CRANberries

Fri, 09 May 2008

Package SeqKnn updated to version 1.0.1 with previous version 1.0.0 dated 2006-02-08

Author: Ki-Yeol Kim and Gwan-Su Yi, CSBio lab., Information and Communications University
Title: Sequential KNN imputation method
Description: This function estimates missing values sequentially from the gene that had least missing rate in microarray data

Diff between SeqKnn versions 1.0.0 dated 2006-02-08 and 1.0.1 dated 2008-05-09

 SeqKnn-1.0.0/SeqKnn/R/SeqKNN.R    |only
 SeqKnn-1.0.0/SeqKnn/R/nnmiss.R    |only
 SeqKnn-1.0.0/SeqKnn/README        |only
 SeqKnn-1.0.0/SeqKnn/man/SeqKNN.Rd |only
 SeqKnn-1.0.1/SeqKnn/CONTENTS      |only
 SeqKnn-1.0.1/SeqKnn/DESCRIPTION   |   20 ++++++++++----------
 SeqKnn-1.0.1/SeqKnn/INDEX         |only
 SeqKnn-1.0.1/SeqKnn/MD5           |only
 SeqKnn-1.0.1/SeqKnn/R/SeqKnn.R    |only
 SeqKnn-1.0.1/SeqKnn/man/SeqKnn.Rd |only
 SeqKnn-1.0.1/SeqKnn/man/khan05.Rd |   17 +++--------------
 SeqKnn-1.0.1/SeqKnn/man/nnmiss.Rd |   19 -------------------
 12 files changed, 13 insertions(+), 43 deletions(-)

More information about SeqKnn at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

Package pbatR updated to version 2.1.1 with previous version 2.0.2 dated 2007-09-27

Author: PBAT: Christoph Lange, pbatR: Thomas Hoffmann
Title: P2BAT
Description: This package provides data analysis via the pbat program, and an alternative internal implementation of the power calculations via simulation only. For analysis, this package provides a frontend to the PBAT software, automatically reading in the output from the pbat program and displaying the corresponding figure when appropriate (i.e. PBAT-logrank). It includes support for multiple processes and clusters. For analysis, users must download PBAT and accept it's license, available on the PBAT webpage. Both the data analysis and power calculations have command line and graphical interfaces using tcltk.

Diff between pbatR versions 2.0.2 dated 2007-09-27 and 2.1.1 dated 2008-05-09

 DESCRIPTION           |    6 +-
 NAMESPACE             |   21 ++++---
 R/cped.R              |only
 R/createCommandfile.R |   30 +++++++---
 R/pbat.R              |   30 +++++++---
 R/pbat.dir.R          |   42 +++++++-------
 R/pbat.m.R            |   32 ++++++----
 R/pbatGUI.R           |   61 ++++++++++++++++----
 R/ped.R               |   23 +++++--
 R/phe.R               |   18 ++++--
 R/power.R             |   58 +++++++++++++------
 R/powerConversions.R  |    4 -
 R/powerGUI.R          |   66 +++++++++++++++-------
 R/version.R           |   15 +++--
 man/cped.Rd           |only
 man/pbat.Rd           |  149 ++++++++++++++++++++++++++------------------------
 man/ped.Rd            |   25 ++++----
 man/phe.Rd            |   14 ++--
 man/power.Rd          |   14 ++--
 src/data.cpp          |   29 +++++++++
 src/kludge.cpp        |   16 +++--
 src/powerSim.cpp      |   54 +++++++++++++-----
 src/wait.cpp          |   20 +++---
 23 files changed, 469 insertions(+), 258 deletions(-)

More information about pbatR at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

Package odfWeave updated to version 0.7.5 with previous version 0.7.4 dated 2008-05-05

Author: Max Kuhn, Steve Weaston
Title: Sweave processing of Open Document Format (ODF) files
Description: Sweave processing of Open Document Format (ODF) files

Diff between odfWeave versions 0.7.4 dated 2008-05-05 and 0.7.5 dated 2008-05-09

 ._odfWeave                                 |only
 odfWeave/._DESCRIPTION                     |only
 odfWeave/._NAMESPACE                       |only
 odfWeave/._R                               |only
 odfWeave/._ToDo                            |only
 odfWeave/._inst                            |only
 odfWeave/._man                             |only
 odfWeave/DESCRIPTION                       |    6 +++---
 odfWeave/R/._RweaveOdf.R                   |only
 odfWeave/R/._addFontDecs.R                 |only
 odfWeave/R/._addStyleDefs.R                |only
 odfWeave/R/._adjustImageSize.R             |only
 odfWeave/R/._figGen.R                      |only
 odfWeave/R/._getExt.R                      |only
 odfWeave/R/._getStyles.R                   |only
 odfWeave/R/._listString.R                  |only
 odfWeave/R/._matrixPaste.R                 |only
 odfWeave/R/._odfCat.R                      |only
 odfWeave/R/._odfDataType.R                 |only
 odfWeave/R/._odfEnv.R                      |only
 odfWeave/R/._odfFigureCaption.R            |only
 odfWeave/R/._odfInsertPlot.R               |only
 odfWeave/R/._odfItemize.R                  |only
 odfWeave/R/._odfPageBreak.R                |only
 odfWeave/R/._odfSetPageStyle.R             |only
 odfWeave/R/._odfStyleGen.R                 |only
 odfWeave/R/._odfTable.R                    |only
 odfWeave/R/._odfTable.character.R          |only
 odfWeave/R/._odfTable.data.frame.R         |only
 odfWeave/R/._odfTable.matrix.R             |only
 odfWeave/R/._odfTable.numeric.R            |only
 odfWeave/R/._odfTableCaption.R             |only
 odfWeave/R/._odfTableGen.R                 |only
 odfWeave/R/._odfTmpDir.R                   |only
 odfWeave/R/._odfTranslate.R                |only
 odfWeave/R/._odfWeave.R                    |only
 odfWeave/R/._odfWeaveControl.R             |only
 odfWeave/R/._pkgVersions.R                 |only
 odfWeave/R/._postproc.R                    |only
 odfWeave/R/._preproc.R                     |only
 odfWeave/R/._procstyles.R                  |only
 odfWeave/R/._tableStyles.R                 |only
 odfWeave/R/._xmlUtils.R                    |only
 odfWeave/R/odfWeave.R                      |   22 +++++++++++-----------
 odfWeave/inst/._doc                        |only
 odfWeave/inst/._examples                   |only
 odfWeave/inst/doc/._RnewsExample.pdf       |only
 odfWeave/inst/doc/._RnewsOut.pdf           |only
 odfWeave/inst/doc/._odfWeave.Rnw           |only
 odfWeave/inst/doc/._odfWeave.pdf           |only
 odfWeave/inst/doc/._odfWeave.tex           |only
 odfWeave/inst/doc/odfWeave.pdf             |binary
 odfWeave/inst/doc/odfWeave.tex             |    8 ++++----
 odfWeave/inst/examples/._Frink.png         |only
 odfWeave/inst/examples/._RunFormatting.R   |only
 odfWeave/inst/examples/._examples.odt      |only
 odfWeave/inst/examples/._formatting.odt    |only
 odfWeave/inst/examples/._formattingOut.odt |only
 odfWeave/inst/examples/._simple.odt        |only
 odfWeave/inst/examples/._testCases.odt     |only
 odfWeave/man/._PreProc.Rd                  |only
 odfWeave/man/._RweaveOdf.Rd                |only
 odfWeave/man/._adjustImageSize.Rd          |only
 odfWeave/man/._announce.Rd                 |only
 odfWeave/man/._listString.Rd               |only
 odfWeave/man/._matrixPaste.Rd              |only
 odfWeave/man/._odfCat.Rd                   |only
 odfWeave/man/._odfFigureCaption.Rd         |only
 odfWeave/man/._odfInsertPlot.Rd            |only
 odfWeave/man/._odfItemize.Rd               |only
 odfWeave/man/._odfPageBreak.Rd             |only
 odfWeave/man/._odfSetPageStyle.Rd          |only
 odfWeave/man/._odfTable.Rd                 |only
 odfWeave/man/._odfTableCaption.Rd          |only
 odfWeave/man/._odfTmpDir.Rd                |only
 odfWeave/man/._odfWeave.Rd                 |only
 odfWeave/man/._odfWeaveControl.Rd          |only
 odfWeave/man/._pkgVersions.Rd              |only
 odfWeave/man/._styles.Rd                   |only
 odfWeave/man/._tableStyles.Rd              |only
 80 files changed, 18 insertions(+), 18 deletions(-)

More information about odfWeave at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

Package Oarray updated to version 1.4-2 with previous version 1.4 dated 2007-10-03

Author: Jonathan Rougier
Title: Arrays with arbitrary offsets
Description: Generalise the starting point of the array index

