Title: Axis Labeling
Diff between labeling versions 0.1 dated 2010-11-22 and 0.2 dated 2013-06-20
Description: Provides a range of axis labeling algorithms
Author: Justin Talbot
Maintainer: Justin Talbot
DESCRIPTION | 16 ++++----
MD5 | 28 +++++++--------
NAMESPACE | 15 +++++---
R/labeling.R | 19 ++++++++--
man/extended.Rd | 52 ++++++++++++++++++++--------
man/extended.figures.Rd | 31 ++++++++++++-----
man/gnuplot.Rd | 33 +++++++++++++-----
man/heckbert.Rd | 34 +++++++++++++-----
man/labeling-package.Rd | 64 +++++++++++++++++++++++------------
man/matplotlib.Rd | 33 +++++++++++++-----
man/nelder.Rd | 39 ++++++++++++++++-----
man/rpretty.Rd | 62 +++++++++++++++++++++++++---------
man/sparks.Rd | 35 ++++++++++++++-----
man/thayer.Rd | 35 ++++++++++++++-----
man/wilkinson.Rd | 87 +++++++++++++++++++++++++++++++++---------------
15 files changed, 413 insertions(+), 170 deletions(-)
Title: Dive analysis and calibration
Diff between diveMove versions 1.3.6 dated 2013-03-28 and 1.3.7 dated 2013-06-20
Description: Utilities to represent, visualize, filter, analyse, and
summarize time-depth recorder (TDR) data. Miscellaneous
functions for handling location data are also provided.
Author: Sebastian P. Luque
Maintainer: Sebastian P. Luque
ChangeLog | 88 +++++++++++++++++++++++++++++++++++++-----------
DESCRIPTION | 12 +++---
MD5 | 45 ++++++++++++------------
NAMESPACE | 10 ++++-
NEWS | 21 ++++++++++-
R/AllMethod.R | 6 ++-
R/austFilter.R | 44 ++++++++++++------------
R/calibrate.R | 5 --
R/distSpeed.R | 43 ++++++++---------------
R/plotTDR.R | 4 +-
R/zoc.R | 3 -
R/zzz.R | 15 ++++++--
inst/doc/diveMove.R |only
inst/doc/diveMove.pdf |binary
man/austFilter.Rd | 12 ++++--
man/distSpeed.Rd | 17 +++++++--
man/diveMove-package.Rd | 4 +-
man/dives.Rd | 10 ++---
man/readLocs.Rd | 7 ++-
man/readTDR.Rd | 11 +++---
man/sealLocs.Rd | 7 +--
tests/calibrations.R | 2 -
tests/class-tests.R | 58 ++++++++++++++++---------------
tests/final-stats.R | 4 --
24 files changed, 258 insertions(+), 170 deletions(-)
Title: Classification and Regression Training
Diff between caret versions 5.16-04 dated 2013-05-17 and 5.16-24 dated 2013-06-20
Description: Misc functions for training and plotting classification
and regression models
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer, Allan Engelhardt and Tony Cooper
Maintainer: Max Kuhn
DESCRIPTION | 31 +++++-------
MD5 | 36 +++++++-------
R/classLevels.R | 1
R/createGrid.R | 25 +++------
R/createModel.R | 123 +++++++++++++++++++++++++++++--------------------
R/misc.R | 44 +++++++++++++++--
R/modelLookup.R | 114 ++++++++++++++++++++++++++++++---------------
R/predictionFunction.R | 30 ++++++++---
R/print.train.R | 7 --
R/probFunction.R | 9 ---
R/rfe.R | 3 +
R/selection.R | 15 +++++
R/train.default.R | 13 +++--
R/workflows.R | 18 +++----
inst/NEWS.Rd | 49 +++++++++++++++++++
inst/doc/caret.pdf |binary
inst/modelKey.txt | 2
man/calibration.Rd | 3 -
man/train.Rd | 3 -
19 files changed, 346 insertions(+), 180 deletions(-)
Title: Truncated Maximum Likelihood fit and Robust Accelerated Failure
Time regression for Gaussian and log-Weibull case.
Diff between RobustAFT versions 1.0 dated 2011-08-20 and 1.2 dated 2013-06-20
Description: R functions for the computation of the truncated maximum
likelihood and the robust accelerated failure time regression
for gaussian and log-Weibull case.
