
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(-)