Title: NCBI2R-An R package to navigate and annotate genes and SNPs
Diff between NCBI2R versions 1.3.5 dated 2012-01-23 and 1.4.0 dated 2012-06-13
Description: NCBI2R is an R package that annotates lists of SNPs and/or
genes, with current information from NCBI, including LD
information. Functions are provided that with one command will
provide annotation of the results from genome wide association
studies to provide a broader context of their meaning. Other
functions enable comparisons between a user's GWA results, and
candidate snp/gene lists that are created from keywords, such
as specific diseases, phenotypes or gene ontology terms.
Commands are simple to follow and designed to work with R
objects to integrate into existing workflows. The output
produces text fields and weblinks to more information for items
such as: gene descriptions, nucleotide positions, OMIM,
pathways, phenotypes, and lists of interacting and neighboring
genes. Annotation can then be used in R for further analysis,
or the objects can be customized for use in spreadsheet
programs or web browsers. The NCBI2R package wasdesigned to
allow those performing genome analysis to produce output that
could easily be understood by a person not familiar with R.
Please see the website at http://NCBI2R.wordpress.com for more
information. The internet is required for almost all of these
functions. Use the function PrintNCBI2RInfo() for information.
Author: Scott Melville
Maintainer: Scott Melville
DESCRIPTION | 8 -
MD5 | 111 +++++++++-------
NAMESPACE | 2
R/AnnotateSNPList.r | 2
R/CompareTaxInfo.r |only
R/GenomeSort.r |only
R/GetGeneInfo.r | 23 +--
R/GetGeneNames.r | 142 ++++++++------------
R/GetGeneTable.r | 16 ++
R/GetLDInfo.r | 2
R/GetNeighGenes.r | 172 ++++++++++++-------------
R/GetPubMed.r | 4
R/GetPublishedGWAS.r |only
R/GetSNPFlankSeq.r | 57 +++-----
R/GetSNPInfo.r | 157 +++-------------------
R/GetTax.r | 2
R/GetTaxInfo.r |only
R/check.batchsize.r |only
R/check.package.r |only
R/check.platform.or.test.r |only
R/checkAllNumerics.r |only
R/checkSNPsAllrs.r |only
R/extract.genenames.from.genetabletxt.r |only
R/get.file.r | 2
R/get.gene.docset.r |only
R/getSNPInfo.cleaning.r |only
R/getSNPInfo.master.docset.r |only
R/getSNPInfo.master.xml.r |only
R/getSNPInfo.singlebatch.trimmednames.docset.r |only
R/getSNPInfo.singlebatch.trimmednames.xml.r |only
R/ncbi2r.options.default.r | 6
R/order.to.original.snplist.r |only
R/parseSNPIDLine.r | 10 +
R/pn.r | 17 +-
R/randomSNP.r | 10 -
R/updateCheck.int.r | 21 +--
data/gwas.rda |binary
man/AdjustRangeAroundGene.Rd | 6
man/AnnotateDataframe.Rd | 6
man/AnnotateSNPFile.Rd | 4
man/AnnotateSNPList.Rd | 2
man/CompareTaxInfo.Rd |only
man/ConvertPubMedHeadings.rd | 2
man/DelayUntil.rd | 11 -
man/DivideString.Rd | 2
man/GenomeSort.Rd |only
man/GetClosestGeneInfo.Rd | 4
man/GetGeneInfo.Rd | 3
man/GetGeneNames.Rd | 5
man/GetGeneTable.Rd | 9 +
man/GetLDInfo.Rd | 2
man/GetNeighGenes.Rd | 12 +
man/GetPathways.Rd | 2
man/GetPhenotypes.Rd | 2
man/GetPublishedGWAS.Rd |only
man/GetSNPFlankSeq.rd | 4
man/GetSNPInfo.Rd | 22 ++-
man/GetSNPProxyInfo.Rd | 2
man/GetTaxInfo.Rd |only
man/MakeExcel.Rd | 2
man/MakeHTML.Rd | 4
man/MergeSNPsGenes.Rd | 4
man/NatureJobs.Rd | 9 -
man/OpenPDF.Rd | 12 -
man/OpenPMID.Rd | 12 -
man/OpenURL.Rd | 6
man/gwas.Rd | 4
67 files changed, 429 insertions(+), 488 deletions(-)
Title: Logic Regression
Diff between LogicReg versions 1.5.1 dated 2012-03-27 and 1.5.2 dated 2012-06-13
Description: Routines for Logic Regression
Author: Charles Kooperberg
Maintainer: Charles Kooperberg
DESCRIPTION | 8 +-
MD5 | 4 -
R/LogicReg.R | 234 +++++++++++++++++++++++++++++------------------------------
3 files changed, 124 insertions(+), 122 deletions(-)
Title: Sparse Lightweight Arrays and Matrices
Diff between slam versions 0.1-23 dated 2011-10-27 and 0.1-24 dated 2012-06-13
Description: Data structures and algorithms for sparse arrays and
matrices, based on index arrays and simple triplet
representations, respectively.
