otuByAutocorr

model

data

ac.cut

<p>Looks at autocorrelation among sampled parameter values.</p>

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.

Mikhail Matz

MCMC.OTU

Bayesian Analysis of Multivariate Counts Data in DNA
Metabarcoding and Ecology

otuByAutocorr function

Selects OTUs for which MCMC-based parameter estimates are reliable. — otuByAutocorr

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

otuByAutocorr: Selects OTUs for which MCMC-based parameter estimates are reliable.

Description

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