raretaxa: Identify Rare Taxa in a Data Set

In labdsv: Ordination and Multivariate Analysis for Ecology

Identify Rare Taxa in a Data Set

Description

Identifies the distribution of rare taxa in a community data.frame, using a specified rareness threshold.

Usage

raretaxa(comm,min=1,log=FALSE,type='b', panel='all')

Arguments

comm	a community data.frame with samples as rows and species as columns
min	the minimum number of occurrences for a species to be considered rare
log	controls whether or not the Y axis on some graphs should be log scaled
type	the plot type. ‘b’ = both points and lines
panel	a switch to control which graphic is displayed. Can be either an integer from 1 to 3 or the word ‘all’.

Details

Rare species are an issue in ecological data sets. This function produces three graphs identifying (1) the distribution of rare species/plot, (2) the mean abundance (when present) of rare species, and (3) the total abundance or rare species/plot.

Value

Produces only graphs and returns no output

Author(s)

David W. Roberts [e-mail]

Examples

data(bryceveg)
raretaxa(bryceveg,min=3,log=TRUE)

labdsv documentation built on April 10, 2023, 5:08 p.m.