Author: Kurt Hornik, David Meyer, Christian Buchta
Maintainer: David Meyer
DESCRIPTION | 13 -
MD5 | 30 ++--
NAMESPACE | 15 +-
R/abind.R |only
R/array.R | 34 +++-
R/matrix.R | 67 +++++++--
R/reduce.R |only
R/rollup.R | 327 ++++++++++++++++++++++++++++++++++------------
R/stm.R | 20 +-
man/abind.Rd |only
man/array.Rd | 39 +++++
man/rollup.Rd | 84 +++++++----
src/sparse.c | 190 ++++++++++++++++++++++++++
src/util.c |only
tests/abind.R |only
tests/abind.Rout.save |only
tests/rollup.R |only
tests/rollup.Rout.save |only
tests/ssa_valid.R |only
tests/ssa_valid.Rout.save |only
tests/util.R |only
tests/util.Rout.save |only
22 files changed, 655 insertions(+), 164 deletions(-)
Title: An interface of MIXMOD
Diff between Rmixmod versions 1.1.2 dated 2012-05-14 and 1.1.3 dated 2012-06-13
Description: Supervised and unsupervised classification with MIXture
MODelling
Author: Remi Lebret and Serge Iovleff and Florent Langrognet, with
contributions from C. Biernacki and G. Celeux and G. Govaert
Maintainer: Remi Lebret
DESCRIPTION | 8 ++++----
MD5 | 10 ++++++----
R/MixmodCluster.R | 4 ++--
R/Rmixmod.R | 40 ++++++++++++++++++++++++++++++++++++++--
data/finance.rda |only
man/Rmixmod-package.Rd | 4 ++--
man/finance.Rd |only
7 files changed, 52 insertions(+), 14 deletions(-)
Title: RMAWGEN (R Multi-site Auto-regressive Weather GENerator): a
package to generate daily time series from monthly mean values
Diff between RMAWGEN versions 1.2.5 dated 2012-05-11 and 1.2.5.1 dated 2012-06-13
Description: This package contains S3 and S4 functions for spatial
multi-site stochastic generation of daily timeseries of
temperature and precipitation. The implemented tools make use
of Vectorial AutoRegressive models (VARs). The VAR is
calibrated by daily instrumental "Gaussinized" time series and
then works with monthly timeseries as input.
Bugs/comments/questions/collaboration of any kind are warmly
welcomed.
Author: Emanuele Cordano, Emanuele Eccel
Maintainer: Emanuele Cordano
DESCRIPTION | 16 ++++++++--------
MD5 | 20 +++++++++++++-------
NAMESPACE | 4 ++++
R/ComprehensivePrecipitationGenerator.R | 18 +++++++++++-------
R/ComprehensiveTemperatureGenerator.R | 19 ++++++++++++++++++-
R/RMAWGEN-package.R | 2 +-
R/qqplot_RMAWGENts.R |only
inst/doc/examples/jss_article |only
inst/doc/examples/marginal_gaussianization1.R |only
inst/doc/examples/precipitation-generator.R | 9 ++-------
man/RMAWGEN-package.Rd | 2 +-
man/qqplot_RMAWGEN_Tx.Rd |only
12 files changed, 58 insertions(+), 32 deletions(-)
Title: Paired Data Analysis
Diff between PairedData versions 0.9.1 dated 2012-04-07 and 0.9.9 dated 2012-06-13
Description: This package provides many datasets and a set of graphics
(based on ggplot2), statistics, effect sizes and hypothesis
tests for analysing paired data with S4 class.
