Fri, 03 Feb 2012

Package tm updated to version 0.5-7.1 with previous version 0.5-7 dated 2011-12-17

Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut, cre]
Maintainer: Ingo Feinerer

Diff between tm versions 0.5-7 dated 2011-12-17 and 0.5-7.1 dated 2012-02-03

 tm-0.5-7.1/tm/DESCRIPTION                |    8 +++---
 tm-0.5-7.1/tm/MD5                        |   29 ++++++++++++---------
 tm-0.5-7.1/tm/R/matrix.R                 |   32 +++++++++++++++---------
 tm-0.5-7.1/tm/R/reader.R                 |    3 +-
 tm-0.5-7.1/tm/R/source.R                 |   13 +--------
 tm-0.5-7.1/tm/inst/NEWS.Rd               |only
 tm-0.5-7.1/tm/inst/doc/extensions.pdf    |binary
 tm-0.5-7.1/tm/inst/doc/tm.pdf            |binary
 tm-0.5-7.1/tm/inst/stopwords/catalan.dat |only
 tm-0.5-7.1/tm/man/PCorpus.Rd             |    5 +++
 tm-0.5-7.1/tm/man/VCorpus.Rd             |    5 +++
 tm-0.5-7.1/tm/man/readPDF.Rd             |    3 --
 tm-0.5-7.1/tm/man/stopwords.Rd           |    4 ++-
 tm-0.5-7.1/tm/man/termFreq.Rd            |   41 +++++++++++++++++--------------
 tm-0.5-7.1/tm/vignettes                  |only
 tm-0.5-7/tm/inst/NEWS                    |only
 tm-0.5-7/tm/inst/doc/references.bib      |only
 17 files changed, 79 insertions(+), 64 deletions(-)

More information about tm at CRAN
Permanent link

Package readMLData updated to version 0.9-5 with previous version 0.9-4 dated 2012-01-31

Title: Reading machine learning benchmark data sets from different sources in their original format.
Description: The data are not part of the package. The package requires to receive a path to a local copy of the data and their description, which consists of an XML file "contents.xml" and R scripts. Each data set is read into R as a data frame using its own R script. An example of the description directory for some of the data sets from UCI Machine Learning Repository is available at "http://www.cs.cas.cz/~savicky/readMLData".
Author: Petr Savicky
Maintainer: Petr Savicky

Diff between readMLData versions 0.9-4 dated 2012-01-31 and 0.9-5 dated 2012-02-03

 ChangeLog                 |   13 ++++++-------
 DESCRIPTION               |   22 +++++++++++-----------
 MD5                       |   38 ++++++++++++++++++++------------------
 NAMESPACE                 |    2 ++
 R/check.R                 |   29 +++++++++++++++++++++++------
 R/functions.R             |   43 ++++++++++++++++++++++++++++---------------
 R/utils.R                 |   20 ++++++++++++++++++++
 R/xml.R                   |    3 ++-
 man/analyzaData.Rd        |    3 +++
 man/checkAvailability.Rd  |only
 man/checkConsistency.Rd   |    3 +++
 man/checkType.Rd          |    3 +++
 man/dsDownload.Rd         |only
 man/dsRead.Rd             |   17 +++++++++++------
 man/dsSearch.Rd           |    5 ++++-
 man/dsSort.Rd             |    5 ++++-
 man/getFields.Rd          |    5 ++++-
 man/getType.Rd            |    3 +++
 man/prepareDSList.Rd      |   23 ++++++++++++++++-------
 man/readMLData-package.Rd |   44 ++++++++++++++++++++++++++++++++++----------
 man/xml.Rd                |    3 +++
 21 files changed, 200 insertions(+), 84 deletions(-)

More information about readMLData at CRAN
Permanent link

Package plotrix updated to version 3.3-6 with previous version 3.3-5 dated 2012-01-25

Title: Various plotting functions
Description: Lots of plots, various labeling, axis and color scaling functions.
Author: Jim Lemon, Ben Bolker, Sander Oom, Eduardo Klein, Barry Rowlingson, Hadley Wickham, Anupam Tyagi, Olivier Eterradossi, Gabor Grothendieck, Michael Toews, John Kane, Rolf Turner, Carl Witthoft, Julian Stander, Thomas Petzoldt, Remko Duursma, Elisa Biancotto, Ofir Levy, Christophe Dutang, Peter Solymos, Robby Engelmann, Michael Hecker, Felix Steinbeck, Hans Borchers
Maintainer: Jim Lemon

