Title: Identification of unique multilocus genotypes
Diff between allelematch versions 2.0 dated 2011-10-08 and 2.01 dated 2012-01-11
Description: This package provides tools for the identification of
unique of multilocus genotypes when both genotyping error and
missing data are present. The package is targeted at those
working with large datasets and databases containing multiple
samples of each individual, a situation that is common in
conservation genetics, and particularly in non-invasive
wildlife sampling applications. Functions explicitly
incorporate missing data, and can tolerate allele mismatches
created by genotyping error.
Author: Paul Galpern
Maintainer: Paul Galpern
allelematch-2.0/allelematch/inst/doc/allelematch_supplement.pdf |only
allelematch-2.0/allelematch/inst/doc/example1_1.csv |only
allelematch-2.0/allelematch/inst/doc/example1_1.html |only
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allelematch-2.0/allelematch/inst/doc/index.html |only
allelematch-2.01/allelematch/DESCRIPTION | 10 ++--
allelematch-2.01/allelematch/MD5 | 24 +---------
allelematch-2.01/allelematch/NAMESPACE |only
allelematch-2.01/allelematch/inst/doc/allelematch_vignette.Rnw |only
allelematch-2.01/allelematch/inst/doc/allelematch_vignette.pdf |only
24 files changed, 9 insertions(+), 25 deletions(-)
Title: A Toolkit for Recursive Partytioning
Diff between partykit versions 0.1-2 dated 2011-12-18 and 0.1-3 dated 2012-01-11
Description: A toolkit with infrastructure for representing,
summarizing, and visualizing tree-structured regression and
classification models. This unified infrastructure can be used
for reading/coercing tree models from different sources (rpart,
RWeka, PMML) yielding objects that share functionality for
print/plot/predict methods. (It will also be the basis for a
re-implementation of the party package. Currently, only a
re-implementation of ctree() is contained in the package.)
Author: Torsten Hothorn [aut, cre], Achim Zeileis [aut]
Maintainer: Torsten Hothorn
DESCRIPTION | 26 +++++++++++++-------------
MD5 | 8 ++++----
NEWS | 6 ++++++
data/WeatherPlay.rda |binary
inst/doc/partykit.pdf |binary
5 files changed, 23 insertions(+), 17 deletions(-)
Title: OpenStreetMap and R
Diff between osmar versions 1.0-01 dated 2011-09-30 and 1.1-0 dated 2012-01-11
Description: This package provides infrastructure to access
OpenStreetMap data from different sources, to work with the
data in common R manner, and to convert data into available
infrastructure provided by existing R packages (e.g., into sp
and igraph objects).
Author: Thomas Schlesinger and Manuel J. A. Eugster
Maintainer: Thomas Schlesinger
osmar-1.0-01/osmar/R/bbox2coords.R |only
osmar-1.0-01/osmar/R/bounds.R |only
osmar-1.0-01/osmar/R/compCheck.r |only
osmar-1.0-01/osmar/R/extractValues.r |only
osmar-1.0-01/osmar/R/findID.r |only
osmar-1.0-01/osmar/R/findKeyValue.r |only
osmar-1.0-01/osmar/R/findTime.r |only
osmar-1.0-01/osmar/R/formatBbox.R |only
osmar-1.0-01/osmar/R/gNode.R |only
osmar-1.0-01/osmar/R/gRelation.R |only
osmar-1.0-01/osmar/R/gWay.R |only
osmar-1.0-01/osmar/R/getBboxXML.R |only
osmar-1.0-01/osmar/R/getElementXML.R |only
osmar-1.0-01/osmar/R/getElementsID.R |only
osmar-1.0-01/osmar/R/getOSMObject.R |only
osmar-1.0-01/osmar/R/getXMLData.R |only
osmar-1.0-01/osmar/R/getXMLMember.R |only
osmar-1.0-01/osmar/R/getXMLMeta.R |only
osmar-1.0-01/osmar/R/id2path.R |only
osmar-1.0-01/osmar/R/kids2df.R |only
osmar-1.0-01/osmar/R/merge.r |only