Author: Stephane Champely
Maintainer: Stephane Champely
PairedData-0.9.1/PairedData/data/HORSEbegin.rda |only
PairedData-0.9.1/PairedData/data/SKIexperts.rda |only
PairedData-0.9.1/PairedData/data/iceskating.rda |only
PairedData-0.9.1/PairedData/data/rugby.rda |only
PairedData-0.9.1/PairedData/data/shoulder.rda |only
PairedData-0.9.1/PairedData/man/HORSEbegin.Rd |only
PairedData-0.9.1/PairedData/man/SKIexperts.Rd |only
PairedData-0.9.1/PairedData/man/bonett.seier.test.Rd |only
PairedData-0.9.1/PairedData/man/grambsch.test.Rd |only
PairedData-0.9.1/PairedData/man/iceskating.Rd |only
PairedData-0.9.1/PairedData/man/pitman.morgan.test.Rd |only
PairedData-0.9.1/PairedData/man/plotBA.Rd |only
PairedData-0.9.1/PairedData/man/plotMcNeil.Rd |only
PairedData-0.9.1/PairedData/man/plotProfiles.Rd |only
PairedData-0.9.1/PairedData/man/plotSliding.Rd |only
PairedData-0.9.1/PairedData/man/rugby.Rd |only
PairedData-0.9.1/PairedData/man/shoulder.Rd |only
PairedData-0.9.1/PairedData/man/yuen.test.Rd |only
PairedData-0.9.9/PairedData/DESCRIPTION | 14
PairedData-0.9.9/PairedData/MD5 | 105 ++-
PairedData-0.9.9/PairedData/R/ClassP1.R | 127 +---
PairedData-0.9.9/PairedData/R/global1.R | 471 ++++++++++++----
PairedData-0.9.9/PairedData/data/Anorexia.rda |only
PairedData-0.9.9/PairedData/data/Barley.rda |only
PairedData-0.9.9/PairedData/data/Blink.rda |only
PairedData-0.9.9/PairedData/data/Blink2.rda |only
PairedData-0.9.9/PairedData/data/BloodLead.rda |only
PairedData-0.9.9/PairedData/data/ChickWeight.rda |only
PairedData-0.9.9/PairedData/data/Corn.rda |only
PairedData-0.9.9/PairedData/data/Datalcoholic.rda |only
PairedData-0.9.9/PairedData/data/Grain.rda |only
PairedData-0.9.9/PairedData/data/Grain2.rda |only
PairedData-0.9.9/PairedData/data/GrapeFruit.rda |only
PairedData-0.9.9/PairedData/data/HorseBeginners.rda |only
PairedData-0.9.9/PairedData/data/IceSkating.rda |only
PairedData-0.9.9/PairedData/data/Iron.rda |only
PairedData-0.9.9/PairedData/data/Meat.rda |only
PairedData-0.9.9/PairedData/data/Rugby.rda |only
PairedData-0.9.9/PairedData/data/Sewage.rda |only
PairedData-0.9.9/PairedData/data/Shoulder.rda |only
PairedData-0.9.9/PairedData/data/SkiExperts.rda |only
PairedData-0.9.9/PairedData/data/Sleep.rda |only
PairedData-0.9.9/PairedData/data/Tobacco.rda |only
PairedData-0.9.9/PairedData/man/Anorexia.Rd |only
PairedData-0.9.9/PairedData/man/Barley.Rd |only
PairedData-0.9.9/PairedData/man/Blink.Rd |only
PairedData-0.9.9/PairedData/man/Blink2.Rd |only
PairedData-0.9.9/PairedData/man/BloodLead.Rd |only
PairedData-0.9.9/PairedData/man/ChickWeight.Rd |only
PairedData-0.9.9/PairedData/man/Corn.Rd |only
PairedData-0.9.9/PairedData/man/Datalcoholic.Rd |only
PairedData-0.9.9/PairedData/man/GDO.Rd | 27
PairedData-0.9.9/PairedData/man/Grain.Rd |only
PairedData-0.9.9/PairedData/man/Grain2.Rd |only
PairedData-0.9.9/PairedData/man/GrapeFruit.Rd |only
PairedData-0.9.9/PairedData/man/HorseBeginners.Rd |only
PairedData-0.9.9/PairedData/man/IceSkating.Rd |only
