abundance {OTUbase}R Documentation

abundance

Description

abundance generates an abundance table. This table can be either weighted or unweighted.

Usage

abundance(object, ...)

Arguments

object

An OTUset or a TAXset object

...

Additional arguments. These will depend on if the object is an OTUset or a TAXset object.

Details

These are other arguments passed to abundance

Value

The returned value will be a data.frame.

Examples


## locate directory with data
dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into OTUset object
soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")

## calculate abundance
abundance(soginOTU, collab="Site")

[Package OTUbase version 1.40.0 Index]