Author: Alfio Marazzi
Maintainer: A. Randriamiharisoa
RobustAFT-1.0/RobustAFT/R/comval.R |only
RobustAFT-1.0/RobustAFT/R/dfcomn.R |only
RobustAFT-1.2/RobustAFT/DESCRIPTION | 11
RobustAFT-1.2/RobustAFT/MD5 | 227 ++++++--------
RobustAFT-1.2/RobustAFT/NAMESPACE | 2
RobustAFT-1.2/RobustAFT/R/AV.MM.gauss.R | 8
RobustAFT-1.2/RobustAFT/R/BtamatG.r | 26 -
RobustAFT-1.2/RobustAFT/R/BtamatW.r | 28 -
RobustAFT-1.2/RobustAFT/R/CandidateG.r | 49 +--
RobustAFT-1.2/RobustAFT/R/ChiSG.r | 10
RobustAFT-1.2/RobustAFT/R/ChiSN.r | 10
RobustAFT-1.2/RobustAFT/R/ChiSw.r | 10
RobustAFT-1.2/RobustAFT/R/Chidlweibul.r | 8
RobustAFT-1.2/RobustAFT/R/Chidnorm.r | 7
RobustAFT-1.2/RobustAFT/R/CutoffW.r | 20 -
RobustAFT-1.2/RobustAFT/R/IChidlweibul.r | 16
RobustAFT-1.2/RobustAFT/R/IChidnorm.r | 14
RobustAFT-1.2/RobustAFT/R/IPsidnorm.r | 14
RobustAFT-1.2/RobustAFT/R/MM.E.gauss.R | 14
RobustAFT-1.2/RobustAFT/R/PsiSG.r | 10
RobustAFT-1.2/RobustAFT/R/PsiSN.r | 10
RobustAFT-1.2/RobustAFT/R/PsiSw.r | 10
RobustAFT-1.2/RobustAFT/R/Psidnorm.r | 7
RobustAFT-1.2/RobustAFT/R/PspSG.r | 12
RobustAFT-1.2/RobustAFT/R/PspSN.r | 12
RobustAFT-1.2/RobustAFT/R/PspSw.r | 12
RobustAFT-1.2/RobustAFT/R/QMatrix.G.r | 67 ++--
RobustAFT-1.2/RobustAFT/R/Qmatrix.W.r | 69 ++--
RobustAFT-1.2/RobustAFT/R/RappN.r | 35 +-
RobustAFT-1.2/RobustAFT/R/RappW.r | 37 +-
RobustAFT-1.2/RobustAFT/R/RefAve2G.r | 30 -
RobustAFT-1.2/RobustAFT/R/RefAve2W.r | 32 -
RobustAFT-1.2/RobustAFT/R/RefBetaG.r | 82 ++---
RobustAFT-1.2/RobustAFT/R/RefBetaW.r | 83 ++---
RobustAFT-1.2/RobustAFT/R/RefSG.r | 94 ++---
RobustAFT-1.2/RobustAFT/R/RefSW.r | 89 ++---
RobustAFT-1.2/RobustAFT/R/RefSigmaG.r | 19 -
RobustAFT-1.2/RobustAFT/R/RefSigmaW.r | 19 -
RobustAFT-1.2/RobustAFT/R/ResExpG.r | 15
RobustAFT-1.2/RobustAFT/R/ResExpW.r | 20 -
RobustAFT-1.2/RobustAFT/R/SparamG.S.r | 128 +++----
RobustAFT-1.2/RobustAFT/R/SparamW.S.r | 138 ++++----
RobustAFT-1.2/RobustAFT/R/TML.Ave2G.r | 46 +-
RobustAFT-1.2/RobustAFT/R/TML.Ave2W.r | 49 +--
RobustAFT-1.2/RobustAFT/R/TML.BetaG.r | 82 ++---
RobustAFT-1.2/RobustAFT/R/TML.BetaW.r | 91 ++---
RobustAFT-1.2/RobustAFT/R/TML.SigmaG.r | 19 -
RobustAFT-1.2/RobustAFT/R/TML.SigmaW.r | 21 -
RobustAFT-1.2/RobustAFT/R/TML.censored.R | 14
RobustAFT-1.2/RobustAFT/R/TML.gauss.R | 2
RobustAFT-1.2/RobustAFT/R/TML.logweibull.R | 2
RobustAFT-1.2/RobustAFT/R/TML.noncensored.R | 8
RobustAFT-1.2/RobustAFT/R/TML1.control.R | 4
RobustAFT-1.2/RobustAFT/R/TML1.noncensored.R | 8
RobustAFT-1.2/RobustAFT/R/TMLG.r | 105 +++---
RobustAFT-1.2/RobustAFT/R/TMLW.r | 112 +++---
RobustAFT-1.2/RobustAFT/R/TMLeqn2W.r | 49 +--
RobustAFT-1.2/RobustAFT/R/TMLjac11.G.r | 41 +-
RobustAFT-1.2/RobustAFT/R/TMLjac11.W.r | 41 +-
RobustAFT-1.2/RobustAFT/R/TMLjac12.G.r | 41 +-
RobustAFT-1.2/RobustAFT/R/TMLjac12.W.r | 41 +-
RobustAFT-1.2/RobustAFT/R/TMLjac21.G.r | 45 +-
RobustAFT-1.2/RobustAFT/R/TMLjac21.W.r | 45 +-
RobustAFT-1.2/RobustAFT/R/TMLjac22.G.r | 45 +-
RobustAFT-1.2/RobustAFT/R/TMLjac22.W.R | 45 +-
RobustAFT-1.2/RobustAFT/R/comval2.R |only
RobustAFT-1.2/RobustAFT/R/dfcomn2.R | 38 --
RobustAFT-1.2/RobustAFT/R/dfvals.R | 94 ++---
RobustAFT-1.2/RobustAFT/R/dlweibul.r | 7
RobustAFT-1.2/RobustAFT/R/ezez.R | 7
RobustAFT-1.2/RobustAFT/R/hysest.R | 6
