[med-svn] [r-bioc-metagenomeseq] 09/09: Updated version 1.16.0 from 'upstream/1.16.0'
Andreas Tille
tille at debian.org
Sun Oct 1 15:31:08 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-bioc-metagenomeseq.
commit 955724898490be213d344cfe5e2964e6fb2f318a
Merge: 02c2fd3 63047b3
Author: Andreas Tille <tille at debian.org>
Date: Sun Oct 1 17:27:58 2017 +0200
Updated version 1.16.0 from 'upstream/1.16.0'
with Debian dir 73a42c4fbb1bcb71fbd77cb91afd25ac60368b2e
DESCRIPTION | 29 +
NAMESPACE | 104 ++++
NEWS | 71 +++
R/MRcoefs.R | 114 ++++
R/MRexperiment2biom.R | 84 +++
R/MRfulltable.R | 136 +++++
R/MRtable.R | 130 +++++
R/aggregateBySample.R | 64 +++
R/aggregateByTaxonomy.R | 77 +++
R/allClasses.R | 308 ++++++++++
R/biom2MRexperiment.R | 41 ++
R/calculateEffectiveSamples.R | 14 +
R/correlationTest.R | 119 ++++
R/cumNorm.R | 53 ++
R/cumNormMat.R | 37 ++
R/cumNormStat.R | 63 +++
R/cumNormStatFast.R | 57 ++
R/deprecated_metagenomeSeq_function.R | 23 +
R/doCountMStep.R | 70 +++
R/doEStep.R | 33 ++
R/doZeroMStep.R | 41 ++
R/exportMat.R | 30 +
R/exportStats.R | 42 ++
R/filterData.R | 21 +
R/fitDO.R | 64 +++
R/fitFeatureModel.R | 73 +++
R/fitLogNormal.R | 71 +++
R/fitPA.R | 61 ++
R/fitTimeSeries.R | 610 ++++++++++++++++++++
R/fitZeroLogNormal.R | 299 ++++++++++
R/fitZig.R | 274 +++++++++
R/getCountDensity.R | 22 +
R/getEpsilon.R | 22 +
R/getNegativeLogLikelihoods.R | 27 +
R/getPi.R | 17 +
R/getZ.R | 29 +
R/isItStillActive.R | 24 +
R/loadBiom.R | 19 +
R/loadMeta.R | 26 +
R/loadMetaQ.R | 28 +
R/loadPhenoData.R | 52 ++
R/mergeMRexperiments.R | 103 ++++
R/misc.R | 70 +++
R/plotBubble.R | 96 ++++
R/plotCorr.R | 35 ++
R/plotFeature.R | 73 +++
R/plotGenus.R | 69 +++
R/plotMRheatmap.R | 37 ++
R/plotOTU.R | 64 +++
R/plotOrd.R | 59 ++
R/plotRare.R | 42 ++
R/zigControl.R | 29 +
README.md | 32 ++
build/vignette.rds | Bin 0 -> 296 bytes
data/lungData.rda | Bin 0 -> 290918 bytes
data/mouseData.rda | Bin 0 -> 197032 bytes
inst/CITATION | 50 ++
inst/doc/fitTimeSeries.R | 120 ++++
inst/doc/fitTimeSeries.Rnw | 278 +++++++++
inst/doc/fitTimeSeries.pdf | Bin 0 -> 241572 bytes
inst/doc/metagenomeSeq.R | 299 ++++++++++
inst/doc/metagenomeSeq.Rnw | 725 ++++++++++++++++++++++++
inst/doc/metagenomeSeq.pdf | Bin 0 -> 998018 bytes
inst/extdata/CHK_NAME.otus.count.csv | 1001 +++++++++++++++++++++++++++++++++
inst/extdata/CHK_clinical.csv | 79 +++
inst/extdata/CHK_otus.taxonomy.csv | 1001 +++++++++++++++++++++++++++++++++
inst/extdata/lungfit.rds | Bin 0 -> 93152 bytes
man/MRcoefs.Rd | 72 +++
man/MRcounts.Rd | 37 ++
man/MRexperiment-class.Rd | 61 ++
man/MRexperiment2biom.Rd | 32 ++
man/MRfulltable.Rd | 77 +++
man/MRtable.Rd | 75 +++