Diff between Oarray versions 1.4 dated 2007-10-03 and 1.4-2 dated 2008-05-09

 DESCRIPTION     |    4 ++--
 R/Oarray.R      |   52 ++++++++++++++++++++++++++++++++++++++++++----------
 man/Oarray.Rd   |   28 +++++++++++++++++++++++-----
 man/internal.Rd |   10 ++++------
 4 files changed, 71 insertions(+), 23 deletions(-)

More information about Oarray at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

Package multipol updated to version 1.0-2 with previous version 1.0-1 dated 2008-04-22

Author: Robin K. S. Hankin
Title: multivariate polynomials
Description: Various utilities to manipulate multivariate polynomials

Diff between multipol versions 1.0-1 dated 2008-04-22 and 1.0-2 dated 2008-05-09

 DESCRIPTION         |    4 ++--
 R/multipol.R        |   11 +++++------
 man/Ops.multipol.Rd |   18 ++++++++++++------
 man/as.array.Rd     |    3 ++-
 man/trim.Rd         |    9 ++++-----
 5 files changed, 25 insertions(+), 20 deletions(-)

More information about multipol at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

Package modeltools updated to version 0.2-15 with previous version 0.2-14 dated 2007-09-26

Author: Torsten Hothorn, Friedrich Leisch, Achim Zeileis
Title: Tools and Classes for Statistical Models
Description: A collection of tools to deal with statistical models. The functionality is experimental and the user interface is likely to change in the future. The documentation is rather terse, but packages `coin' and `party' have some working examples. However, if you find the implemented ideas interesting we would be very interested in a discussion of this proposal. Contributions are more than welcome!

Diff between modeltools versions 0.2-14 dated 2007-09-26 and 0.2-15 dated 2008-05-09

 CHANGES               |   12 ++++++++++++
 DESCRIPTION           |    6 +++---
 NAMESPACE             |    4 ++--
 R/Generics.R          |    4 ++--
 R/Methods.R           |   27 ++++++++++++++++++++++-----
 R/NAhandling.R        |    6 +++---
 inst/CHANGES          |   12 ++++++++++++
 man/Generics.Rd       |    6 +++---
 man/ModelEnv-class.Rd |   16 +++++++++++++---
 tests/regtest.R       |    6 ++++++
 10 files changed, 78 insertions(+), 21 deletions(-)

More information about modeltools at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

Package flexmix updated to version 2.1-0 with previous version 2.0-2 dated 2008-03-26

Author: Friedrich Leisch and Bettina Gruen
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.

Diff between flexmix versions 2.0-2 dated 2008-03-26 and 2.1-0 dated 2008-05-09

 DESCRIPTION                      |    8 
 NAMESPACE                        |    2 
 NEWS                             |   10 
 R/allGenerics.R                  |    6 
 R/flexmix.R                      |    6 
 R/infocrit.R                     |    4 
 R/plot-flexmix.R                 |    4 
 R/plot.R                         |    4 
 R/refit.R                        |    9 
 inst/NEWS                        |   10 
 inst/doc/flexmix-intro.Rnw       |    4 
 inst/doc/flexmix-intro.pdf       | 1619 +++----
 inst/doc/regression-examples.Rnw |   14 
 inst/doc/regression-examples.pdf | 8007 +++++++++++++++++++--------------------
 man/FLXmclust.Rd                 |    6 
 man/flexmix.Rd                   |    6 
 man/patent.Rd                    |    4 
 man/plot-methods.Rd              |    2 
 man/posterior.Rd                 |   10 
 man/salmonellaTA98.Rd            |    4 
 tests/binomial.R                 |    4 
 tests/binomial.Rout.save         |    4 
 tests/restart.R                  |    4 
 23 files changed, 4886 insertions(+), 4865 deletions(-)

More information about flexmix at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

Package flexclust updated to version 0.99-0 with previous version 0.9-1 dated 2007-05-03

Author: Friedrich Leisch
Title: Flexible Cluster Algorithms
Description: The main function kcca implements a general framework for k-centroids cluster analysis supporting arbitrary distance/similarity measures and centroid computation. Further cluster methods include hard competitive learning, neural gas and QT clustering.

Diff between flexclust versions 0.9-1 dated 2007-05-03 and 0.99-0 dated 2008-05-09

 DESCRIPTION            |   10 ++---
 NAMESPACE              |   11 ++++--
 NEWS                   |   43 +++++++++++++++++++++++++
 R/barplot.R            |   55 +++++++++++++++++++++++++-------
 R/cclust.R             |   22 ++++++++-----
 R/info.R               |    7 ++--
 R/kcca.R               |   53 +++++++++++++++++++++++--------
 R/plot.R               |   79 ++++++++++++++++++++++++++++++++++++++---------
 R/predict.R            |    6 +--
 R/projAxes.R           |   14 ++++----
 R/qtclust.R            |   56 ++++++++++++++++++++++++---------
 R/tour.R               |only
 R/utils.R              |   82 ++++++++++++++++++++++++++++++++++++++-----------
 data/dentitio.txt      |    4 +-
 inst/CITATION          |   68 ++++++++++++++++++++++++++++++++++++++--
 inst/NEWS              |   43 +++++++++++++++++++++++++
 man/barplot-methods.Rd |   16 ++++-----
 man/cclust.Rd          |   10 +++--
 man/conversion.Rd      |    6 +--
 man/flxColors.Rd       |only
 man/info.Rd            |    2 -
 man/kcca.Rd            |   47 +++++++++++++++++++++++-----
 man/plot-methods.Rd    |   35 +++++++++++---------
 man/predict-methods.Rd |   16 ++++-----
 man/projAxes.Rd        |    4 +-
 man/qtclust.Rd         |   39 ++++++++++++++++++-----
 man/randomTour.Rd      |only
 man/stepFlexclust.Rd   |    6 ++-
 tests/randomTour.R     |only
 29 files changed, 570 insertions(+), 164 deletions(-)

More information about flexclust at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

Thu, 08 May 2008

Package vcd updated to version 1.0-8 with previous version 1.0-6 dated 2007-10-16

Author: David Meyer, Achim Zeileis, Kurt Hornik
Title: Visualizing Categorical Data
Description: Visualization techniques, data sets, summary and inference procedures aimed particularly at categorical data. Special emphasis is given to highly extensible grid graphics. The package was inspired by the book "Visualizing Categorical Data" by Michael Friendly.

