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.


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install.packages("MCMC.OTU")

1.0.10 by Mikhail V. Matz, 2 years ago


Browse source code at https://github.com/cran/MCMC.OTU


Authors: Mikhail V. Matz


Documentation:   PDF Manual  


GPL-3 license


Depends on MCMCglmm, ggplot2, coda


See at CRAN