osmar-1.0-01/osmar/R/node2SPDF.R |only
osmar-1.0-01/osmar/R/osmclasses.r |only
osmar-1.0-01/osmar/R/plot.r |only
osmar-1.0-01/osmar/R/print.R |only
osmar-1.0-01/osmar/R/removeKids.R |only
osmar-1.0-01/osmar/R/requiredValues.R |only
osmar-1.0-01/osmar/R/summary.R |only
osmar-1.0-01/osmar/R/way2SLDF.R |only
osmar-1.0-01/osmar/man/Node.Rd |only
osmar-1.0-01/osmar/man/OSM.Rd |only
osmar-1.0-01/osmar/man/Relation.Rd |only
osmar-1.0-01/osmar/man/Way.Rd |only
osmar-1.0-01/osmar/man/bbox2coords.Rd |only
osmar-1.0-01/osmar/man/findID.OSM.Rd |only
osmar-1.0-01/osmar/man/findKeyValue.Rd |only
osmar-1.0-01/osmar/man/findTime.Rd |only
osmar-1.0-01/osmar/man/getBboxXML.Rd |only
osmar-1.0-01/osmar/man/getElementXML.Rd |only
osmar-1.0-01/osmar/man/getOSMObject.Rd |only
osmar-1.0-01/osmar/man/osmar-package.Rd |only
osmar-1.0-01/osmar/man/plot-methods.Rd |only
osmar-1.1-0/osmar/DESCRIPTION | 34 ++++++-----
osmar-1.1-0/osmar/MD5 | 83 ++++++++++++---------------
osmar-1.1-0/osmar/NAMESPACE | 89 +++++++++++++++--------------
osmar-1.1-0/osmar/NEWS |only
osmar-1.1-0/osmar/R/as-igraph.R |only
osmar-1.1-0/osmar/R/as-osm.R |only
osmar-1.1-0/osmar/R/as-osmar-elements.R |only
osmar-1.1-0/osmar/R/as-osmar.R |only
osmar-1.1-0/osmar/R/as-sp.R |only
osmar-1.1-0/osmar/R/get.R |only
osmar-1.1-0/osmar/R/osm-descriptors.R |only
osmar-1.1-0/osmar/R/osmar-finding.R |only
osmar-1.1-0/osmar/R/osmar-plotting.R |only
osmar-1.1-0/osmar/R/osmar-subsetting.R |only
osmar-1.1-0/osmar/R/osmar.R |only
osmar-1.1-0/osmar/R/source-api.R |only
osmar-1.1-0/osmar/R/source-file.R |only
osmar-1.1-0/osmar/R/source-osmosis.R |only
osmar-1.1-0/osmar/R/source.R |only
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osmar-1.1-0/osmar/man/as_igraph.Rd |only
osmar-1.1-0/osmar/man/as_osm.Rd |only
osmar-1.1-0/osmar/man/as_osmar.Rd |only
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osmar-1.1-0/osmar/man/binary_grep.Rd |only
osmar-1.1-0/osmar/man/c.osmar.Rd |only
osmar-1.1-0/osmar/man/find.Rd |only
osmar-1.1-0/osmar/man/find_down.Rd |only
osmar-1.1-0/osmar/man/find_nearest_node.Rd |only
osmar-1.1-0/osmar/man/get_osm.Rd |only
osmar-1.1-0/osmar/man/get_osm_elements.Rd |only
osmar-1.1-0/osmar/man/osm_crs.Rd |only
osmar-1.1-0/osmar/man/osm_descriptors.Rd |only
osmar-1.1-0/osmar/man/osmsource_api.Rd |only
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osmar-1.1-0/osmar/man/osmsource_osmosis.Rd |only
osmar-1.1-0/osmar/man/plot.osmar.Rd |only
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81 files changed, 105 insertions(+), 101 deletions(-)
Title: Simultaneous Inference in General Parametric Models
Diff between multcomp versions 1.2-8 dated 2011-10-26 and 1.2-9 dated 2012-01-11
Description: Simultaneous tests and confidence intervals for general
linear hypotheses in parametric models, including linear,
generalized linear, linear mixed effects, and survival models.
The package includes demos reproducing analyzes presented in
the book "Multiple Comparisons Using R" (Bretz, Hothorn,
Westfall, 2010, CRC Press).
Author: Torsten Hothorn, Frank Bretz and Peter Westfall and Richard M.
Heiberger and Andre Schuetzenmeister
Maintainer: Torsten Hothorn
DESCRIPTION | 10 +++++-----
MD5 | 14 +++++++-------
NEWS | 4 ++++
R/helpers.R | 27 +--------------------------
inst/CHANGES | 4 ++++
inst/doc/chfls1.pdf |binary
inst/doc/generalsiminf.pdf |binary
inst/doc/multcomp-examples.pdf |binary
8 files changed, 21 insertions(+), 38 deletions(-)
Title: Tools for parsing and generating XML within R and S-Plus.