Diff between vcd versions 1.0-6 dated 2007-10-16 and 1.0-8 dated 2008-05-08

 DESCRIPTION                                       |    6 
 R/Ord_plot.R                                      |    2 
 R/assoc.R                                         |    2 
 R/cd_plot.R                                       |    2 
 R/cotabplot.R                                     |   58 
 R/distplot.R                                      |    8 
 R/doubledeckerplot.R                              |    2 
 R/fourfold.R                                      |   26 
 R/goodfit.R                                       |   21 
 R/labeling.R                                      |   50 
 R/legends.R                                       |   26 
 R/mosaic.R                                        |    2 
 R/rootogram.R                                     |    2 
 R/sieve.R                                         |    2 
 R/spacings.R                                      |    2 
 R/spine.R                                         |    2 
 R/strucplot.R                                     |   34 
 R/structable.R                                    |   14 
 R/ternaryplot.R                                   |   14 
 demo/mondrian.R                                   |    3 
 inst/CITATION                                     |    3 
 inst/doc/Rplots.ps                                |39208 +++++++++++-----------
 inst/doc/Z.cls                                    |only
 inst/doc/bkde.png                                 |binary
 inst/doc/bkde2.png                                |binary
 inst/doc/class.png                                |binary
 inst/doc/hcl-colors-arthritis1.pdf                |   96 
 inst/doc/hcl-colors-pal-d1.pdf                    |    6 
 inst/doc/hcl-colors-pal-q1.pdf                    |    6 
 inst/doc/hcl-colors-pal-s1.pdf                    |    6 
 inst/doc/hcl-colors-seats1.pdf                    |    6 
 inst/doc/hcl-colors-votes1.pdf                    |    6 
 inst/doc/hcl-colors.aux                           |   18 
 inst/doc/hcl-colors.log                           |  282 
 inst/doc/hcl-colors.pdf                           | 3684 +-
 inst/doc/jss.bst                                  |only
 inst/doc/residual-shadings-Arthritis-classic1.pdf |    6 
 inst/doc/residual-shadings-Punishment-assoc1.pdf  |  346 
 inst/doc/residual-shadings-Punishment-mosaic1.pdf |  202 
 inst/doc/residual-shadings-alzheimer-plot1.pdf    |  106 
 inst/doc/residual-shadings-shadings.pdf           |    6 
 inst/doc/residual-shadings.aux                    |   10 
 inst/doc/residual-shadings.blg                    |    2 
 inst/doc/residual-shadings.log                    |  277 
 inst/doc/residual-shadings.pdf                    | 3609 +-
 inst/doc/strucplot-Arthritis.eps                  |   72 
 inst/doc/strucplot-Arthritis.pdf                  |   94 
 inst/doc/strucplot-Conditioningfig.eps            |   74 
 inst/doc/strucplot-Conditioningfig.pdf            |  100 
 inst/doc/strucplot-Expectedfig.eps                |   98 
 inst/doc/strucplot-Expectedfig.pdf                |  120 
 inst/doc/strucplot-Observedfig.eps                |   98 
 inst/doc/strucplot-Observedfig.pdf                |  104 
 inst/doc/strucplot-PreSex.eps                     |  104 
 inst/doc/strucplot-PreSex.pdf                     |  126 
 inst/doc/strucplot-Residualsfig.eps               |  226 
 inst/doc/strucplot-Residualsfig.pdf               |  248 
 inst/doc/strucplot-Titanic.pdf                    |    6 
 inst/doc/strucplot-UCBAdmissions.eps              |  216 
 inst/doc/strucplot-UCBAdmissions.pdf              |  238 
 inst/doc/strucplot-Variablesfig.pdf               |    6 
 inst/doc/strucplot-arthritisfig.eps               |   74 
 inst/doc/strucplot-arthritisfig.pdf               |   96 
 inst/doc/strucplot-artspinefig.eps                |   26 
 inst/doc/strucplot-artspinefig.pdf                |   32 
 inst/doc/strucplot-bundesligafig.pdf              |    6 
 inst/doc/strucplot-changeplotfig.eps              |  116 
 inst/doc/strucplot-changeplotfig.pdf              |  122 
 inst/doc/strucplot-cotabplotfig.eps               |   76 
 inst/doc/strucplot-cotabplotfig.pdf               |   86 
 inst/doc/strucplot-haireyefig1.pdf                |    6 
 inst/doc/strucplot-haireyefig2.pdf                |    6 
 inst/doc/strucplot-haireyefig3.pdf                |    6 
 inst/doc/strucplot-interpolatefig.pdf             |    6 
 inst/doc/strucplot-label1fig.pdf                  |    6 
 inst/doc/strucplot-label2fig.eps                  |  348 
 inst/doc/strucplot-label2fig.pdf                  |  394 
 inst/doc/strucplot-label3fig.eps                  |  352 
 inst/doc/strucplot-label3fig.pdf                  |  386 
 inst/doc/strucplot-listfig.pdf                    |    6 
 inst/doc/strucplot-ocdoubledecker.pdf             |    6 
 inst/doc/strucplot-ocmosaicnull.eps               |  119 
 inst/doc/strucplot-ocmosaicnull.pdf               |  141 
 inst/doc/strucplot-ocmosaicstage.eps              |   95 
 inst/doc/strucplot-ocmosaicstage.pdf              |  117 
 inst/doc/strucplot-ocpairs.pdf                    |    6 
 inst/doc/strucplot-pairsfig.pdf                   |    6 
 inst/doc/strucplot-recyclingfig.eps               |  136 
 inst/doc/strucplot-recyclingfig.pdf               |  166 
 inst/doc/strucplot-shading1fig.eps                |   20 
 inst/doc/strucplot-shading1fig.pdf                |   26 
 inst/doc/strucplot-sievefig.eps                   | 1330 
 inst/doc/strucplot-sievefig.pdf                   |  736 
 inst/doc/strucplot-spacingfig.eps                 |  104 
 inst/doc/strucplot-spacingfig.pdf                 |  126 
 inst/doc/strucplot-splitfig.eps                   |   98 
 inst/doc/strucplot-splitfig.pdf                   |  120 
 inst/doc/strucplot-ucbfig.eps                     |   20 
 inst/doc/strucplot-ucbfig.pdf                     |   26 
 inst/doc/strucplot-vcdlayout.pdf                  |    6 
 inst/doc/strucplot-viewportnamesfig.eps           |   56 
 inst/doc/strucplot-viewportnamesfig.pdf           |   70 
 inst/doc/strucplot.aux                            |   74 
 inst/doc/strucplot.log                            |  346 
 inst/doc/strucplot.pdf                            |binary
 inst/doc/vcd.bib                                  |only
 man/MSPatients.Rd                                 |    3 
 man/agreementplot.Rd                              |    3 
 man/assocstats.Rd                                 |    2 
 man/labeling_border.Rd                            |    3 
 man/oddsratio.Rd                                  |    2 
 man/strucplot.Rd                                  |    2 
 112 files changed, 28106 insertions(+), 28102 deletions(-)

More information about vcd at CRAN

posted at: 13:18 | path: /cran/updated | permanent link to this entry

Package tseries updated to version 0.10-15 with previous version 0.10-14 dated 2008-02-26

Author: Compiled by Adrian Trapletti
Title: Time series analysis and computational finance
Description: Package for time series analysis and computational finance

Diff between tseries versions 0.10-14 dated 2008-02-26 and 0.10-15 dated 2008-05-08

 ChangeLog     |    7 +++++++
 DESCRIPTION   |    6 +++---
 R/finance.R   |    2 +-
 inst/CITATION |    3 ++-
 4 files changed, 13 insertions(+), 5 deletions(-)

More information about tseries at CRAN

posted at: 13:18 | path: /cran/updated | permanent link to this entry

Package scatterplot3d updated to version 0.3-27 with previous version 0.3-26 dated 2008-05-02

Author: Uwe Ligges
Title: 3D Scatter Plot
Description: Plots a three dimensional (3D) point cloud.

Diff between scatterplot3d versions 0.3-26 dated 2008-05-02 and 0.3-27 dated 2008-05-08

 CHANGES          |    1 +
 DESCRIPTION      |    7 ++++---
 inst/CITATION    |    2 +-
 inst/doc/s3d.pdf |    6 +++---
 4 files changed, 9 insertions(+), 7 deletions(-)

More information about scatterplot3d at CRAN

posted at: 09:18 | path: /cran/updated | permanent link to this entry

Package RFreak updated to version 0.2-1 with previous version 0.2-0 dated 2007-12-24

Author: Robin Nunkesser
Title: R/FrEAK interface
Description: An R interface to a modified version of the Free Evolutionary Algorithm Kit FrEAK. FrEAK is a toolkit written in Java to design and analyze evolutionary algorithms. Both the R interface and an extended version of FrEAK are contained in the RFreak package. For more information on FrEAK see http://sourceforge.net/projects/freak427/.

Diff between RFreak versions 0.2-0 dated 2007-12-24 and 0.2-1 dated 2008-05-08

 DESCRIPTION                                       |   13 
 inst/java/resource/freak/gui/help/footnode.html   |    2 
 inst/java/resource/freak/gui/help/index.html      |  482 +++++++++++-----------
 inst/java/resource/freak/gui/help/node1.html      |    4 
 inst/java/resource/freak/gui/help/node3.html      |  268 ++++++------
 inst/java/resource/freak/gui/help/node4.html      |  284 ++++++------
 inst/java/resource/freak/gui/help/node5.html      |  186 ++++----
 inst/java/resource/freak/gui/help/node6.html      |  375 ++++++++---------
 inst/java/resource/freak/gui/help/node7.html      |    3 
 inst/java/resource/freak/gui/help/node8.html      |    3 
 inst/java/resource/freak/gui/help/usersguide.html |   38 -
 inst/java/run.cmd                                 |    2 
 man/RFreak-package.Rd                             |    9 
 13 files changed, 834 insertions(+), 835 deletions(-)

More information about RFreak at CRAN

posted at: 09:18 | path: /cran/updated | permanent link to this entry

New package BCE with initial version 1.1
Package: BCE
Version: 1.1
Title: Bayesian composition estimator: estimating sample (taxonomic) composition from biomarker data
Author: Karel Van den Meersche , Karline Soetaert
Maintainer: Karel Van den Meersche
Depends: R (>= 2.01), quadprog
Description: Function to estimates taxonomic compositions from biomarker data, using a Bayesian approach.
License: GPL
LazyData: yes
Packaged: Thu May 8 04:31:09 2008; theussl

More information about BCE at CRAN

posted at: 09:18 | path: /cran/new | permanent link to this entry

New package tframePlus with initial version 2008.5-1
Package: tframePlus
Title: Time Frame coding kernel extensions
Description: Extensions and additional tframe utilities.
Depends: R (>= 2.5.0), tframe
Imports: tframe
Suggests: zoo, its
Version: 2008.5-1
Date: 2008-05-02
LazyLoad: yes
License: GPL-2 | file LICENSE
Author: Paul Gilbert
Maintainer: Paul Gilbert
URL: http://www.bank-banque-canada.ca/pgilbert
Packaged: Fri May 2 10:24:00 2008; paul

More information about tframePlus at CRAN

posted at: 05:18 | path: /cran/new | permanent link to this entry

Package tframe updated to version 2008.5-1 with previous version 2007.5-3 dated 2007-07-13

Author: Paul Gilbert
Title: Time Frame coding kernel
Description: Functions for writing code that is independent of the way time is represented. See ?tframe.Intro for more details.

