Identify Rare Taxa in a Data Set
Identifies the distribution of rare taxa in a community data.frame, using a specified rareness threshold.
raretaxa(comm,min=1,log=FALSE,type='b', panel='all')
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’. |
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.
Produces only graphs and returns no output
data(bryceveg) raretaxa(bryceveg,min=3,log=TRUE)
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