PairedData-0.9.9/PairedData/man/Iron.Rd |only
PairedData-0.9.9/PairedData/man/Meat.Rd |only
PairedData-0.9.9/PairedData/man/PairedData-internal.Rd | 13
PairedData-0.9.9/PairedData/man/PairedData-package.Rd | 6
PairedData-0.9.9/PairedData/man/PrisonStress.Rd | 37 +
PairedData-0.9.9/PairedData/man/Rugby.Rd |only
PairedData-0.9.9/PairedData/man/Sewage.Rd |only
PairedData-0.9.9/PairedData/man/Shoulder.Rd |only
PairedData-0.9.9/PairedData/man/SkiExperts.Rd |only
PairedData-0.9.9/PairedData/man/Sleep.Rd |only
PairedData-0.9.9/PairedData/man/Tobacco.Rd |only
PairedData-0.9.9/PairedData/man/anscombe2.Rd | 23
PairedData-0.9.9/PairedData/man/bonettseier.var.test.Rd |only
PairedData-0.9.9/PairedData/man/effect.size.Rd | 9
PairedData-0.9.9/PairedData/man/grambsch.var.test.Rd |only
PairedData-0.9.9/PairedData/man/lambda.table.Rd | 3
PairedData-0.9.9/PairedData/man/paired-class.Rd | 5
PairedData-0.9.9/PairedData/man/paired.Rd | 4
PairedData-0.9.9/PairedData/man/paired.plotBA.Rd |only
PairedData-0.9.9/PairedData/man/paired.plotCor.Rd |only
PairedData-0.9.9/PairedData/man/paired.plotMcNeil.Rd |only
PairedData-0.9.9/PairedData/man/paired.plotProfiles.Rd |only
PairedData-0.9.9/PairedData/man/plot.Rd | 22
PairedData-0.9.9/PairedData/man/rpaired.contaminated.Rd | 2
PairedData-0.9.9/PairedData/man/rpaired.gld.Rd | 4
PairedData-0.9.9/PairedData/man/slidingchart.Rd |only
PairedData-0.9.9/PairedData/man/summary.Rd | 10
PairedData-0.9.9/PairedData/man/t.test.Rd | 2
PairedData-0.9.9/PairedData/man/var.test.Rd |only
PairedData-0.9.9/PairedData/man/wilcox.test.Rd |only
PairedData-0.9.9/PairedData/man/winsor.cor.test.Rd |only
PairedData-0.9.9/PairedData/man/yuen.t.test.Rd |only
89 files changed, 612 insertions(+), 272 deletions(-)
Title: Analysis of evolutionary rates in an OU framework
Diff between OUwie versions 1.21 dated 2012-05-04 and 1.24 dated 2012-06-13
Description: Calculates and compares rate differences of continuous
character evolution under Brownian motion and a new set of
Ornstein-Uhlenbeck-based Hansen models that allow the strength
of selection and stochastic motion to vary across selective
regimes.
Author: Jeremy M. Beaulieu
Maintainer: Jeremy M. Beaulieu
DESCRIPTION | 10 -
MD5 | 24 +-
NAMESPACE | 6
R/OUwie.R | 319 +++++++++++++++++++-------------------
R/OUwie.contour.R | 253 ++++++++++++++++--------------
R/OUwie.fixed.R | 248 ++++++++++++++++--------------
R/OUwie.sim.R | 24 ++
R/varcov.ou.R | 278 +++++++++++++++++----------------
R/weight.mat.R | 436 +++++++++++++++++++++++++++--------------------------
data/sim.ex.rda |binary
data/tworegime.rda |binary
man/OUwie.Rd | 44 +++--
man/OUwie.fixed.Rd | 22 +-
13 files changed, 873 insertions(+), 791 deletions(-)
Title: ISIPTA network analysis
Diff between ISIPTA versions 0.1-7 dated 2012-04-10 and 0.1-8 dated 2012-06-13
Description: A Network Analysis of the Imprecise Probability Community
based on ISIPTA Electronic Proceedings (see
http://www.sipta.org/).