RobustAFT-1.2/RobustAFT/R/intg0.TMLW.r | 7
RobustAFT-1.2/RobustAFT/R/intg0.r | 12
RobustAFT-1.2/RobustAFT/R/intg1.TMLW.r | 7
RobustAFT-1.2/RobustAFT/R/intg2.TMLW.r | 7
RobustAFT-1.2/RobustAFT/R/intg2.r | 7
RobustAFT-1.2/RobustAFT/R/intw0.r | 15
RobustAFT-1.2/RobustAFT/R/intw1.r | 8
RobustAFT-1.2/RobustAFT/R/intxlwbl.r | 10
RobustAFT-1.2/RobustAFT/R/liepsu.R | 2
RobustAFT-1.2/RobustAFT/R/lywalg.R | 4
RobustAFT-1.2/RobustAFT/R/plot.TML.R | 2
RobustAFT-1.2/RobustAFT/R/plot.fits.compare.R | 2
RobustAFT-1.2/RobustAFT/R/plweibul.r | 7
RobustAFT-1.2/RobustAFT/R/ps0.r | 7
RobustAFT-1.2/RobustAFT/R/ps0W.r | 7
RobustAFT-1.2/RobustAFT/R/ps1.r | 7
RobustAFT-1.2/RobustAFT/R/ps1W.r | 7
RobustAFT-1.2/RobustAFT/R/psp0W.r | 7
RobustAFT-1.2/RobustAFT/R/psp1W.r | 7
RobustAFT-1.2/RobustAFT/R/regfal.r | 60 +--
RobustAFT-1.2/RobustAFT/R/rysigm.R | 4
RobustAFT-1.2/RobustAFT/R/rywalg.R | 4
RobustAFT-1.2/RobustAFT/R/s.estim.R | 2
RobustAFT-1.2/RobustAFT/R/summary.TML.R | 6
RobustAFT-1.2/RobustAFT/R/tutl.R | 10
RobustAFT-1.2/RobustAFT/R/ww.r | 8
RobustAFT-1.2/RobustAFT/R/xlwbl.r | 7
RobustAFT-1.2/RobustAFT/R/zez.R | 7
RobustAFT-1.2/RobustAFT/man/RobustAFT.package.Rd | 155 +++++----
RobustAFT-1.2/RobustAFT/man/TML.censored.control.S.rd | 29 +
RobustAFT-1.2/RobustAFT/man/TML.censored.control.ref.rd | 35 +-
RobustAFT-1.2/RobustAFT/man/TML.censored.control.tml.rd | 25 -
RobustAFT-1.2/RobustAFT/man/TML.censored.rd | 97 +++--
RobustAFT-1.2/RobustAFT/man/TML.noncensored.control.rd | 38 +-
RobustAFT-1.2/RobustAFT/man/TML.noncensored.rd | 75 ++--
RobustAFT-1.2/RobustAFT/man/TML1.noncensored.Rd | 55 ++-
RobustAFT-1.2/RobustAFT/man/TML1.noncensored.control.S.Rd | 8
RobustAFT-1.2/RobustAFT/man/TML1.noncensored.control.rd | 9
RobustAFT-1.2/RobustAFT/man/fits.compare.rd | 28 -
RobustAFT-1.2/RobustAFT/man/plot.TML.rd | 39 +-
RobustAFT-1.2/RobustAFT/man/plot.fits.compare.rd | 37 +-
RobustAFT-1.2/RobustAFT/man/predict.TML.rd | 26 -
RobustAFT-1.2/RobustAFT/man/summary.TML.rd | 51 ++-
RobustAFT-1.2/RobustAFT/src/robaft.f | 50 ++-
RobustAFT-1.2/RobustAFT/src/robcom.f | 108 +-----
116 files changed, 1878 insertions(+), 1839 deletions(-)
Title: Meta-Analysis with R
Diff between meta versions 2.4-0 dated 2013-06-17 and 2.4-1 dated 2013-06-20
Description: Fixed and random effects meta-analysis. Functions for
tests of bias, forest and funnel plot.
Author: Guido Schwarzer
Maintainer: Guido Schwarzer
DESCRIPTION | 8 +--
MD5 | 30 +++++++-------
NEWS | 32 +++++++++++++++
R/asin2p.R | 56 ++++++++++++++------------
R/forest.meta.R | 88 +++++++++++++++++++++++++++---------------
R/metaprop.R | 3 +
R/print.meta.R | 16 +++++++
R/print.summary.meta.R | 102 ++++++++++++++++++++++++++++++-------------------
man/forest.meta.Rd | 23 +++++++++++
man/metabin.Rd | 1
man/metacont.Rd | 1
man/metacor.Rd | 2
man/metacr.Rd | 2
man/metagen.Rd | 2
man/metaprop.Rd | 4 +
man/print.meta.Rd | 1
16 files changed, 255 insertions(+), 116 deletions(-)
Title: Syntax highlighter
Diff between highlight versions 0.4.2 dated 2013-06-19 and 0.4.3 dated 2013-06-20
Description: Syntax highlighter for R code based on the results of the
R parser. Rendering in HTML and latex markup. Custom Sweave
driver performing syntax highlighting of R code chunks