Diff between XML versions 3.7-2 dated 2012-01-08 and 3.7-3 dated 2012-01-11
Description: This package provides many approaches for both reading and
creating XML (and HTML) documents (including DTDs), both local
and accessible via HTTP or FTP. It also offers access to an
XPath "interpreter".
Author: Duncan Temple Lang (duncan@wald.ucdavis.edu)
Maintainer: Duncan Temple Lang
Changes | 9 +++++++++
DESCRIPTION | 13 +++++++------
INSTALL | 2 +-
MD5 | 8 ++++----
R/xmlTreeParse.R | 6 ++++--
5 files changed, 25 insertions(+), 13 deletions(-)
Title: Truncated Multivariate Normal and Student t Distribution
Diff between tmvtnorm versions 1.4-3 dated 2012-01-05 and 1.4-4 dated 2012-01-11
Description: Random number generation for the truncated multivariate
normal and Student t distribution. Computes probabilities,
quantiles and densities, including one-dimensional and
bivariate marginal densities. Computes first and second moments
(i.e. mean and covariance matrix) for the double-truncated
multinormal case.
Author: Stefan Wilhelm
Maintainer: Stefan Wilhelm
tmvtnorm-1.4-3/tmvtnorm/Rplots.pdf |only
tmvtnorm-1.4-3/tmvtnorm/inst/user-feedback.txt |only
tmvtnorm-1.4-3/tmvtnorm/release-notes.txt |only
tmvtnorm-1.4-4/tmvtnorm/DESCRIPTION | 20 ++++++----
tmvtnorm-1.4-4/tmvtnorm/MD5 | 13 ++----
tmvtnorm-1.4-4/tmvtnorm/NEWS | 7 +++
tmvtnorm-1.4-4/tmvtnorm/R/rtmvnorm.R | 11 +++--
tmvtnorm-1.4-4/tmvtnorm/inst/doc/GibbsSampler.pdf |binary
tmvtnorm-1.4-4/tmvtnorm/src/rtmvnormgibbs.f90 | 41 +++++-----------------
9 files changed, 41 insertions(+), 51 deletions(-)
Title: Automatic Text Classification via Supervised Learning
Diff between RTextTools versions 1.3.3 dated 2012-01-08 and 1.3.4 dated 2012-01-11
Description: RTextTools is a machine learning package for automatic
text classification that makes it simple for novice users to
get started with machine learning, while allowing experienced
users to easily experiment with different settings and
algorithm combinations. The package includes nine algorithms
for ensemble classification (svm, slda, boosting, bagging,
random forests, glmnet, decision trees, neural networks,
maximum entropy), comprehensive analytics, and thorough
documentation.
Author: Timothy P. Jurka, Loren Collingwood, Amber E. Boydstun,
Emiliano Grossman, Wouter van Atteveldt
Maintainer: Timothy P. Jurka
ChangeLog | 6 ++++++
DESCRIPTION | 21 +++++++++++++++------
MD5 | 12 ++++++------
NAMESPACE | 1 +
R/create_matrix.R | 22 +++++++++++++++++++++-
inst/THANKS | 16 ++++++++--------
man/create_matrix.Rd | 10 ++++++----
7 files changed, 63 insertions(+), 25 deletions(-)
Title: Analysis of Parent-Specific DNA Copy Numbers
Diff between PSCBS versions 0.17.1 dated 2011-11-23 and 0.19.4 dated 2012-01-11
Description: Segments allele-specific DNA copy number data to detect
regions with abnormal copy number within each parental
chromosome
Author: A.B. Olshen, H. Bengtsson, P. Neuvial, P.T. Spellman, R.A.