Diff between plotrix versions 3.3-5 dated 2012-01-25 and 3.3-6 dated 2012-02-03

 DESCRIPTION            |    8 ++++----
 INDEX                  |    2 ++
 MD5                    |   20 ++++++++++++--------
 NAMESPACE              |    2 ++
 R/battleship.plot.R    |only
 R/box.heresy.R         |only
 R/brkdnNest.R          |    2 +-
 R/staxlab.R            |   16 +++++++++++++---
 R/taylor.diagram.R     |   20 +++++++++++---------
 man/battleship.plot.Rd |only
 man/box.heresy.Rd      |only
 man/staxlab.Rd         |    3 ++-
 man/taylor.diagram.Rd  |    3 ++-
 13 files changed, 49 insertions(+), 27 deletions(-)

More information about plotrix at CRAN
Permanent link

Package IBDsim updated to version 0.9-1 with previous version 0.8 dated 2011-10-24

Title: Simulation of chromosomal regions shared by family members.
Description: R package for simulation of IBD sharing among family members. Using sex specific recombination rates from the Decode map (2010) of the human genome, phased chromosomes are simulated for all pedigree members, either by unconditional 'gene dropping' or conditional on a specified IBD pattern. Regions compatible with the query IBD pattern (possibly different from the conditional pattern) are subsequently detected and summarized.
Author: Magnus Dehli Vigeland
Maintainer:

Diff between IBDsim versions 0.8 dated 2011-10-24 and 0.9-1 dated 2012-02-03

 IBDsim-0.8/IBDsim/data/twoloops.rda    |only
 IBDsim-0.8/IBDsim/man/twoloops.Rd      |only
 IBDsim-0.9-1/IBDsim/DESCRIPTION        |   10 +++++-----
 IBDsim-0.9-1/IBDsim/MD5                |   24 +++++++++++-------------
 IBDsim-0.9-1/IBDsim/R/IBDsim.R         |   16 ++++++++--------
 IBDsim-0.9-1/IBDsim/R/genedrop.R       |    2 +-
 IBDsim-0.9-1/IBDsim/R/ibd.runs.R       |    4 ++--
 IBDsim-0.9-1/IBDsim/R/ped_utils.R      |    4 ++--
 IBDsim-0.9-1/IBDsim/R/summary.ibd.R    |    2 +-
 IBDsim-0.9-1/IBDsim/data/DecodeMap.rda |binary
 IBDsim-0.9-1/IBDsim/data/datalist      |    1 -
 IBDsim-0.9-1/IBDsim/data/dominant1.rda |binary
 IBDsim-0.9-1/IBDsim/man/IBDsim.Rd      |    2 +-
 IBDsim-0.9-1/IBDsim/man/dominant1.Rd   |    2 +-
 14 files changed, 32 insertions(+), 35 deletions(-)

More information about IBDsim at CRAN
Permanent link

Package DAAG updated to version 1.12 with previous version 1.10 dated 2012-01-25

Title: Data Analysis And Graphics data and functions
Description: various data sets used in examples and exercises in the book Maindonald, J.H. and Braun, W.J. (2003, 2007, 2010) "Data Analysis and Graphics Using R".
Author: John Maindonald and W. John Braun
Maintainer: W. John Braun

Diff between DAAG versions 1.10 dated 2012-01-25 and 1.12 dated 2012-02-03

 DESCRIPTION             |    6 ++--
 MD5                     |   18 ++++++++------
 NAMESPACE               |    7 +++--
 R/logisticsim.R         |    2 -
 R/plotSampDist.R        |only
 R/simulateSampDist.R    |only
 data/nassCDS.RData      |binary
 man/kiwishade.Rd        |   59 +++++++++++++++++++++--------------------------
 man/nassCDS.Rd          |   60 +++++++++++++++++++++++++++++-------------------
 man/plotSampDist.Rd     |only
 man/science.Rd          |   48 +++++++++++++++++++-------------------
 man/simulateSampDist.Rd |only
 12 files changed, 107 insertions(+), 93 deletions(-)

More information about DAAG at CRAN
Permanent link

Package compareGroups updated to version 1.0 with previous version 0.1-4 dated 2011-04-26

Title: descriptives by groups
Description: This package is meant to facilitate the construction of bivariate table (descriptives of several variables between groups) and generate reports in LaTeX, HTML or (CSV) plain text. Also, it includes a graphical interface (GUI) to build these tables more easily.
Author: Isaac Subirana, Héctor Sanz, Joan Vila
Maintainer: Isaac Subirana

