duarm {labdsv} | R Documentation |
Calculates the degree to which species are either always present or always absent within clusters or types.
duarm(taxa,clustering,sort=FALSE)
taxa |
a matrix or dataframe of samples, species as columns, samples as rows |
clustering |
a vector of numeric cluster memberships for samples, or a
classification object returned from pam ,
or partana |
sort |
if TRUE, return in order of highest value to lowest rather than input order |
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).
a dataframe of species indicator values
The name duarm is a horrible pun on the name duleg, which is an abbreviation for Dufrene and Legendre who defined an alternative indicator species algorithm.
David W. Roberts droberts@montana.edu http://ecology.msu.montana.edu/droberts
http://ecology.msu.montana.edu/labdsv/R
data(bryceveg) dis.bc <- dsvdis(bryceveg,'bray/curtis') clust <- sample(1:5,nrow(bryceveg),replace=TRUE) duarm(bryceveg,clust)