Author: Manuel J. A. Eugster [aut, cre], Gero Walter [aut], Thomas
Augustin [aut]
Maintainer: Manuel J. A. Eugster
DESCRIPTION | 23 ++++++++++++++---------
MD5 | 4 ++--
NEWS | 7 ++++++-
3 files changed, 22 insertions(+), 12 deletions(-)
Title: A package for graphical modelling in R
Diff between gRbase versions 1.5-0 dated 2012-03-03 and 1.5-1 dated 2012-06-13
Description: The gRbase package provides certain general constructs
which are used by other graphical modelling packages. This
includes 1) the concept of gmData (graphical meta data), 2)
several graph algorithms 3) facilities for table operations, 4)
functions for testing for conditional independence. gRbase also
illustrates how hierarchical log-linear models (hllm) may be
implemented.
Author: Søren Højsgaard
Maintainer: Søren Højsgaard
ChangeLog | 6 ++++++
DESCRIPTION | 8 ++++----
MD5 | 42 +++++++++++++++++++++---------------------
data/Nutrimouse.RData |binary
data/ashtrees.RData |binary
data/breastcancer.RData |binary
data/chestSim1000.RData |binary
data/chestSim10000.RData |binary
data/chestSim100000.RData |binary
data/chestSim500.RData |binary
data/chestSim50000.RData |binary
data/dumping.RData |binary
data/lizard.RData |binary
data/mildew.RData |binary
data/reinis.RData |binary
inst/doc/ArrayOps.pdf |binary
inst/doc/ArrayOpsPrim.pdf |binary
inst/doc/Graphs.pdf |binary
inst/doc/gRbase.pdf |binary
vignettes/fig/graph-013.pdf |binary
vignettes/fig/graph-016.pdf |binary
vignettes/fig/graph-019.pdf |binary
22 files changed, 31 insertions(+), 25 deletions(-)
Title: Collection of methods to detect dichotomous differential item
functioning (DIF) in psychometrics
Diff between difR versions 4.2 dated 2012-04-02 and 4.3 dated 2012-06-13
Description: The difR package contains several traditional methods to
detect DIF in dichotomously scored items. Both uniform and
non-uniform DIF effects can be detected, with methods relying
upon item response models or not. Some methods deal with more
than one focal group.
Author: David Magis (U Liege), Sebastien Beland (UQAM) and Gilles
Raiche (UQAM)
Maintainer: David Magis
DESCRIPTION | 10 +++++-----
MD5 | 10 +++++-----
NEWS | 18 ++++++++++++++++++
R/Logistik.r | 2 +-
TODO | 15 ++++++++++++++-
inst/doc/difR-manual.pdf |binary
6 files changed, 43 insertions(+), 12 deletions(-)
Title: Useful libraries for building a Java based GUI under R
Diff between CommonJavaJars versions 1.0-1 dated 2012-01-28 and 1.0-2 dated 2012-06-13
More information about CommonJavaJars at CRAN
Description: Useful libraries for building a Java based GUI under R
Author: Kornelius Rohmeyer
Maintainer: Kornelius Rohmeyer
DESCRIPTION | 7 +++----
MD5 | 10 +++++-----
inst/doc/CommonJavaJars.Rnw | 27 +++++++++++++++++++++++++--
inst/doc/CommonJavaJars.pdf |binary
inst/java/afcommons.jar |binary
man/CommonJavaJars-package.Rd | 2 +-
6 files changed, 34 insertions(+), 12 deletions(-)
Permanent link
Title: Archetypal Analysis
Diff between archetypes versions 2.0-2 dated 2010-08-24 and 2.1-0 dated 2012-06-13
Description: The main function archetypes implements a framework for
archetypal analysis supporting arbitary problem solving
mechanisms for the different conceputal parts of the algorithm.