Diff between compareGroups versions 0.1-4 dated 2011-04-26 and 1.0 dated 2012-02-03

 compareGroups-0.1-4/compareGroups/R/plot.compareGroups.r              |only
 compareGroups-0.1-4/compareGroups/R/zzz.R                             |only
 compareGroups-0.1-4/compareGroups/data/myData.rda                     |only
 compareGroups-0.1-4/compareGroups/inst/doc/Sweave.sty                 |only
 compareGroups-0.1-4/compareGroups/inst/doc/compareGroups_vignette.Rnw |only
 compareGroups-0.1-4/compareGroups/inst/doc/compareGroups_vignette.bib |only
 compareGroups-0.1-4/compareGroups/inst/doc/figures                    |only
 compareGroups-0.1-4/compareGroups/inst/doc/make_latex.r               |only
 compareGroups-0.1-4/compareGroups/inst/doc/tables                     |only
 compareGroups-0.1-4/compareGroups/man/myData.Rd                       |only
 compareGroups-1.0/compareGroups/DESCRIPTION                           |   21 
 compareGroups-1.0/compareGroups/MD5                                   |only
 compareGroups-1.0/compareGroups/NAMESPACE                             |   41 
 compareGroups-1.0/compareGroups/R/Cox.plot.R                          |only
 compareGroups-1.0/compareGroups/R/KM.plot.R                           |only
 compareGroups-1.0/compareGroups/R/KMg.plot.R                          |only
 compareGroups-1.0/compareGroups/R/bar.plot.R                          |only
 compareGroups-1.0/compareGroups/R/bar2.plot.R                         |only
 compareGroups-1.0/compareGroups/R/box.plot.R                          |only
 compareGroups-1.0/compareGroups/R/cGroupsGUI.R                        | 1567 ++++++----
 compareGroups-1.0/compareGroups/R/cbind.createTable.R                 |only
 compareGroups-1.0/compareGroups/R/chisq.test2.R                       |   15 
 compareGroups-1.0/compareGroups/R/compare.i.R                         |  362 +-
 compareGroups-1.0/compareGroups/R/compareGroups.default.R             |  189 +
 compareGroups-1.0/compareGroups/R/compareGroups.formula.R             |  130 
 compareGroups-1.0/compareGroups/R/createTable.R                       |  154 
 compareGroups-1.0/compareGroups/R/descrip.R                           |   32 
 compareGroups-1.0/compareGroups/R/descripSurv.R                       |only
 compareGroups-1.0/compareGroups/R/export2csv.R                        |   82 
 compareGroups-1.0/compareGroups/R/export2html.R                       |only
 compareGroups-1.0/compareGroups/R/export2latex.R                      |   96 
 compareGroups-1.0/compareGroups/R/export2latex.cbind.createTable.R    |only
 compareGroups-1.0/compareGroups/R/export2latex.createTable.R          |only
 compareGroups-1.0/compareGroups/R/logrank.pval.R                      |only
 compareGroups-1.0/compareGroups/R/norm.plot.R                         |   53 
 compareGroups-1.0/compareGroups/R/plot.compareGroups.R                |only
 compareGroups-1.0/compareGroups/R/prepare.R                           |only
 compareGroups-1.0/compareGroups/R/print.cbind.createTable.R           |only
 compareGroups-1.0/compareGroups/R/print.compareGroups.R               |   27 
 compareGroups-1.0/compareGroups/R/print.createTable.R                 |  104 
 compareGroups-1.0/compareGroups/R/print.summary.compareGroups.R       |   22 
 compareGroups-1.0/compareGroups/R/print.summary.createTable.r         |only
 compareGroups-1.0/compareGroups/R/rbind.compareGroups.R               |only
 compareGroups-1.0/compareGroups/R/rbind.createTable.R                 |only
 compareGroups-1.0/compareGroups/R/summ.i.R                            |   10 
 compareGroups-1.0/compareGroups/R/summary.compareGroups.R             |    3 
 compareGroups-1.0/compareGroups/R/summary.createTable.R               |only
 compareGroups-1.0/compareGroups/R/table.i.R                           |  136 
 compareGroups-1.0/compareGroups/R/update.compareGroups.R              |   14 
 compareGroups-1.0/compareGroups/R/update.formula2.R                   |    6 
 compareGroups-1.0/compareGroups/R/z[.cbind.createTable.R              |only
 compareGroups-1.0/compareGroups/R/z[.compareGroups.R                  |only
 compareGroups-1.0/compareGroups/R/z[.createTable.R                    |only
 compareGroups-1.0/compareGroups/R/z[.rbind.compareGroups.R            |only
 compareGroups-1.0/compareGroups/R/z[.rbind.createTable.R              |only
 compareGroups-1.0/compareGroups/compareGroups-Ex.R                    |  483 +--
 compareGroups-1.0/compareGroups/data/regicor.rda                      |binary
 compareGroups-1.0/compareGroups/inst/doc/changelog.txt                |   59 
 compareGroups-1.0/compareGroups/inst/doc/compareGroups_vignette.pdf   |binary
 compareGroups-1.0/compareGroups/man/cGroupsGUI.Rd                     |   10 
 compareGroups-1.0/compareGroups/man/compareGroups-internal.Rd         |   32 
 compareGroups-1.0/compareGroups/man/compareGroups-package.Rd          |    8 
 compareGroups-1.0/compareGroups/man/compareGroups.Rd                  |  146 
 compareGroups-1.0/compareGroups/man/createTable.Rd                    |  114 
 compareGroups-1.0/compareGroups/man/export2csv.Rd                     |   20 
 compareGroups-1.0/compareGroups/man/export2html.Rd                    |only
 compareGroups-1.0/compareGroups/man/export2latex.Rd                   |   56 
 compareGroups-1.0/compareGroups/man/regicor.Rd                        |   55 
 compareGroups-1.0/compareGroups/man/varinfo.Rd                        |   18 
 compareGroups-1.0/compareGroups/vignettes                             |only
 70 files changed, 2717 insertions(+), 1348 deletions(-)

