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MCMC.OTU (version 1.0.10)

Bayesian Analysis of Multivariate Counts Data in DNA Metabarcoding and Ecology

Description

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.

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Version

Install

install.packages('MCMC.OTU')

Monthly Downloads

142

Version

1.0.10

License

GPL-3

Maintainer

Mikhail Matz

Last Published

February 12th, 2016

Functions in MCMC.OTU (1.0.10)

getNormalizedOTUdata

Extracts mcmc.otu model predictions
otuStack

Prepares OTU counts data for MCMC model fitting using mcmc.otu().
OTUsummary

Summarizes and plots results of mcmc.otu() function series.
startedLog

prepares OTU counts data for PCA analysis using started-log transform
summaryPlotOTU

Wrapper function for ggplot2 to make bar and line graphs of mcmc.otu() results
panel.cor

accessory function for pairs() to display Pearson correlations
otuByAutocorr

Selects OTUs for which MCMC-based parameter estimates are reliable.
green.data

Symbiodinium sp. ITS2 OTUs from Orbicella franksi and O. faveolata
signifOTU

Finds differentially represented OTUs.
logLin

prepares OTU counts data for PCA analysis using log-linear-hybrid transform
panel.cor.pval

accessory function for pairs() to display pvalue of the Pearson correlation
mcmc.otu

Analyzes multivariate counts data using poisson-lognormal mixed model
purgeOutliers

Removes outlier samples and OTUs.
padjustOTU

Adjusts p-values in the OTU summary for multiple comparisons.
mcmc.pval

calculates p-value based on Bayesian z-score or MCMC sampling
MCMC.OTU-package

Bayesian analysis of multivariate counts data in DNA metabarcoding and ecology.