Diff between tframe versions 2007.5-3 dated 2007-07-13 and 2008.5-1 dated 2008-05-08

 tframe-2007.5-3/tframe/INDEX               |only
 tframe-2007.5-3/tframe/R/its.R             |only
 tframe-2007.5-3/tframe/R/zoo.R             |only
 tframe-2007.5-3/tframe/help                |only
 tframe-2007.5-3/tframe/tests/zoo.R         |only
 tframe-2007.5-3/tframe/tframe-manual.pdf   |only
 tframe-2008.5-1/tframe/DESCRIPTION         |    8 
 tframe-2008.5-1/tframe/NAMESPACE           |   21 -
 tframe-2008.5-1/tframe/NEWS                |    9 
 tframe-2008.5-1/tframe/R/tframe.R          |    6 
 tframe-2008.5-1/tframe/inst/doc/tframe.pdf |  398 ++++++++++++++---------------
 tframe-2008.5-1/tframe/man/tframe.Rd       |    8 
 tframe-2008.5-1/tframe/man/tfstart.Rd      |   24 -
 tframe-2008.5-1/tframe/man/tfwindow.Rd     |    4 
 tframe-2008.5-1/tframe/tests/utils.R       |   24 +
 15 files changed, 240 insertions(+), 262 deletions(-)

More information about tframe at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

Package ljr updated to version 1.2-0 with previous version 1.1-0 dated 2008-02-24

Author: Michal Czajkowski, Ryan Gill, Greg Rempala
Title: Logistic Joinpoint Regression
Description: Fits and tests logistic joinpoint models.

Diff between ljr versions 1.1-0 dated 2008-02-24 and 1.2-0 dated 2008-05-08

 ljr-1.1-0/ljr/R/ljr02.R           |only
 ljr-1.1-0/ljr/R/ljr12.R           |only
 ljr-1.1-0/ljr/R/ljr2.R            |only
 ljr-1.1-0/ljr/R/ljr22.R           |only
 ljr-1.1-0/ljr/R/ljrb2.R           |only
 ljr-1.1-0/ljr/R/ljrf2.R           |only
 ljr-1.1-0/ljr/man/ljr02.rd        |only
 ljr-1.1-0/ljr/man/ljr12.rd        |only
 ljr-1.1-0/ljr/man/ljr2.rd         |only
 ljr-1.1-0/ljr/man/ljr22.rd        |only
 ljr-1.1-0/ljr/man/ljrb2.rd        |only
 ljr-1.1-0/ljr/man/ljrf2.rd        |only
 ljr-1.1-0/ljr/src/backward2.c     |only
 ljr-1.1-0/ljr/src/fillfreeint.c   |only
 ljr-1.1-0/ljr/src/forward2.c      |only
 ljr-1.1-0/ljr/src/ljr2.c          |only
 ljr-1.1-0/ljr/src/ljr22.c         |only
 ljr-1.1-0/ljr/src/ljr2rmint.c     |only
 ljr-1.1-0/ljr/src/ljr2rmtm.c      |only
 ljr-1.1-0/ljr/src/test02.c        |only
 ljr-1.1-0/ljr/src/test12.c        |only
 ljr-1.2-0/ljr/DESCRIPTION         |   18 +++++++++---------
 ljr-1.2-0/ljr/R/firstlib.R        |    2 +-
 ljr-1.2-0/ljr/R/ljr0.R            |    3 ++-
 ljr-1.2-0/ljr/R/ljr01.R           |    3 ++-
 ljr-1.2-0/ljr/R/ljr1.R            |   14 +++++++-------
 ljr-1.2-0/ljr/R/ljr11.R           |    3 ++-
 ljr-1.2-0/ljr/R/ljrb.R            |    3 ++-
 ljr-1.2-0/ljr/R/ljrf.R            |    3 ++-
 ljr-1.2-0/ljr/R/ljrjk.R           |    5 +++--
 ljr-1.2-0/ljr/R/ljrk.R            |    3 ++-
 ljr-1.2-0/ljr/R/ljrkk.R           |    3 ++-
 ljr-1.2-0/ljr/data                |only
 ljr-1.2-0/ljr/man/kcm.rd          |only
 ljr-1.2-0/ljr/man/ljr0.rd         |   28 ++++++----------------------
 ljr-1.2-0/ljr/man/ljr01.rd        |   28 ++++++----------------------
 ljr-1.2-0/ljr/man/ljr1.rd         |   29 ++++++-----------------------
 ljr-1.2-0/ljr/man/ljr11.rd        |   30 +++++++-----------------------
 ljr-1.2-0/ljr/man/ljrb.rd         |   29 +++++++----------------------
 ljr-1.2-0/ljr/man/ljrf.rd         |   29 +++++++----------------------
 ljr-1.2-0/ljr/man/ljrjk.rd        |   27 ++++++---------------------
 ljr-1.2-0/ljr/man/ljrk.rd         |   27 +++++----------------------
 ljr-1.2-0/ljr/man/ljrkk.rd        |   28 ++++++----------------------
 ljr-1.2-0/ljr/src/fillfixed.c     |    2 ++
 ljr-1.2-0/ljr/src/fillfixedrm.c   |    2 ++
 ljr-1.2-0/ljr/src/fillfreermint.c |only
 ljr-1.2-0/ljr/src/rgi.c           |    3 ++-
 47 files changed, 96 insertions(+), 226 deletions(-)

More information about ljr at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

Package epiR updated to version 0.9-6 with previous version 0.9-5 dated 2008-04-29

Author: Mark Stevenson with contributions from Telmo Nunes, Javier Sanchez, and Ron Thornton.
Title: Functions for analysing epidemiological data
Description: A package for analysing epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.

Diff between epiR versions 0.9-5 dated 2008-04-29 and 0.9-6 dated 2008-05-08

 DESCRIPTION    |    6 
 R/epi.ccc.r    |    2 
 doc/epiR.pdf   | 5775 ++++++++++++++++++++++++++++-----------------------------
 man/epi.ccc.Rd |   32 
 4 files changed, 2903 insertions(+), 2912 deletions(-)

More information about epiR at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

Package ape updated to version 2.2 with previous version 2.1-3 dated 2008-03-21

Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Gangolf Jobb, Christoph Heibl, Vincent Lefort, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Korbinian Strimmer, Damien de Vienne
Title: Analyses of Phylogenetics and Evolution
Description: ape provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading nucleotide sequences, and several tools such as Mantel's test, computation of minimum spanning tree, the population parameter theta based on various approaches, nucleotide diversity, generalized skyline plots, estimation of absolute evolutionary rates and clock-like trees using mean path lengths, non-parametric rate smoothing and penalized likelihood, classifying genes in trees using the Klastorin-Misawa-Tajima approach. Phylogeny estimation can be done with the NJ, BIONJ, ME, and ML methods.

Diff between ape versions 2.1-3 dated 2008-03-21 and 2.2 dated 2008-05-08

 Changes                |   48 ++++++++
 DESCRIPTION            |   13 +-
 R/DNA.R                |    9 -
 R/PGLS.R               |   84 +++++++++++++++
 R/chronopl.R           |  265 ++++++++++++++++++++++++++++++++++---------------
 R/cophyloplot.R        |only
 R/dist.topo.R          |  168 ++++++++++++++++++-------------
 R/drop.tip.R           |   22 ++--
 R/multi2di.R           |    4 
 R/plot.phylo.R         |    9 -
 R/plotPhyloCoor.R      |only
 R/read.dna.R           |    8 -
 R/rtree.R              |   41 +++----
 R/subtreeplot.R        |only
 R/subtrees.R           |only
 R/summary.phylo.R      |    3 
 R/zoom.R               |    8 -
 Thanks                 |   22 ++--
 inst/doc/MoranI.pdf    |binary
 man/ape-internal.Rd    |    2 
 man/boot.phylo.Rd      |    9 +
 man/chronopl.Rd        |   57 ++++++++--
 man/compar.cheverud.Rd |    2 
 man/consensus.Rd       |   13 ++
 man/cophyloplot.Rd     |only
 man/corBlomberg.Rd     |only
 man/corClasses.Rd      |   29 +++--
 man/corPagel.Rd        |only
 man/plot.phylo.Rd      |   10 +
 man/subtreeplot.Rd     |only
 man/subtrees.Rd        |only
 31 files changed, 579 insertions(+), 247 deletions(-)

More information about ape at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

Package TSpadi updated to version 2008.5-1 with previous version 2007.10-1 dated 2007-11-03

Author: Paul Gilbert
Title: TSdbi Interface to PADI Time Series Server (for e.g. Fame)
Description: Provides methods for generics in the TSdbi package to connect through a protocol for application database interface (PADI) to a time series database (e.g. Fame).

