Thu, 12 Jan 2012

New package BTSPAS with initial version 2012.01
Package: BTSPAS
Version: 2012.01
Date: 2012-01-10
Title: Bayesian Time-Strat. Population Analysis
Author: Carl J Schwarz and Simon J Bonner
Maintainer: Carl J Schwarz
Depends: coda, splines, actuar, BRugs, R2OpenBUGS
Description: BTSPAS provides advanced Bayesian methods to estimate abundance and run-timing from temporally-stratified Petersen mark-recapture experiments. Methods include hierarchical modelling of the capture probabilities and spline smoothing of the daily run size.
URL: http://www.stat.sfu.ca/~cschwarz/Consulting/Trinity/Phase2
License: GPL (>= 2)
Repository: CRAN
Repository/R-Forge/Project: btspas
Repository/R-Forge/Revision: 96
Date/Publication: 2012-01-12 21:05:08
Packaged: 2012-01-11 21:42:55 UTC; rforge

More information about BTSPAS at CRAN
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Package MatrixModels updated to version 0.3-1 with previous version 0.2-1 dated 2010-09-21

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 and Martin Maechler
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(-)

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Package M3 updated to version 0.2 with previous version 0.1 dated 2011-06-20

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 -
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 man/get.map.lines.M3.proj.Rd      |   23 +++++++++++++------
 21 files changed, 179 insertions(+), 100 deletions(-)

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Package fts updated to version 0.7.7 with previous version 0.7.6 dated 2009-10-15

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(-)

More information about fts at CRAN
Permanent link

Package editrules updated to version 2.0-3 with previous version 2.0-1 dated 2011-12-08

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

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 editrules-2.0-3/editrules/NEWS                                   |  359 -
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 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 
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 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
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 editrules-2.0-3/editrules/inst/tests/testIsObviouslyRedundant.R  |   48 
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 editrules-2.0-3/editrules/t.R                                    |only
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 220 files changed, 13925 insertions(+), 13824 deletions(-)

More information about editrules at CRAN
Permanent link

Package aroma.core updated to version 2.4.1 with previous version 2.3.2 dated 2011-11-15

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(-)

More information about aroma.core at CRAN
Permanent link

Package aroma.cn updated to version 1.0.0 with previous version 0.9.3 dated 2011-11-15

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 -
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 incl/callAllelicBalanceByBAFs.PairedPSCBS.Rex |    7 --
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 incl/deShearC1C2.PairedPSCBS.Rex              |    4 -
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 inst/NEWS                                     |   17 +++++
 man/TotalCnKernelSmoothing.Rd                 |    3 
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 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(-)

More information about aroma.cn at CRAN
Permanent link

Package aroma.affymetrix updated to version 2.4.0 with previous version 2.3.0 dated 2011-11-02

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
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 aroma.affymetrix-2.4.0/aroma.affymetrix/inst/buildScripts/chipTypes/Sc03b_MF_v04                                                         |only
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 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

Package XML updated to version 3.7-4 with previous version 3.7-3 dated 2012-01-11

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(-)

More information about XML at CRAN
Permanent link

Package vegdata updated to version 0.5.3 with previous version 0.5.1 dated 2011-11-07

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 
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 R/tax.r                    |  479 ++++++++++++++++++++++-----------------------
 R/tv.refl.r                |   42 +--
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 15 files changed, 399 insertions(+), 385 deletions(-)

More information about vegdata at CRAN
Permanent link

Package trio updated to version 1.4.12 with previous version 1.2.9 dated 2011-10-14

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

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More information about trio at CRAN
Permanent link

Package spam updated to version 0.28-0 with previous version 0.27-0 dated 2011-08-18

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 
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 R/diff.R                                  |    2 
 R/dist.R                                  |    2 
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 R/makeprec.R                              |    2 
 R/mle.R                                   |    2 
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 R/profile.R                               |    6 
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 R/spamlist.R                              |    2 
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 data/Oral.rda                             |binary
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 tests/demo_article-jss-example1.R         |    2 
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 tests/demo_article-jss-example2.R         |    2 
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 tests/demo_cholesky.R                     |    2 
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 tests/demo_spam.R                         |    2 
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 tests/demo_timing.R                       |    2 
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 tests/solve.R                             |    2 
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Permanent link