Author: Romain Francois
Maintainer: Romain Francois
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
R/SweaveLatexDriver.R | 9 ++++++---
R/zzz.R | 2 +-
build/highlight.pdf |binary
man/Hweave.Rd | 15 +++++++++++----
man/highlight-package.Rd | 4 ++--
7 files changed, 30 insertions(+), 20 deletions(-)
Title: Tools of the Trade for Discriminant Analysis
Diff between DiscriMiner versions 0.1-22 dated 2012-09-14 and 0.1-25 dated 2013-06-20
Description: Functions for Discriminant Analysis and Classification
purposes covering various methods such as descriptive,
geometric, linear, quadratic, PLS, as well as qualitative
discriminant analyses
Author: Gaston Sanchez [aut, cre], Charles Determan [ctb]
Maintainer: Gaston Sanchez
DESCRIPTION | 30 +++++++---
MD5 | 133 +++++++++++++++++++++++----------------------
NAMESPACE | 84 ++++++++++------------------
R/DiscriMiner-package.R |only
R/FRatio.R | 24 ++++++++
R/betweenCov.R | 33 +++++++++--
R/betweenSS.R | 24 ++++++++
R/binarize.R | 27 ++++++++-
R/classify.R | 47 ++++++++++++++-
R/corRatio.R | 23 +++++++
R/desDA.R | 64 +++++++++++++++++++--
R/discPower.R | 30 +++++++++-
R/disqual.R | 60 ++++++++++++++++++++
R/easyMCA.R | 30 ++++++++++
R/geoDA.R | 56 ++++++++++++++++++
R/getWithin.R | 31 ++++++++++
R/groupMeans.R | 25 ++++++++
R/groupMedians.R | 25 ++++++++
R/groupQuants.R | 26 ++++++++
R/groupStds.R | 25 ++++++++
R/groupVars.R | 25 ++++++++
R/linDA.R | 65 +++++++++++++++++++++
R/my_plsDA.R | 107 +++++++++++++++++++++++++-----------
R/my_plsDA_old.R |only
R/plot.plsda.R | 1
R/plsDA.R | 96 ++++++++++++++++++++++++++++----
R/plsDA_old.R |only
R/print.desda.R | 1
R/print.disqual.R | 1
R/print.geoda.R | 1
R/print.linda.R | 1
R/print.plsda.R | 1
R/print.quada.R | 1
R/print.qualmca.R | 1
R/quaDA.R | 69 ++++++++++++++++++++++-
R/totalCov.R | 27 +++++++++
R/totalSS.R | 21 +++++++
R/withinCov.R | 29 +++++++++
R/withinSS.R | 24 ++++++++
README.md | 45 ++++++++-------
man/DiscriMiner-package.Rd | 51 +++++++++--------
man/FRatio.Rd | 35 ++++++-----
man/betweenCov.Rd | 54 ++++++++++--------
man/betweenSS.Rd | 35 ++++++-----
man/binarize.Rd | 34 ++++++-----
man/bordeaux.Rd | 38 +++++-------
man/classify.Rd | 45 +++++++++------
man/corRatio.Rd | 39 ++++++-------
man/desDA.Rd | 84 +++++++++++++++++-----------
man/discPower.Rd | 44 ++++++++------
man/disqual.Rd | 102 +++++++++++++++++++++++-----------
man/easyMCA.Rd | 45 ++++++++-------
man/geoDA.Rd | 82 +++++++++++++++++----------
man/getWithin.Rd | 41 +++++++------
man/groupMeans.Rd | 36 ++++++------
man/groupMedians.Rd | 36 ++++++------
man/groupQuants.Rd | 41 ++++++++-----
man/groupStds.Rd | 36 ++++++------
man/groupVars.Rd | 37 +++++++-----
man/infarctus.Rd | 44 ++++++--------
man/insurance.Rd | 59 ++++++++++---------
man/linDA.Rd | 93 ++++++++++++++++++++-----------
man/my_plsDA.Rd |only
man/plsDA.Rd | 114 +++++++++++++++++++++++++++-----------
man/plsDA_old.Rd |only
man/quaDA.Rd | 91 +++++++++++++++++++-----------
man/totalCov.Rd | 40 +++++++------
man/totalSS.Rd | 31 +++++-----
man/withinCov.Rd | 44 ++++++++------
man/withinSS.Rd | 35 ++++++-----
70 files changed, 1968 insertions(+), 811 deletions(-)
Title: Tools for parsing and generating XML within R and S-Plus.
