optpart (version 3.0-3)

compare: Compare Species Constancy for Specified Clusters

Description

Extracts specified columns from a constancy table (see const) and identifies species which occur in one of the two clusters (potential diagnostic species) or in both.

Usage

compare(const,left,right,thresh=0.2)

Arguments

const

a constancy table produced by function const

left

a numeric cluster

right

a cluster number

thresh

a minimum differential abundance to list in the table

Value

a list with elements

left

a data.frame of species diagnostic of set ‘left’

right

a data.frame of species diagnostic of set ‘right’

both

species occuring in both sets and diagnostic of neither

Details

compare extracts two columns (left and right) from a constancy table produced by const, and calculates the pairwise differences. Differences greater than the specified threshold appear in the set ‘left’; negative differences less then minus one times the threshold appear in the set ‘right’, and species which occur in both columns but with an absolute value of difference less than the threshold appear in set ‘both’.

References

http://ecology.msu.montana.edu/labdsv/R

Examples

# NOT RUN {
data(shoshveg)        # returns vegetation data set
data(shoshsite)       # returns site data
elev.clust <- as.numeric(factor(cut(shoshsite$elevation,5)))
                      # 5 elevation bands
elev.const <- const(shoshveg,elev.clust)
compare(elev.const,1,2)   # identify diagnostic species 
# }