OTU.diversity: Summarize Diversity Indices for OTU Tables
In RAM: R for Amplicon-Sequencing-Based Microbial-Ecology

Description Usage Arguments Details Value Note Author(s) References Examples

These functions calculate diversity indices for all samples and append outputs as new columns to metadata table.

1	OTU.diversity(data, meta)

`data`	a list of OTU tables.
`meta`	the metadata to append the outputs.

This function summarize the following diversity indices: specnumber, shannon, simpson, invsimpson, true diversity, evenness, chao and ACE indices, for a given otu table. See diversity.indices)

This function return vectors of diversity indices for each sample, which are appended to a given metadata table.

Credit goes to package vegan for the partial argument matching (see References), and for the calculation of all diversity indices except for true diversity and evenness.

Wen Chen.

Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens and Helene Wagner (2013). vegan: Community Ecology Package. R package version 2.0-10. http://CRAN.R-project.org/package=vegan

Diversity index. (2014, May 7). In Wikipedia, The Free Encyclopedia. Retrieved 14:57, May 28, 2014, from http://en.wikipedia.org/w/index.php?title= Diversity_index&oldid=607510424

Blackwood, C. B., Hudleston, D., Zak, D. R., & Buyer, J. S. (2007) Interpreting ecological OTU.diversity applied to terminal restriction fragment length polymorphism data: insights from simulated microbial communities. Applied and Environmental Microbiology, 73(16), 5276-5283.

data(ITS1, ITS2, meta)
data=list(ITS1=ITS1, ITS2=ITS2)
## Not run: 
meta.diversity<-OTU.diversity(data=data, meta=meta)

## End(Not run)

Loading required package: vegan
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Loading required package: lattice
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