Author: Manuel J. A. Eugster [aut, cre], Friedrich Leisch [aut]
Maintainer: Manuel J. A. Eugster
archetypes-2.0-2/archetypes/R/archetypes-deprecated.R |only
archetypes-2.0-2/archetypes/inst/doc/jss.bst |only
archetypes-2.0-2/archetypes/inst/doc/jss.cls |only
archetypes-2.0-2/archetypes/man/archetypes-class.Rd |only
archetypes-2.0-2/archetypes/man/archetypes-deprecated.Rd |only
archetypes-2.0-2/archetypes/man/memento.Rd |only
archetypes-2.1-0/archetypes/DESCRIPTION | 25 -
archetypes-2.1-0/archetypes/MD5 |only
archetypes-2.1-0/archetypes/NAMESPACE | 112 ++----
archetypes-2.1-0/archetypes/NEWS | 28 +
archetypes-2.1-0/archetypes/R/archetypes-class.R | 198 +++++------
archetypes-2.1-0/archetypes/R/archetypes-kit-blocks.R | 55 +--
archetypes-2.1-0/archetypes/R/archetypes-kit.R | 15
archetypes-2.1-0/archetypes/R/archetypes-map.R |only
archetypes-2.1-0/archetypes/R/archetypes-movie.R | 16
archetypes-2.1-0/archetypes/R/archetypes-panorama.R | 13
archetypes-2.1-0/archetypes/R/archetypes-pcplot.R | 3
archetypes-2.1-0/archetypes/R/archetypes-robust.R | 37 --
archetypes-2.1-0/archetypes/R/archetypes-step.R | 146 ++------
archetypes-2.1-0/archetypes/R/archetypes-weighted.R | 36 --
archetypes-2.1-0/archetypes/R/archetypes-xyplot.R | 7
archetypes-2.1-0/archetypes/R/generics.R |only
archetypes-2.1-0/archetypes/R/memento.R | 6
archetypes-2.1-0/archetypes/R/pcplot.R | 12
archetypes-2.1-0/archetypes/R/skeletonplot.R | 5
archetypes-2.1-0/archetypes/inst/doc/archetypes.Rnw | 2
archetypes-2.1-0/archetypes/inst/doc/archetypes.pdf |binary
archetypes-2.1-0/archetypes/inst/doc/rt-002.pdf |binary
archetypes-2.1-0/archetypes/inst/doc/rt-003.pdf |binary
archetypes-2.1-0/archetypes/man/archetypes-generics.Rd | 50 +-
archetypes-2.1-0/archetypes/man/archetypes.Rd | 91 ++---
archetypes-2.1-0/archetypes/man/archetypesFamily.Rd | 33 +
archetypes-2.1-0/archetypes/man/archmap.Rd |only
archetypes-2.1-0/archetypes/man/archmap_projections.Rd |only
archetypes-2.1-0/archetypes/man/as.archetypes.Rd |only
archetypes-2.1-0/archetypes/man/barplot.archetypes.Rd | 58 ++-
archetypes-2.1-0/archetypes/man/bestModel.Rd |only
archetypes-2.1-0/archetypes/man/coef.Rd |only
archetypes-2.1-0/archetypes/man/extract.Rd |only
archetypes-2.1-0/archetypes/man/fitted.Rd |only
archetypes-2.1-0/archetypes/man/kappa.Rd |only
archetypes-2.1-0/archetypes/man/movieplot.Rd | 75 ++--
archetypes-2.1-0/archetypes/man/nparameters.Rd |only
archetypes-2.1-0/archetypes/man/panorama.archetypes.Rd | 75 ++--
archetypes-2.1-0/archetypes/man/parameters.Rd |only
archetypes-2.1-0/archetypes/man/pcplot.Rd | 55 +--
archetypes-2.1-0/archetypes/man/pcplot.archetypes.Rd |only
archetypes-2.1-0/archetypes/man/pcplot.default.Rd |only
archetypes-2.1-0/archetypes/man/predict.Rd |only
archetypes-2.1-0/archetypes/man/residuals.Rd |only
archetypes-2.1-0/archetypes/man/robustArchetypes.Rd |only
