isamic {labdsv} | R Documentation |
Calculates the degree to which species are either always present or always absent within clusters or types.
isamic(taxa,clustering,sort=FALSE)
taxa |
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 |
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 data.frame of species indicator values
This function was previously called ‘duarm’, a horrible pun on the
name duleg
, which is an abbreviation for Dufrene and Legendre who defined
an alternative indicator species algorithm. Following publication of Aho et al. 2008,
it was renamed ‘isamic’ as decribed in that paper.
David W. Roberts droberts@montana.edu
http://ecology.msu.montana.edu/labdsv/R/labdsv 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. In press.
data(bryceveg) dis.bc <- dsvdis(bryceveg,'bray/curtis') clust <- sample(1:5,nrow(bryceveg),replace=TRUE) isamic(bryceveg,clust)