More information about compareGroups at CRAN
Permanent link

New package catdata with initial version 1.0
Package: catdata
Type: Package
Title: Categorical Data
Version: 1.0
Date: 2010-04-13
Encoding: UTF-8
Depends: R (>= 2.10), MASS
Suggests: rms, qvcalc, glmmML, nnet, pscl, VGAM, gee, mlogit, Ecdat, geepack, mgcv, rpart, party, ordinal, lme4, vcdExtra, glmnet, mboost, class, e1071, flexmix, lqa, lpSolve, GAMBoost, penalized
Author: Gerhard Tutz, Marcus Gross, Sarah Maierhofer, Gunther Schauberger
Maintainer: Gunther Schauberger , Gerhard Tutz
Description: This R-package contains examples from the book "Regression for Categorical Data", Tutz 2011, Cambridge University Press. The names of the examples refer to the chapter and the data set that is used.
License: GPL-2
LazyLoad: yes
Packaged: 2012-02-03 10:29:32 UTC; schaubergerg
Repository: CRAN
Date/Publication: 2012-02-03 11:35:05

More information about catdata at CRAN
Permanent link

Package survey updated to version 3.28 with previous version 3.27 dated 2012-01-06

Title: analysis of complex survey samples
Description: Summary statistics, two-sample tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. Predictive margins by direct standardization. PPS sampling without replacement. Principal components, factor analysis.
Author: Thomas Lumley
Maintainer: Thomas Lumley

