MCMC.OTU

Package: MCMC.OTU
Type: Package
Title: Bayesian Analysis of Multivariate Counts Data in DNA
Metabarcoding and Ecology
Version: 1.0.10
Date: 2016-02-10
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz <matz@utexas.edu>
Description: 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.
License: GPL-3
Depends: MCMCglmm, ggplot2, coda
NeedsCompilation: no
Packaged: 2016-02-11 19:23:29 UTC; c-monstr
Repository: CRAN
Date/Publication: 2016-02-12 00:53:04

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'MCMC.OTU' ...
** package 'MCMC.OTU' successfully unpacked and MD5 sums checked
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'MCMC.OTU'
    finding HTML links ... done
    MCMC.OTU-package                        html  
    OTUsummary                              html  
    getNormalizedOTUdata                    html  
    green.data                              html  
    logLin                                  html  
    mcmc.otu                                html  
    mcmc.pval                               html  
    otuByAutocorr                           html  
    otuStack                                html  
    padjustOTU                              html  
    panel.cor                               html  
    panel.cor.pval                          html  
    purgeOutliers                           html  
    signifOTU                               html  
    startedLog                              html  
    summaryPlotOTU                          html  
** building package indices
** testing if installed package can be loaded
* DONE (MCMC.OTU)
Making 'packages.html' ... done