Diff between TSpadi versions 2007.10-1 dated 2007-11-03 and 2008.5-1 dated 2008-05-08

 DESCRIPTION             |    9 +++++----
 NEWS                    |    5 +++++
 inst/doc/TSpadiFame.pdf |binary
 3 files changed, 10 insertions(+), 4 deletions(-)

More information about TSpadi at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

Package TSdbi updated to version 2008.5-1 with previous version 2007.10-1 dated 2007-10-27

Author: Paul Gilbert
Title: Time Series Database Interface
Description: TSdbi provides an common interface to time series databases.

Diff between TSdbi versions 2007.10-1 dated 2007-10-27 and 2008.5-1 dated 2008-05-08

 DESCRIPTION        |    8 ++++----
 NAMESPACE          |    3 ++-
 NEWS               |   10 +++++++++-
 R/TSdbi.R          |   14 ++++++++------
 R/TSquery.R        |only
 S4checks.R.tex     |only
 inst/doc/TSdbi.pdf |binary
 man/TSquery.Rd     |only
 tests/S4checks.R   |only
 9 files changed, 23 insertions(+), 12 deletions(-)

More information about TSdbi at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

Package TSSQLite updated to version 2008.5-1 with previous version 2007.10-1 dated 2007-11-03

Author: Paul Gilbert
Title: Time Series Database Interface extentions for SQLite
Description: TSSQLite provides a SQLite interface for TSdbi.

Diff between TSSQLite versions 2007.10-1 dated 2007-11-03 and 2008.5-1 dated 2008-05-08

 DESCRIPTION           |   10 +++++-----
 Rplots.pdf            |only
 inst/doc/TSSQLite.pdf |binary
 test                  |binary
 4 files changed, 5 insertions(+), 5 deletions(-)

More information about TSSQLite at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

Package TSMySQL updated to version 2008.5-1 with previous version 2007.10-1 dated 2007-11-05

Author: Paul Gilbert
Title: Time Series Database Interface extensions for MySQL
Description: TSMySQL provides a MySQL interface for TSdbi.

Diff between TSMySQL versions 2007.10-1 dated 2007-11-05 and 2008.5-1 dated 2008-05-08

 DESCRIPTION          |   10 +++++-----
 Rplots.pdf           |only
 S4checks.R.tex       |only
 inst/doc/TSMySQL.pdf |binary
 4 files changed, 5 insertions(+), 5 deletions(-)

More information about TSMySQL at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

New package RCurl with initial version 0.9-2
Package: RCurl
Version: 0.9-2
Title: HTTP request interface
Author: Duncan Temple Lang
SystemRequirements: curl (version 7.12.0 or higher) http://curl.haxx.se
Maintainer: Duncan Temple Lang
Description: The package allows one to compose HTTP requests to fetch URIs, post forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting SSL/HTTPS, cookies, redirects, authentication, etc.
License: BSD
LazyLoad: true
Depends: methods
URL: http://www.omegahat.org/RCurl
Limitations: One doesn't yet have full control over the contents of a POST form such as specifying files, content type. Error handling uses a single global variable at present.
Note: This will be used generally to communicate with HTTP servers and specifically in the SOAP package, HTML forms and for accessing data on Web sites that require more state information than simply URL access (e.g. cookies).
Check: To run R CMD check, one really needs network access. It is an HTTP client! This can be problematic as a Web site may be down when you run but the real tests are important.
Packaged: Thu May 8 02:28:19 2008; duncan

More information about RCurl at CRAN

posted at: 05:18 | path: /cran/new | permanent link to this entry

Package GPArotation updated to version 2008.05-1 with previous version 2007.06-1 dated 2007-06-10

Author: Coen Bernaards and Robert Jennrich
Title: GPA Factor Rotation
Description: Gradient Projection Algorithm Rotation for Factor Analysis. See ?GPArotation.Intro for more details.

Diff between GPArotation versions 2007.06-1 dated 2007-06-10 and 2008.05-1 dated 2008-05-08

 GPArotation-2007.06-1/GPArotation/GPArotation-manual.pdf   |only
 GPArotation-2007.06-1/GPArotation/INDEX                    |only
 GPArotation-2007.06-1/GPArotation/help                     |only
 GPArotation-2008.05-1/GPArotation/DESCRIPTION              |    8 ++++----
 GPArotation-2008.05-1/GPArotation/LICENSE                  |    2 +-
 GPArotation-2008.05-1/GPArotation/NAMESPACE                |    9 ++++++---
 GPArotation-2008.05-1/GPArotation/NEWS                     |    9 +++++++++
 GPArotation-2008.05-1/GPArotation/R/GPArotation.R          |    4 ++--
 GPArotation-2008.05-1/GPArotation/R/echelon.R              |only
 GPArotation-2008.05-1/GPArotation/R/eiv.R                  |    4 ++--
 GPArotation-2008.05-1/GPArotation/Rplots.pdf               |only
 GPArotation-2008.05-1/GPArotation/inst/doc/GPArotation.pdf |binary
 GPArotation-2008.05-1/GPArotation/man/GPA.Rd               |    2 +-
 GPArotation-2008.05-1/GPArotation/man/echelon.Rd           |only
 GPArotation-2008.05-1/GPArotation/man/eiv.Rd               |    5 +++--
 GPArotation-2008.05-1/GPArotation/man/rotations.Rd         |    9 ++++++---
 16 files changed, 34 insertions(+), 18 deletions(-)

More information about GPArotation at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

Package EMD updated to version 1.1.0 with previous version 1.0.0 dated 2008-03-29

Author: Donghoh Kim , Hee-Seok Oh
Title: Empirical Mode Decomposition and Hilbert Spectral Analysis
Description: This package carries out empirical mode decompostion and Hilbert spectral analysis.

Diff between EMD versions 1.0.0 dated 2008-03-29 and 1.1.0 dated 2008-05-08

 DESCRIPTION    |    8 ++++----
 R/EMD1d.R      |    6 +++++-
 man/emd2d.Rd   |    2 +-
 man/extrema.Rd |    6 +++---
 4 files changed, 13 insertions(+), 9 deletions(-)

More information about EMD at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

Wed, 07 May 2008

Package qAnalyst updated to version 0.5.2 with previous version 0.5.1 dated 2008-02-19

Author: Andrea Spano' and Giorgio Spedicato
Title: Variables and Attributes Control Charts
Description: qAnalyst performs: control charts for variables and attributes according to Douglas C. Montgomery Introduction to Statistical Quality Control book, Capability analysis for normal and non - normal distributions and Distributions Identification

Diff between qAnalyst versions 0.5.1 dated 2008-02-19 and 0.5.2 dated 2008-05-07

 DESCRIPTION             |    8 ++++----
 R/capabilityNormal.R    |   10 +++++-----
 R/getParameterFun.R     |    4 ++--
 R/spc.R                 |    2 +-
 README                  |    4 ++++
 man/capabilityNormal.Rd |   34 +++++++++++++++++++---------------
 man/spc.Rd              |    5 ++---
 7 files changed, 37 insertions(+), 30 deletions(-)

More information about qAnalyst at CRAN

posted at: 13:19 | path: /cran/updated | permanent link to this entry

New package singlecase with initial version 0.1
Package: singlecase
Type: Package
Title: statistical tests for single case studies in neuropsychology
Version: 0.1
Date: 2008-05-07
Author: Matthieu Dubois
Maintainer: Matthieu Dubois
Description: The singlecase package implements various functions for the single-case research in neuropsychology. Currently, the functions that are implemented were all originally developed by John Crawford, Paul Garthwaite and colleagues. These functions mainly deal with the comparison of a patient's test score (or score difference) to a control or normative sample. These methods also provide a point estimate of the percentage of the population that would obtain a more extreme score (or score difference) and, for some problems, an accompanying interval estimate (i.e., confidence limits) on this percentage.
License: GPL version 2 or newer
URL: http://www.code.ucl.ac.be/MatthieuDubois/r_code.html
Packaged: Wed May 7 16:55:50 2008; hornik

More information about singlecase at CRAN

posted at: 13:19 | path: /cran/new | permanent link to this entry

Package neuralnet updated to version 1.1 with previous version 1.0 dated 2008-04-15

Author: Stefan Fritsch , Frauke Guenther , following earlier work by Marc Suling
Title: Training of neural networks
Description: Training of neural networks using the Resilient Backpropagation with (Riedmiller, 1994) or without Weightbacktracking (Riedmiller, 1993) or the modified globally convergent version by Anastasiadis et. al. (2005). The package allows flexible settings through custom-choice of error- and activation-function. Furthermore the calculation of generalized weights (Intrator O & Intrator N, 1993) is implemented.

Diff between neuralnet versions 1.0 dated 2008-04-15 and 1.1 dated 2008-05-07

 DESCRIPTION              |    8 ++++----
 R/plot.nn.r              |    2 +-
 man/neuralnet-package.Rd |    4 ++--
 3 files changed, 7 insertions(+), 7 deletions(-)

More information about neuralnet at CRAN

posted at: 13:19 | path: /cran/updated | permanent link to this entry

Package gnm updated to version 0.9-4 with previous version 0.9-3 dated 2007-09-10

Author: Heather Turner and David Firth
Title: Generalized Nonlinear Models
Description: Functions to specify and fit generalized nonlinear models, including models with multiplicative interaction terms such as the UNIDIFF model from sociology and the AMMI model from crop science, and many others. Over-parameterized representations of models are used throughout; functions are provided for inference on estimable parameter combinations, as well as standard methods for diagnostics etc.

