[med-svn] [r-bioc-metagenomeseq] 03/06: Updated version 1.18.0 from 'upstream/1.18.0'

[Andreas Tille]

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in repository r-bioc-metagenomeseq.

commit fbeb4129fe0cd73de1009faf0324293f536b82b6
Merge: dd28a59 97840a2
Author: Andreas Tille <tille at debian.org>
Date:   Sun Oct 1 17:36:02 2017 +0200

    Updated version 1.18.0 from 'upstream/1.18.0'
    
    with Debian dir 6730ace2241b56b7962731b6defe6beaf6bd1073

 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(-)

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