New package translate with initial version 0.1
Package: translate
Type: Package
Title: Bindings for the Google Translate API v2
Description: Bindings for the Google Translate API v2
Version: 0.1
Date: 2012-01-11
Author: Peter Danenberg
Maintainer: Peter Danenberg
License: GPL
Imports: RCurl, RJSONIO, functional, lisp
Suggests: debug
Collate: 'translate.R'
Packaged: 2012-01-11 19:42:24 UTC; pcdanenb
Repository: CRAN
Date/Publication: 2012-01-12 09:24:54

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Package R.utils updated to version 1.9.9 with previous version 1.9.7 dated 2011-12-22

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(-)

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New package rstiefel with initial version 0.9
Package: rstiefel
Type: Package
Title: Random orthonormal matrix generation on the Stiefel manifold
Version: 0.9
Date: 2012-01-02
Author: Peter Hoff
Maintainer: Peter Hoff
Description: This package simulates random orthonormal matrices from linear and quadratic exponential family distributions on the Stiefel manifold. The most general type of distribution covered is the matrix-variate Bingham-von Mises-Fisher distribution. Most of the simulation methods are presented in Hoff(2009) "Simulation of the Matrix Bingham-von Mises-Fisher Distribution, With Applications to Multivariate and Relational Data."
License: GPL-3
Packaged: 2012-01-11 17:48:21 UTC; root
Repository: CRAN
Date/Publication: 2012-01-12 09:24:49

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Package R.rsp updated to version 0.7.1 with previous version 0.7.0 dated 2011-11-24

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. "<>>= [...] @". As explained in one of the vignettes, RSP-embedded LaTeX vignettes can easily be included in any R package. In addition to RSP, this package also provides an internal cross-platform web server and built-in dynamic RSP-embedded HTML help pages, which can be launched by browseRsp(). If other packages provide RSP help pages, these are automatically linked to as well.
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

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Package Rook updated to version 1.0-3 with previous version 1.0-2 dated 2011-04-25

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

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Package RInside updated to version 0.2.6 with previous version 0.2.5 dated 2011-12-08

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 ++++
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 MD5                                         |   31 +++-
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Package Rglpk updated to version 0.3-7 with previous version 0.3-6 dated 2011-12-30

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 ++++++++++++++++++++++------------
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 5 files changed, 101 insertions(+), 34 deletions(-)

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Package R.filesets updated to version 1.1.4 with previous version 1.1.3 dated 2011-11-02

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 +++++++---
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 man/getFileSize.GenericDataFile.Rd        |    1 
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 14 files changed, 112 insertions(+), 51 deletions(-)

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Package RecordLinkage updated to version 0.4-1 with previous version 0.3-5 dated 2011-09-12

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 , Murat Sariyar
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 
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 RecordLinkage-0.4-1/RecordLinkage/NAMESPACE                               |    1 
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 RecordLinkage-0.4-1/RecordLinkage/R/compare.r                             |    2 
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 RecordLinkage-0.4-1/RecordLinkage/R/evt.r                                 |  209 ++++-
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Package readMzXmlData updated to version 2.0.1 with previous version 2.0 dated 2011-10-04

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 +++
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 man/readMzXmlData-package.Rd |    4 ++--
 5 files changed, 16 insertions(+), 13 deletions(-)

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Package pomp updated to version 0.40-2 with previous version 0.40-1 dated 2012-01-10

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 ++++----
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Package R2jags updated to version 0.03-02 with previous version 0.02-17 dated 2011-07-27

Title: A Package for Running jags from R
Description: Using this package to call jags from R.
Author: Yu-Sung Su , Masanao Yajima ,
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 +++
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New package opencpu.demo with initial version 0.4
Package: opencpu.demo
Maintainer: Jeroen Ooms
License: AGPL
Encoding: UTF-8
Title: OpenCPU Demo apps.
Type: Package
Author: Various contributors
Description: Some demo R functions and apps for OpenCPU
Version: 0.4
Date: 2012-01-06
Suggests: ggplot2, httpRequest, lattice
Collate: 'liveplot.R' 'nabel.R' 'testplothandlers.R'
Packaged: 2012-01-11 23:55:04 UTC; jeroen
Repository: CRAN
Date/Publication: 2012-01-12 09:24:42