Diff between gnm versions 0.9-3 dated 2007-09-10 and 0.9-4 dated 2008-05-07

 gnm-0.9-3/gnm/R/DrefVariables.R           |only
 gnm-0.9-3/gnm/inst/CHANGES                |only
 gnm-0.9-3/gnm/inst/doc/gnmOverview.Rnw    |only
 gnm-0.9-3/gnm/man/Log.Rd                  |only
 gnm-0.9-3/gnm/man/Logit.Rd                |only
 gnm-0.9-3/gnm/man/Raise.Rd                |only
 gnm-0.9-4/gnm/.directory                  |only
 gnm-0.9-4/gnm/DESCRIPTION                 |   28 
 gnm-0.9-4/gnm/NAMESPACE                   |   13 
 gnm-0.9-4/gnm/R/Const.R                   |   10 
 gnm-0.9-4/gnm/R/Diag.R                    |   11 
 gnm-0.9-4/gnm/R/Exp.R                     |    3 
 gnm-0.9-4/gnm/R/Inv.R                     |   17 
 gnm-0.9-4/gnm/R/Log.R                     |   17 
 gnm-0.9-4/gnm/R/Logit.R                   |   17 
 gnm-0.9-4/gnm/R/Mult.R                    |    6 
 gnm-0.9-4/gnm/R/MultHomog.R               |   21 
 gnm-0.9-4/gnm/R/Nonlin.R                  |    6 
 gnm-0.9-4/gnm/R/Raise.R                   |   17 
 gnm-0.9-4/gnm/R/Symm.R                    |   17 
 gnm-0.9-4/gnm/R/anova.gnm.R               |   40 
 gnm-0.9-4/gnm/R/asGnm.glm.R               |    1 
 gnm-0.9-4/gnm/R/asGnm.lm.R                |    1 
 gnm-0.9-4/gnm/R/checkCall.R               |   12 
 gnm-0.9-4/gnm/R/cholInv.R                 |  156 -
 gnm-0.9-4/gnm/R/cholInv1.R                |   68 
 gnm-0.9-4/gnm/R/confint.gnm.R             |   26 
 gnm-0.9-4/gnm/R/confint.profile.gnm.R     |   50 
 gnm-0.9-4/gnm/R/fitted.gnm.R              |only
 gnm-0.9-4/gnm/R/getData.R                 |   12 
 gnm-0.9-4/gnm/R/gnm.R                     |   75 
 gnm-0.9-4/gnm/R/gnmStart.R                |    8 
 gnm-0.9-4/gnm/R/gnmTerms.R                |   25 
 gnm-0.9-4/gnm/R/gnmTools.R                |   23 
 gnm-0.9-4/gnm/R/hashSplit.R               |   42 
 gnm-0.9-4/gnm/R/hatvalues.gnm.R           |    4 
 gnm-0.9-4/gnm/R/instances.R               |   22 
 gnm-0.9-4/gnm/R/nonlinTerms.R             |  421 +--
 gnm-0.9-4/gnm/R/ofInterest.R              |    6 
 gnm-0.9-4/gnm/R/ofInterestReplacement.R   |   22 
 gnm-0.9-4/gnm/R/parameters.R              |    4 
 gnm-0.9-4/gnm/R/pickCoef.R                |   48 
 gnm-0.9-4/gnm/R/plot.gnm.R                |   96 
 gnm-0.9-4/gnm/R/plot.profile.gnm.R        |   42 
 gnm-0.9-4/gnm/R/predict.gnm.R             |   94 
 gnm-0.9-4/gnm/R/print.gnm.R               |    7 
 gnm-0.9-4/gnm/R/print.profile.gnm.R       |   29 
 gnm-0.9-4/gnm/R/print.summary.gnm.R       |   18 
 gnm-0.9-4/gnm/R/profile.gnm.R             |  276 +-
 gnm-0.9-4/gnm/R/qrSolve.R                 |   78 
 gnm-0.9-4/gnm/R/residuals.gnm.R           |   12 
 gnm-0.9-4/gnm/R/rstandard.gnm.R           |    2 
 gnm-0.9-4/gnm/R/sumExpression.R           |   14 
 gnm-0.9-4/gnm/R/termPredictors.gnm.R      |   11 
 gnm-0.9-4/gnm/R/weighted.MM.R             |   22 
 gnm-0.9-4/gnm/R/weights.gnm.R             |only
 gnm-0.9-4/gnm/R/zzz.R                     |    6 
 gnm-0.9-4/gnm/demo/gnm.R                  |   64 
 gnm-0.9-4/gnm/inst/.directory             |only
 gnm-0.9-4/gnm/inst/CITATION               |   32 
 gnm-0.9-4/gnm/inst/NEWS                   |only
 gnm-0.9-4/gnm/inst/doc/.directory         |only
 gnm-0.9-4/gnm/inst/doc/gnmOverview.pdf    | 3630 ++++++++++++++----------------
 gnm-0.9-4/gnm/man/Const.Rd                |   78 
 gnm-0.9-4/gnm/man/Exp.Rd                  |   94 
 gnm-0.9-4/gnm/man/Inv.Rd                  |  100 
 gnm-0.9-4/gnm/man/confint.gnm.Rd          |  212 -
 gnm-0.9-4/gnm/man/gnm.Rd                  |   20 
 gnm-0.9-4/gnm/man/instances.Rd            |   90 
 gnm-0.9-4/gnm/man/model.matrix.gnm.Rd     |   64 
 gnm-0.9-4/gnm/man/nonlin.function.Rd      |  353 +-
 gnm-0.9-4/gnm/man/ofInterest.Rd           |  130 -
 gnm-0.9-4/gnm/man/parameters.Rd           |   66 
 gnm-0.9-4/gnm/man/pickCoef.Rd             |  122 -
 gnm-0.9-4/gnm/man/predict.gnm.Rd          |only
 gnm-0.9-4/gnm/man/profile.gnm.Rd          |  362 +-
 gnm-0.9-4/gnm/man/qrSolve.Rd              |  122 -
 gnm-0.9-4/gnm/tests/RC.Rout.save          |   94 
 gnm-0.9-4/gnm/tests/RChomog.Rout.save     |   96 
 gnm-0.9-4/gnm/tests/biplot.Rout.save      |   70 
 gnm-0.9-4/gnm/tests/diagonalRef.Rout.save |  100 
 gnm-0.9-4/gnm/tests/gammi.Rout.save       |   76 
 gnm-0.9-4/gnm/tests/nls.R                 |   18 
 gnm-0.9-4/gnm/tests/stereotype.Rout.save  |   96 
 gnm-0.9-4/gnm/tests/unidiff.Rout.save     |   84 
 85 files changed, 4118 insertions(+), 4011 deletions(-)

More information about gnm at CRAN

posted at: 13:18 | path: /cran/updated | permanent link to this entry

Package gRc updated to version 0.2.1 with previous version 0.2.0 dated 2008-04-25

Author: Søren Højsgaard Steffen L. Lauritzen
Title: Inference in Graphical Gaussian Models with Edge and Vertex Symmetries
Description: Estimation, model selection and other aspects of statistical inference in Graphical Gaussian models with edge and vertex symmetries (Graphical Gaussian models with colours)

Diff between gRc versions 0.2.0 dated 2008-04-25 and 0.2.1 dated 2008-05-07

 gRc-0.2.0/gRc/src/rconipm.c               |only
 gRc-0.2.1/gRc/ChangeLog                   |    6 +
 gRc-0.2.1/gRc/DESCRIPTION                 |    4 
 gRc-0.2.1/gRc/R/getScoreAndInformation4.R |    1 
 gRc-0.2.1/gRc/R/rcox-Scoring.R            |    7 +
 gRc-0.2.1/gRc/R/sets-SetOp-Lists.R        |   44 -------
 gRc-0.2.1/gRc/R/switchThetaK4.R           |   84 +++++++++++++++
 gRc-0.2.1/gRc/R/xxx2yyy.R                 |   20 +--
 gRc-0.2.1/gRc/src/clevertrace.c           |  118 ++++++++++-----------
 gRc-0.2.1/gRc/src/rconipm2.c              |only
 gRc-0.2.1/gRc/src/shd_utils.c             |  167 +++++++++++++++++++++++-------
 gRc-0.2.1/gRc/src/shd_utils.h             |    5 
 12 files changed, 304 insertions(+), 152 deletions(-)

More information about gRc at CRAN

posted at: 13:18 | path: /cran/updated | permanent link to this entry

Package gRain updated to version 0.3.2 with previous version 0.3.1 dated 2008-05-02

Author: Søren Højsgaard
Title: Graphical Independence Networks
Description: A package for probability propagation in graphical independence networks, also known as probabilistic expert systems (which includes Bayesian networks as a special case).

