labdsv (version 1.8-0)

raretaxa: Identify Rare Taxa in a Data Set

Description

Identifes the distribution of rare taxa in a taxon dataframe, using a specified rareness threshold.

Usage

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

Arguments

taxa

a taxon dataframe 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’.

Value

Produces only graphs and returns no output

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.

Examples

# NOT RUN {
data(bryceveg)
# }
# NOT RUN {
raretaxa(bryceveg,min=3,log=TRUE)
# }