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New package mobForest with initial version 1.0
Package: mobForest
Type: Package
Title: Model based Random Forest analysis
Version: 1.0
Date: 2011-12-12
Author: Nikhil Garge and Barry Eggleston
Maintainer: Nikhil Garge
Description: This package implements random forest method for model based recursive partitioning. The mob() function, developed by Zeileis et al (2008), within party package, is modified to contruct model-based decesion trees based on random forest methodology. The main input function mobForestAnalysis() takes all input parameters to construct trees, compute out-of-bag errors, predictions, and overall accuracy of forest. The algorithm performs parallel computation using clusterApply() function within 'parallel' package.
License: GPL (>= 2)
LazyLoad: yes
Depends: parallel, party
Imports: methods, modeltools
Suggests: mlbench
Packaged: 2012-01-10 21:00:03 UTC; ngarge
Repository: CRAN
Date/Publication: 2012-01-12 09:30:27

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Package MCPAN updated to version 1.1-14 with previous version 1.1-13 dated 2011-11-02

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 +--
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 man/mosaicplot.Shannonci.Rd |   13 +++++------
 7 files changed, 30 insertions(+), 71 deletions(-)

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Package maxLik updated to version 1.1-0 with previous version 1.0-2 dated 2011-10-17

Title: Maximum Likelihood Estimation
Description: Tools for Maximum Likelihood Estimation
Author: Ott Toomet , Arne Henningsen , with contributions from Spencer Graves and Yves Croissant
Maintainer: Arne Henningsen

Diff between maxLik versions 1.0-2 dated 2011-10-17 and 1.1-0 dated 2012-01-12

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 24 files changed, 5039 insertions(+), 4902 deletions(-)

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Package maps updated to version 2.2-4 with previous version 2.2-3 dated 2011-12-13

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 . Enhancements by Thomas P Minka .
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 +++-
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 7 files changed, 34 insertions(+), 23 deletions(-)

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New package lisp with initial version 0.1
Package: lisp
Type: Package
Encoding: UTF-8
Title: List-processing à la SRFI-1
Version: 0.1
Date: 2010-03-02
Author: Peter Danenberg
Maintainer: Peter Danenberg
Description: Though SRFI-1 scopes both list-processing and higher-order programming, we'll save some list-orthogonal functions for the `functional' package; this is freely a mixture of implementation and API.
License: GPL (>= 2)
LazyLoad: yes
Suggests: RUnit
Collate: 'lisp.R'
Packaged: 2012-01-11 18:27:18 UTC; pcdanenb
Repository: CRAN
Date/Publication: 2012-01-12 09:24:37

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New package intReg with initial version 0.1-2
Package: intReg
Version: 0.1-2
Date: 2012-01-12
Title: Interval Regression
Author: Ott Toomet
Maintainer: Ott Toomet
Depends: R (>= 2.7.0), maxLik (>= 1.0-3), sets
Imports: sets
Suggests: Ecdat
Description: Estimating interval regression models. Both common and observation-specific boundaries may be specified.
License: GPL (>= 2)
URL: http://CRAN.R-project.org, http://www.sampleSelection.org
Packaged: 2012-01-12 06:57:05 UTC; siim
Repository: CRAN
Date/Publication: 2012-01-12 09:24:36

More information about intReg at CRAN
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Package gstudio updated to version 0.6 with previous version 0.5 dated 2011-12-31

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

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Package gridBase updated to version 0.4-4 with previous version 0.4-3 dated 2006-04-24

Title: Integration of base and grid graphics
Description: Integration of base and grid graphics
Author: Paul Murrell
Maintainer: Paul Murrell

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Package ggm updated to version 1.99-2 with previous version 1.99-1 dated 2011-12-11

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

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Package GeoXp updated to version 1.5.2 with previous version 1.5.0 dated 2010-05-01

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

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Package flexmix updated to version 2.3-6 with previous version 2.3-5 dated 2011-04-24

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

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Package coefplot updated to version 1.1.5 with previous version 1.1.4 dated 2012-01-04

Title: Plots Coefficients from Fitted Models
Description: Plots the coefficients from a model object
Author: Jared P. Lander
Maintainer:

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Package analogue updated to version 0.8-0 with previous version 0.7-0 dated 2011-05-26

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

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