Package: MCMC.OTU 1.0.10

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.

Authors:Mikhail V. Matz

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MCMC.OTU/json (API)

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This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

14 exports 0.00 score 36 dependencies 32 scripts 119 downloads

Last updated 9 years agofrom:cb3053f9d3. Checks:OK: 7. Indexed: yes.

Exports:getNormalizedOTUdatalogLinmcmc.otumcmc.pvalotuByAutocorrotuStackOTUsummarypadjustOTUpanel.corpanel.cor.pvalpurgeOutlierssignifOTUstartedLogsummaryPlotOTU

Dependencies:apeclicodacolorspacecorpcorcubaturedigestfansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixMCMCglmmmgcvmunsellnlmepillarpkgconfigR6RColorBrewerRcpprlangscalestensorAtibbleutf8vctrsviridisLitewithr