Diff between survey versions 3.27 dated 2012-01-06 and 3.28 dated 2012-02-03

 survey-3.27/survey/inst/doc/epi.dvi            |only
 survey-3.28/survey/DESCRIPTION                 |   20 ++++--
 survey-3.28/survey/MD5                         |   74 +++++++++++------------
 survey-3.28/survey/NAMESPACE                   |   13 ++++
 survey-3.28/survey/R/anova.svyglm.R            |    6 -
 survey-3.28/survey/R/multistage.R              |    2 
 survey-3.28/survey/R/multivariate.R            |    4 -
 survey-3.28/survey/R/regtest.R                 |    8 +-
 survey-3.28/survey/R/survey.R                  |    1 
 survey-3.28/survey/R/surveygraph.R             |    4 -
 survey-3.28/survey/R/surveyrep.R               |   79 +++++++++++++++++++++++--
 survey-3.28/survey/R/transform.R               |only
 survey-3.28/survey/R/twophase.R                |   14 ++--
 survey-3.28/survey/THANKS                      |    7 +-
 survey-3.28/survey/inst/NEWS                   |   11 +++
 survey-3.28/survey/inst/doc/domain.pdf         |binary
 survey-3.28/survey/inst/doc/epi.pdf            |binary
 survey-3.28/survey/inst/doc/phase1.pdf         |binary
 survey-3.28/survey/inst/doc/pps.pdf            |binary
 survey-3.28/survey/inst/doc/survey.pdf         |binary
 survey-3.28/survey/man/update.survey.design.Rd |    4 +
 survey-3.28/survey/man/withReplicates.Rd       |   37 +++++++++--
 survey-3.28/survey/tests/DBIcheck.Rout.save    |   10 +--
 survey-3.28/survey/tests/api.Rout.save         |    2 
 survey-3.28/survey/tests/caleg.Rout.save       |   22 +++---
 survey-3.28/survey/tests/check.Rout.save       |   10 +--
 survey-3.28/survey/tests/deff.Rout.save        |   12 +++
 survey-3.28/survey/tests/domain.Rout.save      |   23 ++-----
 survey-3.28/survey/tests/fpc.Rout.save         |   12 +++
 survey-3.28/survey/tests/kalton.Rout.save      |   10 +--
 survey-3.28/survey/tests/lonely.psu.Rout.save  |   12 +--
 survey-3.28/survey/tests/multistage.Rout.save  |   10 +--
 survey-3.28/survey/tests/nwts-cch.Rout.save    |    2 
 survey-3.28/survey/tests/nwts.Rout.save        |   20 +++---
 survey-3.28/survey/tests/pps.Rout.save         |   21 ++----
 survey-3.28/survey/tests/quantile.Rout.save    |   14 ++--
 survey-3.28/survey/tests/rakecheck.Rout.save   |   10 +--
 survey-3.28/survey/tests/regpredict.Rout.save  |   10 +--
 survey-3.28/survey/tests/twophase.Rout.save    |   10 +--
 39 files changed, 312 insertions(+), 182 deletions(-)

More information about survey at CRAN
Permanent link

Package readBrukerFlexData updated to version 1.2.4 with previous version 1.2.3 dated 2012-01-29

Title: Reads mass spectrometry data in Bruker *flex format
Description: Reads files generated by MALDI-TOF MS of Bruker Daltonics' *flex series. Successfully tested for Bruker Daltonics' Autoflex MS.
Author: Sebastian Gibb
Maintainer: Sebastian Gibb

Diff between readBrukerFlexData versions 1.2.3 dated 2012-01-29 and 1.2.4 dated 2012-02-03

 readBrukerFlexData-1.2.3/readBrukerFlexData/inst/Examples/2010_05_19_Gibb_C8_A1/0_A1/1/1SLin/acqus  |only
 readBrukerFlexData-1.2.3/readBrukerFlexData/inst/Examples/2010_05_19_Gibb_C8_A1/0_A1/1/1SLin/pdata  |only
 readBrukerFlexData-1.2.3/readBrukerFlexData/inst/Examples/2010_05_19_Gibb_C8_A1/0_A1/1/1SLin/sptype |only
 readBrukerFlexData-1.2.3/readBrukerFlexData/inst/Examples/2010_05_19_Gibb_C8_A1/0_A2/1/1SLin/acqus  |only
 readBrukerFlexData-1.2.3/readBrukerFlexData/inst/Examples/2010_05_19_Gibb_C8_A1/0_A2/1/1SLin/pdata  |only
 readBrukerFlexData-1.2.3/readBrukerFlexData/inst/Examples/2010_05_19_Gibb_C8_A1/0_A2/1/1SLin/sptype |only
 readBrukerFlexData-1.2.3/readBrukerFlexData/inst/Examples/hpc/fid/0_A20/1/1SRef/acqus               |only
 readBrukerFlexData-1.2.3/readBrukerFlexData/inst/Examples/hpc/fid/0_A20/1/1SRef/pdata               |only
 readBrukerFlexData-1.2.3/readBrukerFlexData/inst/Examples/hpc/fid/0_A20/1/1SRef/sptype              |only
 readBrukerFlexData-1.2.4/readBrukerFlexData/DESCRIPTION                                             |    8 
 readBrukerFlexData-1.2.4/readBrukerFlexData/MD5                                                     |   27 --
 readBrukerFlexData-1.2.4/readBrukerFlexData/NEWS                                                    |    4 
 readBrukerFlexData-1.2.4/readBrukerFlexData/R/double2singlePrecision.R                              |    2 
 readBrukerFlexData-1.2.4/readBrukerFlexData/R/mqReadBrukerFlex.R                                    |    2 
 readBrukerFlexData-1.2.4/readBrukerFlexData/R/readBrukerFlexData.R                                  |   95 +++++-----
 readBrukerFlexData-1.2.4/readBrukerFlexData/man/readBrukerFlexData-package.Rd                       |   12 -
 16 files changed, 74 insertions(+), 76 deletions(-)

