isamic {labdsv} | R Documentation |
Indicator Species Analysis Minimizing Intermediate Occurrences
Description
Calculates the degree to which species are either always present or always absent within clusters or types.
Usage
isamic(comm,clustering,sort=FALSE)
Arguments
comm |
a matrix or data.frame of samples, species as columns, samples as rows |
clustering |
a vector of numeric cluster memberships for samples, or a
classification object returned from |
sort |
if TRUE, return in order of highest value to lowest rather than input order |
Details
Calculates the constancy (fractional occurrence of each species in every type), and then calculates twice the the sum of the absolute values of the constancy - 0.5, normalized to the number of clusters (columns).
Value
A data.frame of species indicator values
Author(s)
David W. Roberts droberts@montana.edu
References
Aho, K., D.W. Roberts, and T.W. Weaver. 2008. Using geometric and non-geometric internal evaluators to compare eight vegetation classification methods. J. Veg. Sci. 19(4):549-562.
See Also
Examples
data(bryceveg)
data(brycesite)
clust <- cut(brycesite$elev,5,labels=FALSE)
isamic(bryceveg,clust)