Diff between gRain versions 0.3.1 dated 2008-05-02 and 0.3.2 dated 2008-05-07

 ChangeLog                |    6 ++++++
 DESCRIPTION              |    4 ++--
 inst/doc/gRain-intro.pdf |binary
 3 files changed, 8 insertions(+), 2 deletions(-)

More information about gRain at CRAN

posted at: 13:18 | path: /cran/updated | permanent link to this entry

New package empiricalBayes with initial version 2.0
Bundle: empiricalBayes
Contains: HighProbability localFDR
Version: 2.0
Date: 2008-03-05
Author: David R. Bickel , Zahra Montazeri
Maintainer: David. R. Bickel
BundleDescription: EmpiricalBayes provides a simple solution to the extreme multiple testing problem by estimating local false discovery rates. It contains two packages, localFDR and HighProbability. Given a vector of p- values, localFDR estimates local false discovery rates and HighProbability determines which p-values are low enough that their alternative hypotheses can be considered highly probable .
License: Mozilla Public License 1.1
Packaged: Wed May 7 16:51:03 2008; hornik

More information about empiricalBayes at CRAN

posted at: 13:18 | path: /cran/new | permanent link to this entry

Package XML updated to version 1.95-1 with previous version 1.93-2 dated 2007-10-03

Author: Duncan Temple Lang (duncan@wald.ucdavis.edu)
Title: Tools for parsing and generating XML within R and S-Plus.
Description: Parsing facilities for arbitrary XML files, DTDs and HTML, offering both event and tree based parsers which are customizable with R functions.

Diff between XML versions 1.93-2 dated 2007-10-03 and 1.95-1 dated 2008-05-07

 XML-1.93-2/XML/inst/Docs/MathML.pdf           |only
 XML-1.93-2/XML/inst/Docs/Outline.pdf          |only
 XML-1.93-2/XML/inst/Docs/Tour.pdf             |only
 XML-1.93-2/XML/inst/Docs/WritingXML.html      |only
 XML-1.93-2/XML/inst/Docs/description.pdf      |only
 XML-1.93-2/XML/inst/Docs/manual.pdf           |only
 XML-1.93-2/XML/inst/examples/obis.R           |only
 XML-1.95-1/XML/Changes                        |  101 
 XML-1.95-1/XML/DESCRIPTION                    |    4 
 XML-1.95-1/XML/INSTALL                        |    2 
 XML-1.95-1/XML/NAMESPACE                      |   39 
 XML-1.95-1/XML/R/XMLClasses.R                 |  232 +
 XML-1.95-1/XML/R/accessors.R                  |  123 
 XML-1.95-1/XML/R/catalog.R                    |   74 
 XML-1.95-1/XML/R/createNode.R                 |   11 
 XML-1.95-1/XML/R/error.R                      |only
 XML-1.95-1/XML/R/hashTree.R                   |   15 
 XML-1.95-1/XML/R/htmlParse.R                  |   11 
 XML-1.95-1/XML/R/parseDTD.R                   |   10 
 XML-1.95-1/XML/R/tree.R                       |    2 
 XML-1.95-1/XML/R/xmlErrorEnums.R              |only
 XML-1.95-1/XML/R/xmlEventParse.R              |   24 
 XML-1.95-1/XML/R/xmlInternalSource.R          |  104 
 XML-1.95-1/XML/R/xmlNodes.R                   |  337 +
 XML-1.95-1/XML/R/xmlTree.R                    |   44 
 XML-1.95-1/XML/R/xmlTreeParse.R               |   94 
 XML-1.95-1/XML/R/zzz.R                        |    2 
 XML-1.95-1/XML/configure                      | 4956 ++++++++++----------------
 XML-1.95-1/XML/configure.in                   |   12 
 XML-1.95-1/XML/inst/exampleData/Rsource.xml   |    7 
 XML-1.95-1/XML/inst/exampleData/entity.xml-   |only
 XML-1.95-1/XML/inst/exampleData/iTunes.plist  |only
 XML-1.95-1/XML/inst/exampleData/largeText.xml |only
 XML-1.95-1/XML/inst/exampleData/same.xml      |only
 XML-1.95-1/XML/inst/exampleData/utf.xml       |only
 XML-1.95-1/XML/inst/examples/CIS.R            |only
 XML-1.95-1/XML/inst/examples/DiGIR.R          |only
 XML-1.95-1/XML/inst/examples/catalog.R        |only
 XML-1.95-1/XML/inst/examples/event.R          |    6 
 XML-1.95-1/XML/inst/examples/itunesSax.R      |only
 XML-1.95-1/XML/inst/examples/mi1.R            |only
 XML-1.95-1/XML/man/XMLInternalDocument.Rd     |    2 
 XML-1.95-1/XML/man/addChildren.Rd             |   49 
 XML-1.95-1/XML/man/addSibling.Rd              |only
 XML-1.95-1/XML/man/catalogResolve.Rd          |   24 
 XML-1.95-1/XML/man/catalogs.Rd                |only
 XML-1.95-1/XML/man/docName.Rd                 |only
 XML-1.95-1/XML/man/dtdIsAttribute.Rd          |    4 
 XML-1.95-1/XML/man/free.Rd                    |    4 
 XML-1.95-1/XML/man/getNodeSet.Rd              |   59 
 XML-1.95-1/XML/man/getXMLErrors.Rd            |only
 XML-1.95-1/XML/man/newXMLDoc.Rd               |   63 
 XML-1.95-1/XML/man/parseDTD.Rd                |    5 
 XML-1.95-1/XML/man/processXInclude.Rd         |only
 XML-1.95-1/XML/man/saveXML.Rd                 |   10 
 XML-1.95-1/XML/man/xmlAttributeType.Rd        |    2 
 XML-1.95-1/XML/man/xmlAttrs.Rd                |    5 
 XML-1.95-1/XML/man/xmlChildren.Rd             |    8 
 XML-1.95-1/XML/man/xmlEventParse.Rd           |   58 
 XML-1.95-1/XML/man/xmlFlatListTree.Rd         |    2 
 XML-1.95-1/XML/man/xmlGetAttr.Rd              |   15 
 XML-1.95-1/XML/man/xmlNamespace.Rd            |   10 
 XML-1.95-1/XML/man/xmlNamespaceDefinitions.Rd |   16 
 XML-1.95-1/XML/man/xmlNode.Rd                 |    7 
 XML-1.95-1/XML/man/xmlSource.Rd               |   53 
 XML-1.95-1/XML/man/xmlStopParser.Rd           |only
 XML-1.95-1/XML/man/xmlStructuredStop.Rd       |only
 XML-1.95-1/XML/man/xmlTreeParse.Rd            |  165 
 XML-1.95-1/XML/src/DocParse.c                 |  373 +
 XML-1.95-1/XML/src/DocParse.h                 |    2 
 XML-1.95-1/XML/src/EventParse.c               |   98 
 XML-1.95-1/XML/src/EventParse.h               |    7 
 XML-1.95-1/XML/src/HTMLParse.c                |    3 
 XML-1.95-1/XML/src/RSDTD.c                    |   17 
 XML-1.95-1/XML/src/RSDTD.h                    |    2 
 XML-1.95-1/XML/src/RS_XML.h                   |    1 
 XML-1.95-1/XML/src/RUtils.c                   |  139 
 XML-1.95-1/XML/src/Utils.c                    |  168 
 XML-1.95-1/XML/src/Utils.h                    |   63 
 XML-1.95-1/XML/src/XMLEventParse.c            |  161 
 XML-1.95-1/XML/src/XMLTree.c                  |  244 +
 XML-1.95-1/XML/src/catalog.c                  |   97 
 XML-1.95-1/XML/src/xpath.c                    |   37 
 83 files changed, 4612 insertions(+), 3571 deletions(-)

More information about XML at CRAN

posted at: 13:18 | path: /cran/updated | permanent link to this entry

Package GenABEL updated to version 1.3-9 with previous version 1.3-7 dated 2008-04-17

Author: Yurii Aulchenko, Maksim Struchalin, with contributions from Stephan Ripke and Toby Johnson
Title: genome-wide SNP association analysis
Description: a package for genome-wide association analysis between quantitative or binary traits and single-nucleiotide polymorphisms (SNPs).