More information about readBrukerFlexData at CRAN
Permanent link

Package mmod updated to version 0.2.1 with previous version 0.2 dated 2012-01-27

Title: Modern measures of population differentiation
Description: mmod provides functions for measuring population divergence from genotypic data
Author: David Winter
Maintainer: David Winter

Diff between mmod versions 0.2 dated 2012-01-27 and 0.2.1 dated 2012-02-03

 mmod-0.2.1/mmod/.gitignore                  |    2 
 mmod-0.2.1/mmod/DESCRIPTION                 |    7 +
 mmod-0.2.1/mmod/MD5                         |   48 ++++++------
 mmod-0.2.1/mmod/NAMESPACE                   |    1 
 mmod-0.2.1/mmod/NEWS                        |   20 ++++-
 mmod-0.2.1/mmod/R/D_Jost.R                  |   13 +--
 mmod-0.2.1/mmod/R/Gst_Hedrick.R             |   24 +++---
 mmod-0.2.1/mmod/R/Gst_Nei.R                 |   13 +--
 mmod-0.2.1/mmod/R/chao_bootstrap.R          |   39 +++++++---
 mmod-0.2.1/mmod/R/diff_stats.R              |   12 +--
 mmod-0.2.1/mmod/R/jacknife_pop.R            |   11 +-
 mmod-0.2.1/mmod/R/pairwise_D.R              |   15 +---
 mmod-0.2.1/mmod/R/pairwise_Gst_Hedrick.R    |    2 
 mmod-0.2.1/mmod/R/rgenotypes.R              |only
 mmod-0.2.1/mmod/R/summarise_bootstrap.R     |   12 +--
 mmod-0.2.1/mmod/inst/doc/mmod-demo.Rnw      |  104 ++++++++++++++--------------
 mmod-0.2.1/mmod/inst/doc/mmod-demo.pdf      |binary
 mmod-0.2.1/mmod/man/Gst_Hedrick.Rd          |    6 +
 mmod-0.2.1/mmod/man/chao_bootstrap.Rd       |   26 ++++++-
 mmod-0.2.1/mmod/man/diff_stats.Rd           |    4 +
 mmod-0.2.1/mmod/man/jacknife_populations.Rd |    9 +-
 mmod-0.2.1/mmod/man/pairwise_D.Rd           |    6 -
 mmod-0.2.1/mmod/man/pairwise_Gst_Hedrick.Rd |    4 -
 mmod-0.2.1/mmod/man/rgenotypes.Rd           |only
 mmod-0.2.1/mmod/man/summarise_bootsrap.Rd   |    2 
 mmod-0.2.1/mmod/mmod_0.2.1.tar.gz           |only
 mmod-0.2/mmod/chao_bootstrap.R              |only
 mmod-0.2/mmod/mmod_0.2.tar.gz               |only
 mmod-0.2/mmod/test/demo.Rnw                 |only
 29 files changed, 219 insertions(+), 161 deletions(-)

More information about mmod at CRAN
Permanent link

Package lmbc updated to version 0.9.1 with previous version 0.9 dated 2011-12-15

Title: Linear Model Bias Correction for RNA-Seq Data
Description: This is the package for implementing the method in "Bias Correction in RNA-Seq Short-read Counts using Penalized Regression." It first using a penalized regression to determine an appropriate surrounding sequence, then refits the model using the dinucleotide expansion.
Author: David Dalpiaz
Maintainer: David Dalpiaz

Diff between lmbc versions 0.9 dated 2011-12-15 and 0.9.1 dated 2012-02-03

 DESCRIPTION |   14 +++++--
 MD5         |    4 +-
 man/lmbc.Rd |  106 ++++--------------------------------------------------------
 3 files changed, 19 insertions(+), 105 deletions(-)

More information about lmbc at CRAN
Permanent link

Package GrapheR updated to version 1.9-75-2 with previous version 1.9-71 dated 2011-12-27

