[med-svn] [r-bioc-metagenomeseq] branch master updated (9557248 -> 75654a2)

[Andreas Tille]

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

      from  9557248   Updated version 1.16.0 from 'upstream/1.16.0'
       new  dd28a59   Move packaging from SVN to Git
       new  97840a2   New upstream version 1.18.0
       new  fbeb412   Updated version 1.18.0 from 'upstream/1.18.0'
       new  2c72ec2   New upstream version
       new  6914330   Standards-Version: 4.1.1
       new  75654a2   Add README.source to document binary data files, upload to unstable

The 6 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
 debian/README.source             |  16 ++++++
 debian/changelog                 |   9 ++++
 debian/control                   |   6 +--
 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 +-
 88 files changed, 161 insertions(+), 167 deletions(-)
 create mode 100644 debian/README.source

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