archetypes-2.1-0/archetypes/man/rss.Rd |only
archetypes-2.1-0/archetypes/man/screeplot.stepArchetypes.Rd | 24 -
archetypes-2.1-0/archetypes/man/skeletonplot.Rd | 76 ++--
archetypes-2.1-0/archetypes/man/stepArchetypes.Rd | 98 ++---
archetypes-2.1-0/archetypes/man/summary.Rd |only
archetypes-2.1-0/archetypes/man/weightedArchetypes.Rd |only
archetypes-2.1-0/archetypes/man/weights.Rd |only
archetypes-2.1-0/archetypes/man/xyplot.Rd | 57 ---
archetypes-2.1-0/archetypes/man/xyplot.archetypes.Rd |only
archetypes-2.1-0/archetypes/man/xyplot.robustArchetypes.Rd |only
archetypes-2.1-0/archetypes/man/xyplot.stepArchetypes.Rd |only
archetypes-2.1-0/archetypes/man/xyplot.weightedArchetypes.Rd |only
63 files changed, 685 insertions(+), 723 deletions(-)
More information about RcmdrPlugin.StatisticalURV at CRAN
Permanent link
Title: Political Science Computational Laboratory, Stanford University
Diff between pscl versions 1.04.1 dated 2011-10-23 and 1.04.4 dated 2012-06-13
Description: Bayesian analysis of item-response theory (IRT) models,
roll call analysis; computing highest density regions; maximum
likelihood estimation of zero-inflated and hurdle models for
count data; goodness-of-fit measures for GLMs; data sets used
in writing and teaching at the Political Science Computational
Laboratory; seats-votes curves.
Author: Simon Jackman, with contributions from Alex Tahk, Achim
Zeileis, Christina Maimone and Jim Fearon
Maintainer: Simon Jackman
pscl-1.04.1/pscl/inst/doc/auto |only
pscl-1.04.4/pscl/DESCRIPTION | 8 ++--
pscl-1.04.4/pscl/MD5 | 21 +++++------
pscl-1.04.4/pscl/NEWS | 6 +++
pscl-1.04.4/pscl/R/ideal.r | 60 +++++++++++++++++++--------------
pscl-1.04.4/pscl/R/plot.ideal.r | 2 -
pscl-1.04.4/pscl/R/postProcess.r | 9 ++++
pscl-1.04.4/pscl/R/readKH.r | 2 -
pscl-1.04.4/pscl/data/absentee.rda |binary
pscl-1.04.4/pscl/inst/doc/countreg.pdf |binary
pscl-1.04.4/pscl/man/dropRollCall.Rd | 2 -
pscl-1.04.4/pscl/man/ideal.Rd | 4 +-
12 files changed, 69 insertions(+), 45 deletions(-)
Title: Less Code, More Results
Diff between lessR versions 2.3 dated 2012-06-11 and 2.3.1 dated 2012-06-13
Description: Each function accomplishes the work of several or more
standard R functions. For example, two function calls, Read()
and CountAll(), read the data and generate descriptive
statistics for all variables in the data frame, plus histograms
and bar charts as appropriate. Other functions provide for
descriptive statistics, a comprehensive regression analysis,
anova and t-test, color plotting, color bar chart, color
histogram, color box plot, color density curves, a calibrated
power curve, and the reading and display of csv and other
formatted data. The function Help provides a help system that
suggests specific analyses and functions. Variable labels, and
color themes with the set function, are also available.