Olshen, V.E. Seshan
Maintainer: Henrik Bengtsson
PSCBS-0.17.1/PSCBS/incl/segmentByPairedPSCBS,knownSegments.Rex |only
PSCBS-0.19.4/PSCBS/DESCRIPTION | 21 +-
PSCBS-0.19.4/PSCBS/MD5 | 99 +++++-----
PSCBS-0.19.4/PSCBS/R/AbstractCBS.HCLUST.R |only
PSCBS-0.19.4/PSCBS/R/AbstractCBS.PLOT.R | 5
PSCBS-0.19.4/PSCBS/R/AbstractCBS.R | 5
PSCBS-0.19.4/PSCBS/R/CBS.CALL.R | 30 ++-
PSCBS-0.19.4/PSCBS/R/CBS.EXTS.R | 20 +-
PSCBS-0.19.4/PSCBS/R/CBS.IO.R | 79 +++++--
PSCBS-0.19.4/PSCBS/R/CBS.PLOT.R | 23 ++
PSCBS-0.19.4/PSCBS/R/CBS.PRUNE.R | 22 +-
PSCBS-0.19.4/PSCBS/R/CBS.R | 28 ++
PSCBS-0.19.4/PSCBS/R/CBS.updateMeansTogether.R |only
PSCBS-0.19.4/PSCBS/R/PSCBS.EXTS.R | 52 ++++-
PSCBS-0.19.4/PSCBS/R/PSCBS.IO.R |only
PSCBS-0.19.4/PSCBS/R/PairedPSCBS.BOOT2.R | 30 ++-
PSCBS-0.19.4/PSCBS/R/PairedPSCBS.EXTS.R | 58 +++++
PSCBS-0.19.4/PSCBS/R/PairedPSCBS.PLOT.R | 47 ++++
PSCBS-0.19.4/PSCBS/R/PairedPSCBS.RESTRUCT.R | 11 +
PSCBS-0.19.4/PSCBS/R/PairedPSCBS.callROH.R | 14 +
PSCBS-0.19.4/PSCBS/R/PairedPSCBS.updateMeansTogether.R |only
PSCBS-0.19.4/PSCBS/R/callSegmentationOutliers.R | 33 +++
PSCBS-0.19.4/PSCBS/R/findLargeGaps.R |only
PSCBS-0.19.4/PSCBS/R/gapsToSegments.R |only
PSCBS-0.19.4/PSCBS/R/segmentByCBS.R | 19 +
PSCBS-0.19.4/PSCBS/R/zzz.R | 9
PSCBS-0.19.4/PSCBS/incl/999.missingdocs.txt | 7
PSCBS-0.19.4/PSCBS/incl/segmentByCBS,tests.Rex | 12 -
PSCBS-0.19.4/PSCBS/incl/segmentByPairedPSCBS,allLOH.Rex | 8
PSCBS-0.19.4/PSCBS/incl/segmentByPairedPSCBS.Rex | 24 +-
PSCBS-0.19.4/PSCBS/inst/NEWS | 89 ++++++++
PSCBS-0.19.4/PSCBS/inst/data-ex/PairedPSCBS,exData,chr01.Rbin |binary
PSCBS-0.19.4/PSCBS/inst/doc |only
PSCBS-0.19.4/PSCBS/man/CBS.Rd | 2
PSCBS-0.19.4/PSCBS/man/Non-documented_objects.Rd | 12 +
PSCBS-0.19.4/PSCBS/man/PSCBS-package.Rd | 5
PSCBS-0.19.4/PSCBS/man/PSCBS.Rd | 3
PSCBS-0.19.4/PSCBS/man/PairedPSCBS.Rd | 4
PSCBS-0.19.4/PSCBS/man/callGainsAndLosses.CBS.Rd | 2
PSCBS-0.19.4/PSCBS/man/callROH.PairedPSCBS.Rd | 4
PSCBS-0.19.4/PSCBS/man/extractSegmentMeansByLocus.CBS.Rd | 2
PSCBS-0.19.4/PSCBS/man/findLargeGaps.Rd |only
PSCBS-0.19.4/PSCBS/man/gapsToSegments.data.frame.Rd |only
PSCBS-0.19.4/PSCBS/man/getSegments.AbstractCBS.Rd | 1
PSCBS-0.19.4/PSCBS/man/getSegments.PSCBS.Rd | 4
PSCBS-0.19.4/PSCBS/man/hclustCNs.AbstractCBS.Rd |only
PSCBS-0.19.4/PSCBS/man/pruneByHClust.AbstractCBS.Rd |only
PSCBS-0.19.4/PSCBS/man/pruneBySdUndo.CBS.Rd | 3
PSCBS-0.19.4/PSCBS/man/segmentByCBS.Rd | 27 +-
PSCBS-0.19.4/PSCBS/man/segmentByPairedPSCBS.Rd | 47 +++-
PSCBS-0.19.4/PSCBS/man/updateMeansTogether.AbstractCBS.Rd |only
PSCBS-0.19.4/PSCBS/man/writeSegments.CBS.Rd | 7
PSCBS-0.19.4/PSCBS/man/writeSegments.PSCBS.Rd |only
PSCBS-0.19.4/PSCBS/tests/segmentByPairedPSCBS,knownSegments.R | 52 ++---
PSCBS-0.19.4/PSCBS/tests/segmentByPairedPSCBS,noNormalBAFs.R | 40 ++--
PSCBS-0.19.4/PSCBS/tests/segmentByPairedPSCBS.R |only
56 files changed, 730 insertions(+), 230 deletions(-)
Title: Phylogenetic Tools for comparative biology (and other things)
Diff between phytools versions 0.1-5 dated 2011-12-18 and 0.1-6 dated 2012-01-11
Description: phytools provides various functions for phylogenetic
analysis, mostly relevant to comparative biology.
