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 |

**getNormalizedOTUdata:** Extracts mcmc.otu model predictions

**green.data:** Symbiodinium sp. ITS2 OTUs from Orbicella franksi and O....

**logLin:** prepares OTU counts data for PCA analysis using...

**mcmc.otu:** Analyzes multivariate counts data using poisson-lognormal...

**MCMC.OTU-package:** Bayesian analysis of multivariate counts data in DNA...

**mcmc.pval:** calculates p-value based on Bayesian z-score or MCMC sampling

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

**otuStack:** Prepares OTU counts data for MCMC model fitting using...

**OTUsummary:** Summarizes and plots results of mcmc.otu() function series.

**padjustOTU:** Adjusts p-values in the OTU summary for multiple comparisons.

**panel.cor:** accessory function for pairs() to display Pearson...

**panel.cor.pval:** accessory function for pairs() to display pvalue of the...

**purgeOutliers:** Removes outlier samples and OTUs.

**signifOTU:** Finds differentially represented OTUs.

**startedLog:** prepares OTU counts data for PCA analysis using started-log...

**summaryPlotOTU:** Wrapper function for ggplot2 to make bar and line graphs of...

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
Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

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