Diff between XML versions 3.96-1.1 dated 2013-03-28 and 3.98-1.1 dated 2013-06-20
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@r-project.org)
Maintainer: Duncan Temple Lang
XML-3.96-1.1/XML/INSTALL_R |only
XML-3.96-1.1/XML/INSTALL_S |only
XML-3.98-1.1/XML/Changes | 19 +++++
XML-3.98-1.1/XML/DESCRIPTION | 10 +-
XML-3.98-1.1/XML/DESCRIPTION.in | 6 +
XML-3.98-1.1/XML/MD5 | 83 +++++++++++-----------
XML-3.98-1.1/XML/NAMESPACE | 4 -
XML-3.98-1.1/XML/R/getRelativeURL.R | 12 +--
XML-3.98-1.1/XML/R/namespaces.R | 23 ++++++
XML-3.98-1.1/XML/R/simplifyPath.R |only
XML-3.98-1.1/XML/R/xincludes.R | 2
XML-3.98-1.1/XML/R/xmlIncludes.R |only
XML-3.98-1.1/XML/R/xmlInternalSource.R | 52 +++++++------
XML-3.98-1.1/XML/Todo.xml | 10 ++
XML-3.98-1.1/XML/VersionInfo | 2
XML-3.98-1.1/XML/a.out.dSYM |only
XML-3.98-1.1/XML/index.html | 22 ++---
XML-3.98-1.1/XML/inst/exampleData/redundantNS.xml |only
XML-3.98-1.1/XML/libxml2.9.R |only
XML-3.98-1.1/XML/man/Doctype-class.Rd | 4 -
XML-3.98-1.1/XML/man/Doctype.Rd | 8 +-
XML-3.98-1.1/XML/man/SAXState-class.Rd | 3
XML-3.98-1.1/XML/man/addChildren.Rd | 7 +
XML-3.98-1.1/XML/man/asXMLTreeNode.Rd | 3
XML-3.98-1.1/XML/man/catalogs.Rd | 33 ++++----
XML-3.98-1.1/XML/man/getChildrenStrings.Rd | 4 -
XML-3.98-1.1/XML/man/getNodeSet.Rd | 14 ++-
XML-3.98-1.1/XML/man/getRelativeURL.Rd | 4 -
XML-3.98-1.1/XML/man/getXIncludes.Rd | 21 +++++
XML-3.98-1.1/XML/man/makeClassTemplate.Rd | 4 -
XML-3.98-1.1/XML/man/newXMLDoc.Rd | 5 +
XML-3.98-1.1/XML/man/readHTMLTable.Rd | 12 +--
XML-3.98-1.1/XML/man/xmlAttrs.Rd | 3
XML-3.98-1.1/XML/man/xmlCleanNamespaces.Rd |only
XML-3.98-1.1/XML/man/xmlClone.Rd | 3
XML-3.98-1.1/XML/man/xmlEventParse.Rd | 13 ++-
XML-3.98-1.1/XML/man/xmlFlatListTree.Rd | 3
XML-3.98-1.1/XML/man/xmlNode.Rd | 3
XML-3.98-1.1/XML/man/xmlParseDoc.Rd | 3
XML-3.98-1.1/XML/man/xmlSource.Rd | 14 ++-
XML-3.98-1.1/XML/man/xmlTree.Rd | 11 ++
XML-3.98-1.1/XML/man/xmlTreeParse.Rd | 8 +-
XML-3.98-1.1/XML/src/XMLEventParse.c | 51 ++++++++++---
XML-3.98-1.1/XML/src/XMLHashTree.c | 4 -
XML-3.98-1.1/XML/src/XMLTree.c | 60 ++++++++++++---
XML-3.98-1.1/XML/src/xpath.c | 2
46 files changed, 365 insertions(+), 180 deletions(-)
Title: A swiss army knife for population genetic & genomic analysis
Diff between PopGenome versions 1.2.3 dated 2013-02-21 and 1.2.5 dated 2013-06-20
Description: PopGenome is an R-package for Population Genetic & Genomic
Analysis
Author: Bastian Pfeifer, Ulrich Wittelsbuerger
Maintainer: Bastian Pfeifer
PopGenome-1.2.3/PopGenome/man/concatenate_to_whole_genome.Rd |only
PopGenome-1.2.3/PopGenome/man/popGetBial-methods.Rd |only
PopGenome-1.2.3/PopGenome/vignettes/XXX.png |only
PopGenome-1.2.3/PopGenome/vignettes/ZZZ2.png |only
PopGenome-1.2.5/PopGenome/DESCRIPTION | 17
PopGenome-1.2.5/PopGenome/MD5 | 114 ++-
PopGenome-1.2.5/PopGenome/NAMESPACE | 12
PopGenome-1.2.5/PopGenome/NEWS | 43 +
PopGenome-1.2.5/PopGenome/R/BAYESRETURN.R | 3
PopGenome-1.2.5/PopGenome/R/GENOME.R | 94 ++
PopGenome-1.2.5/PopGenome/R/PG_plot.biallelic.matrix.R |only
PopGenome-1.2.5/PopGenome/R/calc.R2.R |only
PopGenome-1.2.5/PopGenome/R/calc_sxsfss.R | 14
PopGenome-1.2.5/PopGenome/R/complike.R | 37 -
PopGenome-1.2.5/PopGenome/R/concatenate.R | 16
PopGenome-1.2.5/PopGenome/R/concatenate.classes.R |only
PopGenome-1.2.5/PopGenome/R/concatenate.regions.R |only
PopGenome-1.2.5/PopGenome/R/fisherextest.R | 6
PopGenome-1.2.5/PopGenome/R/fstcalc.R | 18
PopGenome-1.2.5/PopGenome/R/get.biallelic.matrix.R |only
PopGenome-1.2.5/PopGenome/R/get.codons.R |only
PopGenome-1.2.5/PopGenome/R/get.individuals.R |only
PopGenome-1.2.5/PopGenome/R/get_data.R | 8
PopGenome-1.2.5/PopGenome/R/get_gff_info.R | 18
PopGenome-1.2.5/PopGenome/R/getsyn.R | 2
PopGenome-1.2.5/PopGenome/R/import_export_slim.R | 7
PopGenome-1.2.5/PopGenome/R/intern.calc.R2.R |only
