makess {bio.infer}

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

See Also

get.otu, load.revised.otu

Examples

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