makess: Make a site-OTU matrix

In bio.infer: Predict Environmental Conditions from Biological Observations

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)

bio.infer documentation built on Sept. 2, 2020, 5:08 p.m.