PopGenome-1.2.5/PopGenome/R/mult.linkage.stats.R | 71 --
PopGenome-1.2.5/PopGenome/R/my_math.R | 1
PopGenome-1.2.5/PopGenome/R/pair_linkdisequ_FAST.R |only
PopGenome-1.2.5/PopGenome/R/read.ms.output.R | 3
PopGenome-1.2.5/PopGenome/R/readData.R | 24
PopGenome-1.2.5/PopGenome/R/readMS.R |only
PopGenome-1.2.5/PopGenome/R/readSNP.R | 14
PopGenome-1.2.5/PopGenome/R/readVCF.R | 9
PopGenome-1.2.5/PopGenome/R/set.outgroup.R |only
PopGenome-1.2.5/PopGenome/R/slim.R | 17
PopGenome-1.2.5/PopGenome/R/splitting.data.R | 5
PopGenome-1.2.5/PopGenome/R/splitting.data.sep.R | 2
PopGenome-1.2.5/PopGenome/R/sweeps.stats.R | 23
PopGenome-1.2.5/PopGenome/R/update_slim.R | 9
PopGenome-1.2.5/PopGenome/inst/doc/Integration_of_new_Methods.R |only
PopGenome-1.2.5/PopGenome/inst/doc/Integration_of_new_Methods.Rnw | 2
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PopGenome-1.2.5/PopGenome/man/BayeScanR.Rd | 4
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PopGenome-1.2.5/PopGenome/man/calc.R2-methods.Rd |only
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PopGenome-1.2.5/PopGenome/man/concatenate.regions.Rd |only
PopGenome-1.2.5/PopGenome/man/detail.stats-methods.Rd | 19
PopGenome-1.2.5/PopGenome/man/get.biallelic.matrix-methods.Rd |only
PopGenome-1.2.5/PopGenome/man/get.codons-methods.Rd |only
PopGenome-1.2.5/PopGenome/man/get.individuals-methods.Rd |only
PopGenome-1.2.5/PopGenome/man/get_gff_info.Rd | 6
PopGenome-1.2.5/PopGenome/man/linkage.stats-methods.Rd | 3
PopGenome-1.2.5/PopGenome/man/mult.linkage.stats.Rd | 19
PopGenome-1.2.5/PopGenome/man/readData.Rd | 6
PopGenome-1.2.5/PopGenome/man/readMS.Rd |only
PopGenome-1.2.5/PopGenome/man/readSNP.Rd | 7
PopGenome-1.2.5/PopGenome/man/region.as.fasta.Rd | 6
PopGenome-1.2.5/PopGenome/man/set.outgroup-methods.Rd |only
PopGenome-1.2.5/PopGenome/man/sliding.window.transform-methods.Rd | 9
PopGenome-1.2.5/PopGenome/man/sweeps.stats-methods.Rd | 40 -
PopGenome-1.2.5/PopGenome/src/R2_C.c | 330 +++++++++-
PopGenome-1.2.5/PopGenome/src/get_gff_info_C.c | 12
PopGenome-1.2.5/PopGenome/src/whopgenome/readdnapp.cpp | 2
PopGenome-1.2.5/PopGenome/vignettes/Integration_of_new_Methods.Rnw | 2
PopGenome-1.2.5/PopGenome/vignettes/XXX.pdf |only
PopGenome-1.2.5/PopGenome/vignettes/XYZ.pdf |only
72 files changed, 824 insertions(+), 244 deletions(-)
Title: Fit high dimensional mixtures of Poisson GLMs
Diff between poisson.glm.mix versions 1.0 dated 2012-07-29 and 1.1 dated 2013-06-20
More information about poisson.glm.mix at CRAN
Description: High dimensional mixtures of Poisson Generalized Linear
models with three different parameterizations of Poisson means
are considered. Moreover, partitioning the response variables
into a set of blocks is possible. The package estimates
parameters via EM algorithm. For an efficient initialization, a
random splitting small-EM is introduced.
Author: Panagiotis Papastamoulis, Marie-Laure Martin-Magniette, Cathy
Maugis-Rabusseau
Maintainer: Panagiotis Papastamoulis
DESCRIPTION | 11 ++++++-----
MD5 | 34 +++++++++++++++++-----------------
R/bjkmodel.R | 4 ++--
R/bjmodel.R | 4 ++--
R/bkmodel.R | 4 ++--
R/init1.1.jk.j.R | 7 ++++---
R/init1.2.jk.j.R | 12 +++++++-----
R/init1.k.R | 6 ++++--
R/init2.jk.j.R | 16 ++++++++++------
R/init2.k.R | 10 +++++++---
R/pois.glm.mix.R | 15 ++++++++-------
man/init1.1.jk.j.Rd | 9 ++++++---
man/init1.2.jk.j.Rd | 19 +++++++++++--------
man/init1.k.Rd | 7 +++++--
man/init2.jk.j.Rd | 15 +++++++++------
man/init2.k.Rd | 9 ++++++---
man/pois.glm.mix.Rd | 7 +++++--
man/poisson.glm.mix.Rd | 2 +-
18 files changed, 112 insertions(+), 79 deletions(-)
Permanent link
Title: basic tools for the analysis of disease outbreaks.
Diff between epibase versions 0.1-0 dated 2013-05-22 and 0.1-1 dated 2013-06-20
Description: basic tools for the analysis of disease outbreaks.