man/aggregateBySample.Rd | 39 ++
man/aggregateByTaxonomy.Rd | 49 ++
man/biom2MRexperiment.Rd | 29 +
man/calcNormFactors.Rd | 29 +
man/calcPosComponent.Rd | 22 +
man/calcShrinkParameters.Rd | 24 +
man/calcStandardError.Rd | 28 +
man/calcZeroAdjustment.Rd | 28 +
man/calcZeroComponent.Rd | 22 +
man/calculateEffectiveSamples.Rd | 24 +
man/correctIndices.Rd | 36 ++
man/correlationTest.Rd | 61 ++
man/cumNorm.Rd | 32 ++
man/cumNormMat.Rd | 33 ++
man/cumNormStat.Rd | 39 ++
man/cumNormStatFast.Rd | 36 ++
man/doCountMStep.Rd | 45 ++
man/doEStep.Rd | 37 ++
man/doZeroMStep.Rd | 38 ++
man/expSummary.Rd | 31 +
man/exportMat.Rd | 40 ++
man/exportStats.Rd | 35 ++
man/extractMR.Rd | 30 +
man/filterData.Rd | 29 +
man/fitDO.Rd | 51 ++
man/fitFeatureModel.Rd | 53 ++
man/fitLogNormal.Rd | 46 ++
man/fitMultipleTimeSeries.Rd | 45 ++
man/fitPA.Rd | 45 ++
man/fitSSTimeSeries.Rd | 73 +++
man/fitTimeSeries.Rd | 68 +++
man/fitZeroLogNormal.Rd | 43 ++
man/fitZig.Rd | 75 +++
man/getCountDensity.Rd | 32 ++
man/getEpsilon.Rd | 31 +
man/getNegativeLogLikelihoods.Rd | 33 ++
man/getPi.Rd | 26 +
man/getZ.Rd | 33 ++
man/isItStillActive.Rd | 30 +
man/libSize-set.Rd | 32 ++
man/libSize.Rd | 30 +
man/loadBiom.Rd | 28 +
man/loadMeta.Rd | 30 +
man/loadMetaQ.Rd | 27 +
man/loadPhenoData.Rd | 33 ++
man/lungData.Rd | 12 +
man/makeLabels.Rd | 27 +
man/mergeMRexperiments.Rd | 32 ++
man/mergeTable.Rd | 20 +
man/metagenomeSeq-deprecated.Rd | 30 +
man/metagenomeSeq-package.Rd | 21 +
man/mouseData.Rd | 12 +
man/newMRexperiment.Rd | 46 ++
man/normFactors-set.Rd | 32 ++
man/normFactors.Rd | 29 +
man/plotBubble.Rd | 55 ++
man/plotClassTimeSeries.Rd | 46 ++
man/plotCorr.Rd | 40 ++
man/plotFeature.Rd | 54 ++
man/plotGenus.Rd | 60 ++
man/plotMRheatmap.Rd | 46 ++
man/plotOTU.Rd | 55 ++
man/plotOrd.Rd | 51 ++
man/plotRare.Rd | 37 ++
man/plotTimeSeries.Rd | 41 ++
man/posteriorProbs.Rd | 41 ++
man/returnAppropriateObj.Rd | 31 +
man/ssFit.Rd | 48 ++
man/ssIntervalCandidate.Rd | 34 ++
man/ssPerm.Rd | 28 +
man/ssPermAnalysis.Rd | 41 ++
man/trapz.Rd | 37 ++
man/ts2MRexperiment.Rd | 46 ++
man/uniqueFeatures.Rd | 31 +
man/zigControl.Rd | 38 ++
tests/testthat.R | 17 +
tests/testthat/test-fitZig.R | 58 ++
tests/testthat/test-norm.R | 35 ++
vignettes/fitTimeSeries.Rnw | 278 +++++++++
vignettes/fitTimeSeries.bib | 40 ++
vignettes/metagenomeSeq.Rnw | 725 ++++++++++++++++++++++++
vignettes/metagenomeSeq.bib | 33 ++
vignettes/metagenomeSeq_figure1.png | Bin 0 -> 26433 bytes
vignettes/metagenomeSeq_figure2.png | Bin 0 -> 313594 bytes
vignettes/overview.pdf | Bin 0 -> 36144 bytes
158 files changed, 12082 insertions(+)
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