Diff between GenABEL versions 1.3-7 dated 2008-04-17 and 1.3-9 dated 2008-05-07

 CHANGES.LOG                       |    8 
 DESCRIPTION                       |   10 
 NAMESPACE                         |    4 
 R/GASurv.R                        |only
 R/convert.snp.affymetrix.R        |only
 R/merge.snp.data.R                |   20 
 R/mlreg.R                         |only
 TODO                              |   25 
 inst/doc/GenABEL-tutorial.pdf     | 3453 +++++++++++++++++++-------------------
 man/GASurv.Rd                     |only
 man/GenABEL-package.Rd            |   22 
 man/HWE.show.Rd                   |    3 
 man/Xfix.Rd                       |    2 
 man/add.plot.Rd                   |    1 
 man/as.character.gwaa.data.Rd     |   10 
 man/as.character.snp.coding.Rd    |   10 
 man/as.character.snp.data.Rd      |   10 
 man/as.character.snp.strand.Rd    |   10 
 man/as.data.frame.gwaa.data.Rd    |    6 
 man/as.double.gwaa.data.Rd        |   10 
 man/as.double.snp.data.Rd         |   10 
 man/as.genotype.Rd                |   10 
 man/as.genotype.gwaa.data.Rd      |   10 
 man/as.genotype.snp.data.Rd       |   10 
 man/as.hsgeno.Rd                  |   10 
 man/as.hsgeno.gwaa.data.Rd        |   10 
 man/as.hsgeno.snp.data.Rd         |   10 
 man/catable.Rd                    |   10 
 man/convert.snp.affymetrix.Rd     |only
 man/crnames.Rd                    |   12 
 man/descriptives.marker.Rd        |   14 
 man/descriptives.scan.Rd          |   14 
 man/descriptives.trait.Rd         |   14 
 man/emp.ccfast.Rd                 |    5 
 man/emp.qtscore.Rd                |    7 
 man/formetascore.Rd               |    1 
 man/gwaa.data-class.Rd            |    4 
 man/hom.Rd                        |    6 
 man/merge.snp.data.Rd             |    2 
 man/mlreg.Rd                      |only
 man/qtscore.Rd                    |    3 
 man/qvaluebh95.Rd                 |    8 
 man/scan.glm.2D.Rd                |    4 
 man/scan.glm.Rd                   |    4 
 man/show.ncbi.Rd                  |   18 
 man/snp.names.Rd                  |    2 
 man/srdta.Rd                      |   18 
 man/sset.Rd                       |   12 
 src/Chip.cpp                      |only
 src/Chip.h                        |only
 src/chinv2.cpp                    |only
 src/cholesky2.cpp                 |only
 src/chsolve2.cpp                  |only
 src/convert.snp.affymetrix.cpp    |only
 src/convert_snp_merlin.cpp        |    2 
 src/convert_snp_merlin_wslash.cpp |    6 
 src/coxfit2.cpp                   |only
 src/dmatrix.cpp                   |only
 src/gtps_container.cpp            |   37 
 src/gtps_container.h              |   16 
 src/gwaa.c                        |    1 
 src/lm_gwaa.cpp                   |only
 src/mematri1.h                    |only
 src/mematriR.h                    |only
 src/mematrix.h                    |only
 src/merge.snp.data.cpp            |   96 -
 src/reg1.h                        |only
 src/reg1data.h                    |only
 src/survS.h                       |only
 src/survproto.h                   |only
 70 files changed, 2013 insertions(+), 1977 deletions(-)

More information about GenABEL at CRAN

posted at: 13:18 | path: /cran/updated | permanent link to this entry

Package lpSolve updated to version 5.6.2 with previous version 5.6.1 dated 2008-04-28

Author: Michel Berkelaar and others
Title: Interface to Lp_solve v. 5.5 to solve linear/integer programs
Description: Lp_solve is freely available (under LGPL 2) software for solving linear, integer and mixed integer programs. In this implementation we supply a "wrapper" function in C and some R functions that solve general linear/integer problems, assignment problems, and transportation problems. This version calls lp_solve version 5.5.

Diff between lpSolve versions 5.6.1 dated 2008-04-28 and 5.6.2 dated 2008-05-07

 DESCRIPTION     |    6 +++---
 src/lpslink56.c |    1 -
 2 files changed, 3 insertions(+), 4 deletions(-)

More information about lpSolve at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

Package knncat updated to version 1.1.11 with previous version 1.1.10 dated 2006-05-29

Author: Sam Buttrey
Title: Nearest-neighbor classification with categorical variables
Description: This program scales categorical variables in such a way as to make NN classification as accurate as possible. It also handles continuous variables and prior probabilities, and does intelligent variable selection and estimation of error rates and the right number of NN's.

Diff between knncat versions 1.1.10 dated 2006-05-29 and 1.1.11 dated 2008-05-07

 DESCRIPTION  |   24 ++++++++++++------------
 src/matrix.c |    2 +-
 src/utilsR.c |    1 -
 3 files changed, 13 insertions(+), 14 deletions(-)

More information about knncat at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

Package knnTree updated to version 1.2.4 with previous version 1.2.3 dated 2004-11-16

Author: Sam Buttrey
Title: k-nn classification with variable selection inside leaves of a tree
Description: Construct or predict with k-nearest-neighbor classifiers, using cross-validation to select k, choose variables (by forward or backwards selection), and choose scaling (from among no scaling, scaling each column by its SD, or scaling each column by its MAD). The finished classifier will consist of a classification tree with one such k-nn classifier in each leaf.

Diff between knnTree versions 1.2.3 dated 2004-11-16 and 1.2.4 dated 2008-05-07

 DESCRIPTION   |   27 ++++++++++++++-------------
 src/knnTree.c |    1 -
 src/matrix.c  |    2 +-
 src/utils.c   |    1 -
 4 files changed, 15 insertions(+), 16 deletions(-)

More information about knnTree at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

Package Rsac updated to version 0.1-6 with previous version 0.1-5 dated 2007-10-14

Author: Eric M. Thompson and Jonathan M. Lees
Title: Seismic analysis tools in R
Description: The functions in this package are mostly designed to reproduce the most commonly used functions in the LLNL software Seismic Analysis Code (SAC, http://www.llnl.gov/sac/). This includes reading standard binary SAC (and also SEGY) files, plotting arrays of seismic recordings (the "SAC" plotting style), filtering (highpass, lowpass, and bandpass IIR filters), integration, and differentiation.

Diff between Rsac versions 0.1-5 dated 2007-10-14 and 0.1-6 dated 2008-05-07

 DESCRIPTION      |   13 +++++++------
 R/GET.seis.R     |    2 +-
 R/NumCalculus.R  |    4 ++--
 R/firstlib.r     |    4 ++--
 R/gcp.R          |    4 ++--
 R/getunits.R     |    2 +-
 R/iir.R          |   16 ++++++++--------
 R/mul.R          |    6 +++---
 R/plot.rsac.R    |   22 +++++++++++++++-------
 R/rotate.R       |    2 +-
 R/rsac.R         |    2 +-
 R/rtrend.R       |    7 ++-----
 R/section.R      |only
 R/spect.R        |    2 +-
 R/sync.R         |    2 +-
 R/taper.R        |    4 ++--
 data/sumatra.rda |binary
 man/section.Rd   |only
 man/spect.Rd     |    2 +-
 man/sumatra.Rd   |    4 ++--
 src/LLNfilt.c    |    3 ++-
 src/get_seis.c   |    2 +-
 22 files changed, 55 insertions(+), 48 deletions(-)

More information about Rsac at CRAN

posted at: 05:18 | path: /cran/updated | permanent link to this entry

Tue, 06 May 2008

New package mrdrc with initial version 1.0-0
Package: mrdrc
Title: Model-robust concentration-response analysis
LazyLoad: yes
LazyData: yes
Version: 1.0-0
Author: Christian Ritz , Mads Jeppe Tarp-Johansen,
Maintainer: Christian Ritz
Description: Model-robust, semi-parametric modelling of continuous and quantal concentration/dose-response data.
License: GNU GPL (>= 2)
Depends: R (>= 2.6.0), drc, locfit, EffectiveDose
Date: 2008-05-05
URL: http://www.r-project.org
Packaged: Tue May 6 07:46:20 2008; ritz

More information about mrdrc at CRAN

posted at: 17:18 | path: /cran/new | permanent link to this entry

New package nparcomp with initial version 1.0-0
Package: nparcomp
Type: Package
Title: nparcomp-package
Version: 1.0-0
Date: 2008-05-04
Author: Frank Konietschke
Maintainer: Frank Konietschke
Depends: multcomp, mvtnorm
Description: With this package, it is possible to compute nonparametric simultaneous confidence intervals for relative contrast effects in the unbalanced one way layout. Moreover, it computes simultaneous p-values. The simultaneous confidence intervals can be computed using multivariate normal distribution, multivariate t-distribution with a Satterthwaite Approximation of the degree of freedom or using multivariate range preserving transformations with Logit or Probit as transformation function. 2 sample comparisons can be performed with the same methods described above. There is no assumption on the underlying distribution function, only that the data have to be at least ordinal numbers.
License: GPL
Packaged: Tue May 6 11:45:42 2008; manager

More information about nparcomp at CRAN

posted at: 17:18 | path: /cran/new | permanent link to this entry