Title: A multiplatform GUI for drawing customizable graphs in R
Description: GrapheR is a multiplatform user interface for drawing highly customizable graphs in R. It aims to be a valuable help to quickly draw publishable graphs without any knowledge of R commands. Six kinds of graph are available: histogram, box-and-whisker plot, bar plot, pie chart, curve and scatter plot.
Author: Maxime Hervé
Maintainer: Maxime Hervé

Diff between GrapheR versions 1.9-71 dated 2011-12-27 and 1.9-75-2 dated 2012-02-03

 DESCRIPTION                     |   15 +
 MD5                             |  343 +++++++++++++++++++++++-----------------
 NAMESPACE                       |   11 -
 NEWS                            |only
 R/active.erreur.R               |    1 
 R/active.legende.R              |    1 
 R/active.legende2.R             |    1 
 R/affine.R                      |    1 
 R/aide.R                        |    2 
 R/barres.moy.R                  |    3 
 R/barres.prop.R                 |    3 
 R/code.ask.R                    |    1 
 R/code.data.R                   |   11 +
 R/code.graph.R                  |    3 
 R/code.graph.axes.R             |   36 +++-
 R/code.graph.barres.R           |  213 ++++++++++++++++--------
 R/code.graph.barres.erreurs.R   |    2 
 R/code.graph.moust.R            |   42 +++-
 R/code.graph.nuage.R            |  245 ++++++++++++++++++++++++++--
 R/code.graph.posleg.R           |    2 
 R/code.graph.titre.R            |   82 ++++++---
 R/code.graphtype.R              |    2 
 R/code.open.R                   |    1 
 R/col.barres.R                  |    1 
 R/col.bordures.R                |    1 
 R/col.parts.R                   |    1 
 R/col.symboles.R                |    1 
 R/convert.variable.R            |    8 
 R/courbe.moy.R                  |    1 
 R/courbe.prop.R                 |    1 
 R/data.load1.R                  |    8 
 R/data.load2.R                  |    8 
 R/distrib.R                     |    5 
 R/enregistrer.R                 |   54 ++++--
 R/fermer.GrapheR.R              |    1 
 R/fr1.close.R                   |    1 
 R/fr1.openB.R                   |   43 ++---
 R/fr1.openCa.R                  |    5 
 R/fr1.openCo.R                  |    5 
 R/fr1.openD.R                   |    1 
 R/fr1.openH.R                   |    5 
 R/fr1.openM.R                   |   55 +++++-
 R/fr1.openN.R                   |   29 ++-
 R/fr2.close.R                   |    1 
 R/fr2.openD.R                   |    1 
 R/fr2.opengraphe.R              |    5 
 R/fr3.close.R                   |    1 
 R/fr3.openB.R                   |   45 ++---
 R/fr3.openCa.R                  |    1 
 R/fr3.openCoN.R                 |   49 +++--
 R/fr3.openD.R                   |    1 
 R/fr3.openH.R                   |   37 ++--
 R/fr3.openM.R                   |   45 ++---
 R/fr4.close.R                   |    1 
 R/fr4.openB.R                   |    1 
 R/fr4.openCa.R                  |    1 
 R/fr4.openCo.R                  |    1 
 R/fr4.openD.R                   |    1 
 R/fr4.openH.R                   |    1 
 R/fr4.openM.R                   |   55 ++++--
 R/fr4.openN.R                   |   52 +-----
 R/fr5.close.R                   |    1 
 R/fr5.openB.R                   |    1 
 R/fr5.openCa.R                  |    1 
 R/fr5.openCo.R                  |    1 
 R/fr5.openD.R                   |only
 R/fr5.openH.R                   |    1 
 R/fr5.openM.R                   |   26 ---
 R/fr5.openN.R                   |   95 +++++++----
 R/fr6.close.R                   |    1 
 R/fr6.openB.R                   |    1 
 R/fr6.openCo.R                  |    1 
 R/fr6.openM.R                   |   22 --
 R/fr6.openN.R                   |only
 R/fr7.close.R                   |    1 
 R/graphe.axes.R                 |   16 +
 R/graphe.box.R                  |    1 
 R/graphe.erreurs.calculer.R     |    2 
 R/graphe.erreurs.calculer2.R    |    1 
 R/graphe.erreurs.tracer.R       |    1 
 R/graphe.hachures.R             |    1 
 R/graphe.legende.R              |   25 ++
