R: Make a site-OTU matrix

makess {bio.infer}

R Documentation

Make a site-OTU matrix

Description

makess generates a site-OTU matrix based on a benthic count file. The script assumes that the benthic count file has a field entitled 'OTU' on which the matrix is based.

Usage

makess(bcnt, tname = "OTU", plothist=FALSE, prints = FALSE, nview = 0)

Arguments

`bcnt`	a benthic count file that results from running `get.otu` or `load.revised.otu`.
`tname`	Character string specifying the field in bcnt in which the name of the taxon is stored.
`plothist`	Set to `TRUE` to plot a histogram of the proportion of abundance at each site that is included in the OTU designations
`prints`	Set to `TRUE` to view statistics on the proportion of abundance at each site that is included in the OTU designations
`nview`	Selects the number of sites to view in which the proportion of abundance included is low

Value

A site-OTU matrix.

Author(s)

Lester L. Yuan

Examples

data(bcnt.otu.OR)
ss.OR <- makess(bcnt.otu.OR)

[Package bio.infer version 1.3-6 Index]