Author: {The Hackout team (In alphabetic order: David Aanensen, Marc
Baguelin, Paul Birrell, Simon Cauchemez, Anton Camacho,
Caroline Colijn, Anne Cori, Xavier Didelot, Ken Eames,
Christophe Fraser, Simon Frost, Niel Hens, Joseph Hugues,
Thibaut Jombart, Lulla Opatowski, Oliver Ratmann, Samuel
Soubeyrand, Marc Suchard, Jacco Wallinga, Rolf Ypma)}
Maintainer: Thibaut Jombart
epibase-0.1-0/epibase/vignettes/cache |only
epibase-0.1-0/epibase/vignettes/epibase.aux |only
epibase-0.1-0/epibase/vignettes/epibase.log |only
epibase-0.1-0/epibase/vignettes/epibase.out |only
epibase-0.1-0/epibase/vignettes/epibase.toc |only
epibase-0.1-0/epibase/vignettes/figs |only
epibase-0.1-1/epibase/DESCRIPTION | 14 -
epibase-0.1-1/epibase/MD5 | 285 ----------------------------
epibase-0.1-1/epibase/NAMESPACE | 58 +++--
epibase-0.1-1/epibase/R/make.phylo.R | 8
epibase-0.1-1/epibase/inst/doc/epibase.R | 3
epibase-0.1-1/epibase/inst/doc/epibase.Rnw | 3
epibase-0.1-1/epibase/inst/doc/epibase.pdf |binary
epibase-0.1-1/epibase/man/make.phylo.Rd | 7
epibase-0.1-1/epibase/man/uniqSequences.Rd | 5
epibase-0.1-1/epibase/vignettes/epibase.Rnw | 3
epibase-0.1-1/epibase/vignettes/texput.log |only
17 files changed, 75 insertions(+), 311 deletions(-)
Title: Analysis of animal movements
Diff between adehabitatLT versions 0.3.11 dated 2013-03-22 and 0.3.12 dated 2013-06-20
Description: A collection of tools for the analysis of animal movements
Author: Clement Calenge, contributions from Stephane Dray and Manuela
Royer
Maintainer: Clement Calenge
DESCRIPTION | 8 ++++----
MD5 | 7 ++++---
R/gdltraj.r | 4 ++--
inst/doc/adehabitatLT.R |only
src/tests.c | 2 +-
5 files changed, 11 insertions(+), 10 deletions(-)
Title: An R package for changepoint analysis
Diff between changepoint versions 1.0.6 dated 2013-06-08 and 1.1 dated 2013-06-20
Description: Implements various mainstream and specialised changepoint
methods for finding single and multiple changepoints within
data. Many popular non-parametric and frequentist methods are
included. The cpt.mean, cpt.var, cpt.meanvar functions should
be your first point of call.
Author: Rebecca Killick
Maintainer: Rebecca Killick
DESCRIPTION | 8 ++---
MD5 | 30 +++++++++++-----------
NEWS | 6 ++++
R/exp.R | 27 +++++++++++++++----
R/gamma.R | 10 +++++--
R/multiple.nonparametric.R | 5 ++-
R/multiple.norm.R | 6 ++++
R/poisson.R | 2 +
R/single.norm.R | 61 ++++++++++++++++++++++++++++++++++++---------
man/cpt.mean.Rd | 2 -
man/cpt.meanvar.Rd | 2 -
man/cpt.var.Rd | 2 -
man/single.mean.norm.Rd | 2 -
man/single.meanvar.exp.Rd | 2 -
man/single.meanvar.norm.Rd | 2 -
man/single.var.norm.Rd | 2 -
16 files changed, 122 insertions(+), 47 deletions(-)
Title: Bradley-Terry Models
Diff between BradleyTerry2 versions 1.0-0 dated 2012-05-14 and 1.0-1 dated 2013-06-20
Description: Specify and fit the Bradley-Terry model and structured
versions
Author: Heather Turner and David Firth
Maintainer: Heather Turner
BradleyTerry2-1.0-0/BradleyTerry2/R/predict.glmmPQL.R |only
BradleyTerry2-1.0-0/BradleyTerry2/R/print.glmmPQL.R |only
BradleyTerry2-1.0-0/BradleyTerry2/R/summary.glmmPQL.R |only
BradleyTerry2-1.0-0/BradleyTerry2/R/vcov.glmmPQL.R |only
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BradleyTerry2-1.0-0/BradleyTerry2/vignettes/.Rhistory |only
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BradleyTerry2-1.0-0/BradleyTerry2/vignettes/BradleyTerry.blg |only
BradleyTerry2-1.0-1/BradleyTerry2/DESCRIPTION | 16
BradleyTerry2-1.0-1/BradleyTerry2/MD5 | 57
BradleyTerry2-1.0-1/BradleyTerry2/NAMESPACE | 11
BradleyTerry2-1.0-1/BradleyTerry2/R/BTm.R | 4
BradleyTerry2-1.0-1/BradleyTerry2/R/glmmPQL.R | 2
BradleyTerry2-1.0-1/BradleyTerry2/R/predict.BTglmmPQL.R |only
BradleyTerry2-1.0-1/BradleyTerry2/R/print.BTglmmPQL.R |only
BradleyTerry2-1.0-1/BradleyTerry2/R/print.summary.glmmPQL.R | 2
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BradleyTerry2-1.0-1/BradleyTerry2/R/vcov.BTglmmPQL.R |only
BradleyTerry2-1.0-1/BradleyTerry2/data/CEMS.rda |binary
BradleyTerry2-1.0-1/BradleyTerry2/data/baseball.rda |binary
BradleyTerry2-1.0-1/BradleyTerry2/data/chameleons.rda |binary
BradleyTerry2-1.0-1/BradleyTerry2/data/citations.rda |binary
BradleyTerry2-1.0-1/BradleyTerry2/data/flatlizards.rda |binary
BradleyTerry2-1.0-1/BradleyTerry2/data/icehockey.rda |binary
BradleyTerry2-1.0-1/BradleyTerry2/data/seeds.rda |binary
BradleyTerry2-1.0-1/BradleyTerry2/data/sound.fields.rda |binary
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BradleyTerry2-1.0-1/BradleyTerry2/inst/doc/BradleyTerry.R |only
BradleyTerry2-1.0-1/BradleyTerry2/inst/doc/BradleyTerry.Rnw | 2
BradleyTerry2-1.0-1/BradleyTerry2/inst/doc/BradleyTerry.pdf |binary
BradleyTerry2-1.0-1/BradleyTerry2/man/glmmPQL.Rd | 4
BradleyTerry2-1.0-1/BradleyTerry2/man/predict.BTglmmPQL.Rd |only
BradleyTerry2-1.0-1/BradleyTerry2/tests/flatlizards.R | 1
BradleyTerry2-1.0-1/BradleyTerry2/tests/flatlizards.Rout.save | 742 +++++-----
BradleyTerry2-1.0-1/BradleyTerry2/tests/predict.R | 2
BradleyTerry2-1.0-1/BradleyTerry2/tests/predict.Rout.save | 51
BradleyTerry2-1.0-1/BradleyTerry2/vignettes/BradleyTerry.Rnw | 2
37 files changed, 457 insertions(+), 439 deletions(-)
Title: Using gene expression data to improve flux balance analysis
predictions
Diff between sybilEFBA versions 0.0.1 dated 2013-06-05 and 1.0.0 dated 2013-06-20
Description: three different approaches to use gene expression data (or
protein measurements) for improving FBA predictions.
