[med-svn] [r-bioc-metagenomeseq] branch upstream updated (63047b3 -> 97840a2)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch upstream
in repository r-bioc-metagenomeseq.

      from  63047b3   New upstream version 1.16.0
       new  97840a2   New upstream version 1.18.0

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 DESCRIPTION                      |   6 +--
 R/aggregateByTaxonomy.R          | 105 ++++++++++++++++++++++-----------------
 R/fitTimeSeries.R                |  60 ++++++++++++++--------
 build/vignette.rds               | Bin 296 -> 295 bytes
 inst/doc/fitTimeSeries.pdf       | Bin 241572 -> 242261 bytes
 inst/doc/metagenomeSeq.Rnw       |   2 +-
 inst/doc/metagenomeSeq.pdf       | Bin 998018 -> 998910 bytes
 man/MRcoefs.Rd                   |   1 -
 man/MRcounts.Rd                  |   1 -
 man/MRexperiment2biom.Rd         |   1 -
 man/MRfulltable.Rd               |   1 -
 man/MRtable.Rd                   |   1 -
 man/aggregateBySample.Rd         |   4 +-
 man/aggregateByTaxonomy.Rd       |  14 ++++--
 man/biom2MRexperiment.Rd         |   1 -
 man/calcNormFactors.Rd           |   1 -
 man/calcPosComponent.Rd          |   1 -
 man/calcShrinkParameters.Rd      |   1 -
 man/calcStandardError.Rd         |   1 -
 man/calcZeroAdjustment.Rd        |   1 -
 man/calcZeroComponent.Rd         |   1 -
 man/calculateEffectiveSamples.Rd |   1 -
 man/correctIndices.Rd            |   1 -
 man/correlationTest.Rd           |   3 +-
 man/cumNorm.Rd                   |   1 -
 man/cumNormMat.Rd                |   1 -
 man/cumNormStat.Rd               |   1 -
 man/cumNormStatFast.Rd           |   1 -
 man/doCountMStep.Rd              |   1 -
 man/doEStep.Rd                   |   1 -
 man/doZeroMStep.Rd               |   1 -
 man/expSummary.Rd                |   1 -
 man/exportMat.Rd                 |   1 -
 man/exportStats.Rd               |   1 -
 man/extractMR.Rd                 |   1 -
 man/filterData.Rd                |   1 -
 man/fitDO.Rd                     |   1 -
 man/fitFeatureModel.Rd           |   1 -
 man/fitLogNormal.Rd              |   1 -
 man/fitMultipleTimeSeries.Rd     |   5 +-
 man/fitPA.Rd                     |   1 -
 man/fitSSTimeSeries.Rd           |   5 +-
 man/fitTimeSeries.Rd             |   5 +-
 man/fitZeroLogNormal.Rd          |   1 -
 man/fitZig.Rd                    |   1 -
 man/getCountDensity.Rd           |   1 -
 man/getEpsilon.Rd                |   1 -
 man/getNegativeLogLikelihoods.Rd |   1 -
 man/getPi.Rd                     |   1 -
 man/getZ.Rd                      |   1 -
 man/isItStillActive.Rd           |   1 -
 man/libSize-set.Rd               |   1 -
 man/libSize.Rd                   |   1 -
 man/loadBiom.Rd                  |   1 -
 man/loadMeta.Rd                  |   1 -
 man/loadMetaQ.Rd                 |   1 -
 man/loadPhenoData.Rd             |   1 -
 man/makeLabels.Rd                |   1 -
 man/mergeMRexperiments.Rd        |   1 -
 man/mergeTable.Rd                |   1 -
 man/metagenomeSeq-deprecated.Rd  |   7 ++-
 man/newMRexperiment.Rd           |   1 -
 man/normFactors-set.Rd           |   1 -
 man/normFactors.Rd               |   1 -
 man/plotBubble.Rd                |   1 -
 man/plotClassTimeSeries.Rd       |   1 -
 man/plotCorr.Rd                  |   1 -
 man/plotFeature.Rd               |   1 -
 man/plotGenus.Rd                 |   3 +-
 man/plotMRheatmap.Rd             |   1 -
 man/plotOTU.Rd                   |   1 -
 man/plotOrd.Rd                   |   1 -
 man/plotRare.Rd                  |   1 -
 man/plotTimeSeries.Rd            |   1 -
 man/posteriorProbs.Rd            |   1 -
 man/returnAppropriateObj.Rd      |   1 -
 man/ssFit.Rd                     |   1 -
 man/ssIntervalCandidate.Rd       |   1 -
 man/ssPerm.Rd                    |   1 -
 man/ssPermAnalysis.Rd            |   1 -
 man/trapz.Rd                     |   1 -
 man/ts2MRexperiment.Rd           |   6 ++-
 man/uniqueFeatures.Rd            |   1 -
 man/zigControl.Rd                |   3 +-
 vignettes/metagenomeSeq.Rnw      |   2 +-
 85 files changed, 133 insertions(+), 164 deletions(-)

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-metagenomeseq.git