 R/graphe.log.R                  |    1 
 R/graphe.symboles.R             |    1 
 R/graphe.titre.R                |   30 ++-
 R/hachures.R                    |    1 
 R/hachures2.R                   |    1 
 R/horizontal.R                  |    1 
 R/language.R                    |    1 
 R/language.change.R             |    6 
 R/load.GrapheR.R                |   24 ++
 R/msg.R                         |    5 
 R/navigation.R                  |   10 -
 R/new.window.R                  |    1 
 R/ouvrir.GrapheR.R              |    9 -
 R/pretracer.R                   |    1 
 R/pval.R                        |    1 
 R/reinit.fr7.R                  |    4 
 R/reinit.variables.R            |   16 +
 R/rename.legende.R              |    1 
 R/rename.legende2.R             |   10 -
 R/rename.noms1.R                |    5 
 R/rename.nomsparts.R            |    1 
 R/rename.nomsprop.fac.R         |    1 
 R/rename.variable.R             |    8 
 R/run.GrapheR.R                 |    1 
 R/symboles.R                    |    1 
 R/texte.R                       |    1 
 R/tracer.R                      |    9 -
 R/tracer.barres.limites.R       |    1 
 R/tracer.barres.moyplusieurs.R  |   16 +
 R/tracer.barres.moyun.R         |   16 +
 R/tracer.barres.propplusieurs.R |   19 +-
 R/tracer.barres.propun.R        |   13 +
 R/tracer.cam.R                  |    1 
 R/tracer.courbe.limites.R       |    1 
 R/tracer.courbe.moyplusieurs.R  |    1 
 R/tracer.courbe.moyun.R         |    1 
 R/tracer.courbe.propplusieurs.R |    1 
 R/tracer.courbe.propun.R        |    1 
 R/tracer.hist.R                 |    1 
 R/tracer.hist.limites.R         |    1 
 R/tracer.moust.R                |   16 +
 R/tracer.nuage.limites.R        |    1 
 R/tracer.nuage.plusieurs.R      |   53 +++++-
 R/tracer.nuage.un.R             |   46 +++++
 R/type.ligne.R                  |    1 
 R/type.trait.R                  |    1 
 R/variables.class.R             |    1 
 R/vertical.R                    |    1 
 R/zzzz.R                        |    2 
 inst/doc/manual_de.Rnw          |only
 inst/doc/manual_de.pdf          |only
 inst/doc/manual_en.Rnw          |only
 inst/doc/manual_en.pdf          |binary
 inst/doc/manual_fr.Rnw          |only
 inst/doc/manual_fr.pdf          |binary
 inst/images/Lab10d.gif          |only
 inst/images/Lab11d.gif          |only
 inst/images/Lab12d.gif          |only
 inst/images/Lab13d.gif          |only
 inst/images/Lab14d.gif          |only
 inst/images/Lab15d.gif          |only
 inst/images/Lab16d.gif          |only
 inst/images/Lab17d.gif          |only
 inst/images/Lab18a.gif          |binary
 inst/images/Lab18b.gif          |binary
 inst/images/Lab18c.gif          |binary
 inst/images/Lab18d.gif          |only
 inst/images/Lab19a.gif          |only
 inst/images/Lab19b.gif          |only
 inst/images/Lab19c.gif          |only
 inst/images/Lab19d.gif          |only
 inst/images/Lab1d.gif           |only
 inst/images/Lab20a.gif          |only
 inst/images/Lab20b.gif          |only
 inst/images/Lab20c.gif          |only
 inst/images/Lab20d.gif          |only
 inst/images/Lab2d.gif           |only
 inst/images/Lab3d.gif           |only
 inst/images/Lab4d.gif           |only
 inst/images/Lab5d.gif           |only
 inst/images/Lab6d.gif           |only
 inst/images/Lab7d.gif           |only
 inst/images/Lab8d.gif           |only
 inst/images/Lab9d.gif           |only
 inst/lang/Images_de.csv         |only
 inst/lang/Images_en.csv         |    2 
 inst/lang/Images_es.csv         |    2 
 inst/lang/Images_fr.csv         |    2 
 inst/lang/Language_de.csv       |only
 inst/lang/Language_en.csv       |   31 +++
 inst/lang/Language_es.csv       |   29 +++
 inst/lang/Language_fr.csv       |   27 +++
 man/GrapheR-package.Rd          |    4 
 man/active.erreur.Rd            |    3 
 vignettes                       |only
 177 files changed, 1477 insertions(+), 722 deletions(-)

More information about GrapheR at CRAN
Permanent link


Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.