Author: Abdelmoneim Amer Desouki [aut, cre]
Maintainer: Abdelmoneim Amer Desouki
DESCRIPTION | 15 ++++-----
MD5 | 20 ++++++------
NAMESPACE | 3 -
R/eFBA_gene.R | 78 ++++++++++++++++++++++++------------------------
R/eFBA_rxn.R | 64 +++++++++++++++++++--------------------
R/findFluxGeneExpr.R |only
R/findMDCFlux.R | 26 ++++++++--------
man/FECorr.Rd | 1
man/eFBA_gene.Rd | 4 +-
man/findFluxGeneExpr.Rd |only
man/findMDCFlux.Rd | 4 --
man/iND750.Rd | 2 -
12 files changed, 107 insertions(+), 110 deletions(-)
Title: BEFdata R package
Diff between rbefdata versions 0.3.1 dated 2013-06-12 and 0.3.2 dated 2013-06-20
Description: Basic R package to access the data structures offered by
the BEFdata portal.
Author: Claas-Thido Pfaff
Maintainer: Claas-Thido Pfaff
rbefdata-0.3.1/rbefdata/R/rbefdata-defunct.R |only
rbefdata-0.3.1/rbefdata/man/rbefdata-defunct.Rd |only
rbefdata-0.3.2/rbefdata/DESCRIPTION | 10 +-
rbefdata-0.3.2/rbefdata/MD5 | 37 +++++-----
rbefdata-0.3.2/rbefdata/NEWS | 7 +
rbefdata-0.3.2/rbefdata/R/bef.portal.get.R | 2
rbefdata-0.3.2/rbefdata/R/bef.portal.get.attachment.R | 2
rbefdata-0.3.2/rbefdata/R/bef.portal.get.dataset.R | 2
rbefdata-0.3.2/rbefdata/R/bef.portal.get.dataset_list.R | 5 -
rbefdata-0.3.2/rbefdata/R/bef.portal.get.keywords.R | 1
rbefdata-0.3.2/rbefdata/R/bef.portal.get.metadata.R | 21 ++++-
rbefdata-0.3.2/rbefdata/R/bef.portal.get.proposal.R | 2
rbefdata-0.3.2/rbefdata/R/helper.R | 21 ++++-
rbefdata-0.3.2/rbefdata/R/rbefdata-deprecated.R |only
rbefdata-0.3.2/rbefdata/R/rbefdata-package.R | 13 ++-
rbefdata-0.3.2/rbefdata/inst/fixtures |only
rbefdata-0.3.2/rbefdata/inst/tests/test.1.bef.options.R |only
rbefdata-0.3.2/rbefdata/inst/tests/test.bef.portal.get.attachment.R |only
rbefdata-0.3.2/rbefdata/inst/tests/test.bef.portal.get.dataset.R | 25 ++++--
rbefdata-0.3.2/rbefdata/inst/tests/test.bef.portal.get.metadata.R |only
rbefdata-0.3.2/rbefdata/inst/tests/test.helpers.R |only
rbefdata-0.3.2/rbefdata/man/rbefdata-deprecated.Rd |only
rbefdata-0.3.2/rbefdata/man/rbefdata-package.Rd | 12 ++-
rbefdata-0.3.2/rbefdata/tests/run-all.R | 1
24 files changed, 114 insertions(+), 47 deletions(-)
Title: L-moments
Diff between lmom versions 2.0 dated 2013-06-17 and 2.1 dated 2013-06-20
Description: Functions related to L-moments: computation of L-moments
and trimmed L-moments of distributions and data samples;
parameter estimation; L-moment ratio diagram; plot vs.
quantiles of an extreme-value distribution.
Author: J. R. M. Hosking
Maintainer: J. R. M. Hosking
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
NEWS | 6 ++++++
src/dqagie.f | 7 +++----
src/dqagse.f | 7 +++----
src/dqk15i.f | 13 ++++++-------
src/dqk21.f | 13 ++++++-------
7 files changed, 34 insertions(+), 32 deletions(-)