RAM (version 1.2.1.3)

OTU.diversity: Summarize Diversity Indices for OTU Tables

Description

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

Usage

OTU.diversity(data, meta)

Arguments

data

a list of OTU tables.

meta

the metadata to append the outputs.

Value

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

Details

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)

References

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.

Examples

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