Author: David W. Gerbing, School of Business Administration, Portland
State University
Maintainer: David W. Gerbing
DESCRIPTION | 6 +++---
MD5 | 4 ++--
R/to.R | 30 ++++++++++++++++--------------
3 files changed, 21 insertions(+), 19 deletions(-)
Title: Various R programming tools for data manipulation
Diff between gdata versions 2.10.5 dated 2012-06-09 and 2.10.6 dated 2012-06-13
Description: Various R programming tools for data manipulation
Author: Gregory R. Warnes, with contributions from Ben Bolker, Gregor
Gorjanc, Gabor Grothendieck, Ales Korosec, Thomas Lumley, Don
MacQueen, Arni Magnusson, Jim Rogers, and others
Maintainer: Gregory Warnes
ChangeLog | 53 +++++++++++++++++++++++++++++++++++++++++++++++++
DESCRIPTION | 6 ++---
MD5 | 16 +++++++-------
NEWS | 25 ++++++++++++++++++++++-
R/nobs.R | 5 +---
inst/ChangeLog | 53 +++++++++++++++++++++++++++++++++++++++++++++++++
inst/NEWS | 25 ++++++++++++++++++++++-
inst/doc/mapLevels.pdf |binary
inst/doc/unknown.pdf |binary
9 files changed, 167 insertions(+), 16 deletions(-)
Title: Analyses of Phylogenetics and Evolution
Diff between ape versions 3.0-3 dated 2012-04-24 and 3.0-4 dated 2012-06-13
Description: ape provides functions for reading, writing, plotting, and
manipulating phylogenetic trees, analyses of comparative data
in a phylogenetic framework, ancestral character analyses,
analyses of diversification and macroevolution, computing
distances from allelic and nucleotide data, reading and writing
nucleotide sequences, and several tools such as Mantel's test,
minimum spanning tree, generalized skyline plots, graphical
exploration of phylogenetic data (alex, trex, kronoviz),
estimation of absolute evolutionary rates and clock-like trees
using mean path lengths and penalized likelihood. Phylogeny
estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and
triangle methods, and several methods handling incomplete
distance matrices (NJ*, BIONJ*, MVR*, and the corresponding
triangle method). Some functions call external applications
(PhyML, Clustal, T-Coffee, Muscle) whose results are returned
into R.
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre
Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer
Opgen-Rhein, Andrei-Alin Popescu, Klaus Schliep, Korbinian
Strimmer, Damien de Vienne
Maintainer: Emmanuel Paradis
ape-3.0-3/ape/R/ape-defunct.R |only
ape-3.0-3/ape/man/GC.content.Rd |only
ape-3.0-3/ape/man/ape-defunct.Rd |only
ape-3.0-3/ape/src/newick.c |only
ape-3.0-4/ape/DESCRIPTION | 8
ape-3.0-4/ape/MD5 | 76 +-
ape-3.0-4/ape/NEWS | 34 +
ape-3.0-4/ape/R/DNA.R | 2
ape-3.0-4/ape/R/me.R | 68 +-
ape-3.0-4/ape/R/nj.R | 2
ape-3.0-4/ape/R/read.dna.R | 84 +--
ape-3.0-4/ape/R/write.dna.R | 8
ape-3.0-4/ape/inst/doc/MoranI.pdf |binary
ape-3.0-4/ape/man/CADM.global.Rd | 40 -
ape-3.0-4/ape/man/ace.Rd | 2
ape-3.0-4/ape/man/base.freq.Rd | 19
ape-3.0-4/ape/man/bionj.Rd | 4
ape-3.0-4/ape/man/compar.cheverud.Rd | 4
ape-3.0-4/ape/man/del.gaps.Rd | 3
ape-3.0-4/ape/man/dist.topo.Rd | 4
ape-3.0-4/ape/man/fastme.Rd | 2
ape-3.0-4/ape/man/howmanytrees.Rd | 2
ape-3.0-4/ape/man/pcoa.Rd | 2
ape-3.0-4/ape/man/rTraitCont.Rd | 6
ape-3.0-4/ape/man/read.dna.Rd | 22
ape-3.0-4/ape/man/rlineage.Rd | 4
ape-3.0-4/ape/man/seg.sites.Rd | 4
ape-3.0-4/ape/man/varcomp.Rd | 6
ape-3.0-4/ape/src/BIONJ.c | 908 ++++++++++-------------------------
ape-3.0-4/ape/src/NNI.c | 7
ape-3.0-4/ape/src/SPR.c | 12
ape-3.0-4/ape/src/TBR.c | 12
ape-3.0-4/ape/src/bNNI.c | 7
ape-3.0-4/ape/src/delta_plot.c | 27 -
ape-3.0-4/ape/src/dist_dna.c | 46 -
ape-3.0-4/ape/src/heap.c | 7
ape-3.0-4/ape/src/me.c | 61 +-
ape-3.0-4/ape/src/me.h | 31 -
ape-3.0-4/ape/src/me_balanced.c | 12
ape-3.0-4/ape/src/me_ols.c | 12
ape-3.0-4/ape/src/tree_phylo.c | 32 -
41 files changed, 602 insertions(+), 978 deletions(-)