MCMC.OTU: Bayesian Analysis of Multivariate Counts Data in DNA Metabarcoding and Ecology

Poisson-lognormal generalized linear mixed model analysis of multivariate counts data using MCMC, aiming to infer the changes in relative proportions of individual variables. The package was originally designed for sequence-based analysis of microbial communities ("metabarcoding", variables = operational taxonomic units, OTUs), but can be used for other types of multivariate counts, such as in ecological applications (variables = species). The results are summarized and plotted using 'ggplot2' functions. Includes functions to remove sample and variable outliers and reformat counts into normalized log-transformed values for correlation and principal component/coordinate analysis. Walkthrough and examples: http://www.bio.utexas.edu/research/matz_lab/matzlab/Methods_files/walkthroughExample_mcmcOTU_R.txt.

Author
Mikhail V. Matz
Date of publication
2016-02-12 00:53:04
Maintainer
Mikhail V. Matz <matz@utexas.edu>
License
GPL-3
Version
1.0.10

View on CRAN

Man pages

getNormalizedOTUdata
Extracts mcmc.otu model predictions
green.data
Symbiodinium sp. ITS2 OTUs from Orbicella franksi and O....
logLin
prepares OTU counts data for PCA analysis using...
mcmc.otu
Analyzes multivariate counts data using poisson-lognormal...
MCMC.OTU-package
Bayesian analysis of multivariate counts data in DNA...
mcmc.pval
calculates p-value based on Bayesian z-score or MCMC sampling
otuByAutocorr
Selects OTUs for which MCMC-based parameter estimates are...
otuStack
Prepares OTU counts data for MCMC model fitting using...
OTUsummary
Summarizes and plots results of mcmc.otu() function series.
padjustOTU
Adjusts p-values in the OTU summary for multiple comparisons.
panel.cor
accessory function for pairs() to display Pearson...
panel.cor.pval
accessory function for pairs() to display pvalue of the...
purgeOutliers
Removes outlier samples and OTUs.
signifOTU
Finds differentially represented OTUs.
startedLog
prepares OTU counts data for PCA analysis using started-log...
summaryPlotOTU
Wrapper function for ggplot2 to make bar and line graphs of...

Files in this package

MCMC.OTU
MCMC.OTU/NAMESPACE
MCMC.OTU/data
MCMC.OTU/data/green.data.rda
MCMC.OTU/R
MCMC.OTU/R/getNormalizedOTUdata.R
MCMC.OTU/R/purgeOutliers.R
MCMC.OTU/R/otuStack.R
MCMC.OTU/R/OTUsummary.R
MCMC.OTU/R/summaryPlotOTU.R
MCMC.OTU/R/padjustOTU.R
MCMC.OTU/R/panel.cor.R
MCMC.OTU/R/panel.cor.pval.R
MCMC.OTU/R/signifOTU.R
MCMC.OTU/R/otuByAutocorr.R
MCMC.OTU/R/startedLog.R
MCMC.OTU/R/mcmc.otu.R
MCMC.OTU/R/MCMC.OTU-internal.R
MCMC.OTU/R/mcmc.pval.R
MCMC.OTU/R/logLin.R
MCMC.OTU/MD5
MCMC.OTU/DESCRIPTION
MCMC.OTU/man
MCMC.OTU/man/mcmc.pval.Rd
MCMC.OTU/man/green.data.Rd
MCMC.OTU/man/purgeOutliers.Rd
MCMC.OTU/man/summaryPlotOTU.Rd
MCMC.OTU/man/signifOTU.Rd
MCMC.OTU/man/getNormalizedOTUdata.Rd
MCMC.OTU/man/logLin.Rd
MCMC.OTU/man/MCMC.OTU-package.Rd
MCMC.OTU/man/panel.cor.Rd
MCMC.OTU/man/otuByAutocorr.Rd
MCMC.OTU/man/panel.cor.pval.Rd
MCMC.OTU/man/padjustOTU.Rd
MCMC.OTU/man/startedLog.Rd
MCMC.OTU/man/mcmc.otu.Rd
MCMC.OTU/man/otuStack.Rd
MCMC.OTU/man/OTUsummary.Rd