# 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.

- Author
- Mikhail V. Matz
- Date of publication
- 2016-02-12 00:53:04
- Maintainer
- Mikhail V. Matz <matz@utexas.edu>
- License
- GPL-3
- Version
- 1.0.10

## Man pages

- getNormalizedOTUdata
- Extracts mcmc.otu model predictions
- getNormalizedOTUdata
- Extracts mcmc.otu model predictions
- green.data
- Symbiodinium sp. ITS2 OTUs from Orbicella franksi and O....
- green.data
- Symbiodinium sp. ITS2 OTUs from Orbicella franksi and O....
- logLin
- prepares OTU counts data for PCA analysis using...
- logLin
- prepares OTU counts data for PCA analysis using...
- mcmc.otu
- Analyzes multivariate counts data using poisson-lognormal...
- mcmc.otu
- Analyzes multivariate counts data using poisson-lognormal...
- MCMC.OTU-package
- Bayesian analysis of multivariate counts data in DNA...
- MCMC.OTU-package
- Bayesian analysis of multivariate counts data in DNA...
- mcmc.pval
- calculates p-value based on Bayesian z-score or MCMC sampling
- mcmc.pval
- calculates p-value based on Bayesian z-score or MCMC sampling
- otuByAutocorr
- Selects OTUs for which MCMC-based parameter estimates are...
- otuByAutocorr
- Selects OTUs for which MCMC-based parameter estimates are...
- otuStack
- Prepares OTU counts data for MCMC model fitting using...
- otuStack
- Prepares OTU counts data for MCMC model fitting using...
- OTUsummary
- Summarizes and plots results of mcmc.otu() function series.
- OTUsummary
- Summarizes and plots results of mcmc.otu() function series.
- padjustOTU
- Adjusts p-values in the OTU summary for multiple comparisons.
- padjustOTU
- Adjusts p-values in the OTU summary for multiple comparisons.
- panel.cor
- accessory function for pairs() to display Pearson...
- panel.cor
- accessory function for pairs() to display Pearson...
- panel.cor.pval
- accessory function for pairs() to display pvalue of the...
- panel.cor.pval
- accessory function for pairs() to display pvalue of the...
- purgeOutliers
- Removes outlier samples and OTUs.
- signifOTU
- Finds differentially represented OTUs.
- signifOTU
- Finds differentially represented OTUs.
- startedLog
- prepares OTU counts data for PCA analysis using started-log...
- startedLog
- prepares OTU counts data for PCA analysis using started-log...
- summaryPlotOTU
- Wrapper function for ggplot2 to make bar and line graphs of...
- summaryPlotOTU
- Wrapper function for ggplot2 to make bar and line graphs of...

## Files in this package

MCMC.OTU |

MCMC.OTU/NAMESPACE |

MCMC.OTU/data |

MCMC.OTU/data/green.data.rda |

MCMC.OTU/R |

MCMC.OTU/R/getNormalizedOTUdata.R |

MCMC.OTU/R/purgeOutliers.R |

MCMC.OTU/R/otuStack.R |

MCMC.OTU/R/OTUsummary.R |

MCMC.OTU/R/summaryPlotOTU.R |

MCMC.OTU/R/padjustOTU.R |

MCMC.OTU/R/panel.cor.R |

MCMC.OTU/R/panel.cor.pval.R |

MCMC.OTU/R/signifOTU.R |

MCMC.OTU/R/otuByAutocorr.R |

MCMC.OTU/R/startedLog.R |

MCMC.OTU/R/mcmc.otu.R |

MCMC.OTU/R/MCMC.OTU-internal.R |

MCMC.OTU/R/mcmc.pval.R |

MCMC.OTU/R/logLin.R |

MCMC.OTU/MD5 |

MCMC.OTU/DESCRIPTION |

MCMC.OTU/man |

MCMC.OTU/man/mcmc.pval.Rd |

MCMC.OTU/man/green.data.Rd |

MCMC.OTU/man/purgeOutliers.Rd |

MCMC.OTU/man/summaryPlotOTU.Rd |

MCMC.OTU/man/signifOTU.Rd |

MCMC.OTU/man/getNormalizedOTUdata.Rd |

MCMC.OTU/man/logLin.Rd |

MCMC.OTU/man/MCMC.OTU-package.Rd |

MCMC.OTU/man/panel.cor.Rd |

MCMC.OTU/man/otuByAutocorr.Rd |

MCMC.OTU/man/panel.cor.pval.Rd |

MCMC.OTU/man/padjustOTU.Rd |

MCMC.OTU/man/startedLog.Rd |

MCMC.OTU/man/mcmc.otu.Rd |

MCMC.OTU/man/otuStack.Rd |

MCMC.OTU/man/OTUsummary.Rd |