Author: Liam J. Revell
Maintainer: Liam J. Revell
DESCRIPTION | 12 ++++-----
MD5 | 28 +++++++++++++---------
NAMESPACE | 6 ++--
R/evolvcv.lite.R |only
R/mcmcBM.full.R | 1
R/mcmcLambda.R | 18 ++++++++++----
R/pbtree.R |only
R/phenogram.R | 39 ++++++++++++++++++++++++------
R/phylosig.R | 66 +++++++++++++++++++++++++++++++++-------------------
R/plotTree.R | 54 +++++++++---------------------------------
R/sampleFrom.R |only
man/evolvcv.lite.Rd |only
man/pbtree.Rd |only
man/phenogram.Rd | 9 +++----
man/phylANOVA.Rd | 2 -
man/phylosig.Rd | 1
man/plotTree.Rd | 15 +++++++----
man/sampleFrom.Rd |only
18 files changed, 141 insertions(+), 110 deletions(-)
Title: Importing Vector Graphics
Diff between grImport versions 0.8-1 dated 2011-09-01 and 0.8-2 dated 2012-01-11
Description: Functions for converting, importing, and drawing
PostScript pictures in R plots.
Author: Paul Murrell and Richard Walton.
Maintainer: Paul Murrell
DESCRIPTION | 6 +++---
MD5 | 16 +++++++++-------
R/PostScript2RGML.R | 9 +++++++--
inst/doc/circleRas.pdf |binary
inst/doc/fiddledplot.pdf |binary
inst/doc/import.pdf |binary
inst/doc/importText.pdf |binary
inst/doc/todo.txt | 5 +++++
inst/xsl |only
9 files changed, 24 insertions(+), 12 deletions(-)
Title: Functions for analysing epidemiological data
Diff between epiR versions 0.9-32 dated 2011-05-10 and 0.9-35 dated 2012-01-11
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.
Author: Mark Stevenson
Maintainer: Mark Stevenson
DESCRIPTION | 12 -
MD5 |only
NAMESPACE |only
R/epi.kappa.R | 109 ++++++++++++----
R/epi.prev.R | 311 +++++++++++++++++++++++++++++++++++++++---------
R/zzz.R | 11 +
doc/epiR.pdf |binary
man/epi.2by2.Rd | 3
man/epi.RtoBUGS.Rd | 12 -
man/epi.about.Rd | 15 --
man/epi.asc.Rd | 16 --
man/epi.bohning.Rd | 13 --
man/epi.ccc.Rd | 9 -
man/epi.cluster1size.Rd | 12 -
man/epi.cluster2size.Rd | 9 -
man/epi.clustersize.Rd | 9 -
man/epi.conf.Rd | 12 -
man/epi.convgrid.Rd | 16 --
man/epi.cp.Rd | 9 -
man/epi.cpresids.Rd | 9 -
man/epi.descriptives.Rd | 18 --
man/epi.detectsize.Rd | 9 -
man/epi.dgamma.Rd | 11 -
man/epi.directadj.Rd | 10 -
man/epi.dms.Rd | 18 --
man/epi.dsl.Rd | 3
man/epi.edr.Rd | 12 -
man/epi.empbayes.Rd | 9 -
man/epi.epidural.Rd | 5
man/epi.herdtest.Rd | 6
man/epi.indirectadj.Rd | 6
man/epi.insthaz.Rd | 11 -
man/epi.interaction.Rd | 9 -
man/epi.iv.Rd | 3
man/epi.kappa.Rd | 52 ++++----
man/epi.ltd.Rd | 6
man/epi.mh.Rd | 3
man/epi.nomogram.Rd | 12 -
man/epi.offset.Rd | 9 -
man/epi.pooled.Rd | 12 -
man/epi.popsize.Rd | 11 -
man/epi.prcc.Rd | 9 -
man/epi.prev.Rd | 68 ++++++----
man/epi.simplesize.Rd | 8 -
man/epi.smd.Rd | 6
man/epi.stratasize.Rd | 6
man/epi.studysize.Rd | 6
man/epi.tests.Rd | 6
48 files changed, 417 insertions(+), 514 deletions(-)