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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.
| Version: | 1.0.10 |
| Depends: | MCMCglmm, ggplot2, coda |
| Published: | 2016-02-12 |
| DOI: | 10.32614/CRAN.package.MCMC.OTU |
| Author: | Mikhail V. Matz |
| Maintainer: | Mikhail V. Matz <matz at utexas.edu> |
| License: | GPL-3 |
| NeedsCompilation: | no |
| CRAN checks: | MCMC.OTU results |
| Reference manual: | MCMC.OTU.pdf |
| Package source: | MCMC.OTU_1.0.10.tar.gz |
| Windows binaries: | r-devel: MCMC.OTU_1.0.10.zip, r-release: MCMC.OTU_1.0.10.zip, r-oldrel: MCMC.OTU_1.0.10.zip |
| macOS binaries: | r-release (arm64): MCMC.OTU_1.0.10.tgz, r-oldrel (arm64): MCMC.OTU_1.0.10.tgz, r-release (x86_64): MCMC.OTU_1.0.10.tgz, r-oldrel (x86_64): MCMC.OTU_1.0.10.tgz |
| Old sources: | MCMC.OTU archive |
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These binaries (installable software) and packages are in development.
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