Bayesian Analysis of Multivariate Counts Data in DNA Metabarcoding and Ecology

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Documentation for package ‘MCMC.OTU’ version 1.0.10

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MCMC.OTU-package Bayesian analysis of multivariate counts data in DNA metabarcoding and ecology.
getNormalizedOTUdata Extracts mcmc.otu model predictions
green.data Symbiodinium sp. ITS2 OTUs from Orbicella franksi and O. faveolata
logLin prepares OTU counts data for PCA analysis using log-linear-hybrid transform
MCMC.OTU Bayesian analysis of multivariate counts data in DNA metabarcoding and ecology.
mcmc.otu Analyzes multivariate counts data using poisson-lognormal mixed model
mcmc.pval calculates p-value based on Bayesian z-score or MCMC sampling
otuByAutocorr Selects OTUs for which MCMC-based parameter estimates are reliable.
otuStack Prepares OTU counts data for MCMC model fitting using mcmc.otu().
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 correlations
panel.cor.pval accessory function for pairs() to display pvalue of the Pearson correlation
purgeOutliers Removes outlier samples and OTUs.
signifOTU Finds differentially represented OTUs.
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