labdsv (version 1.8-0)

isamic: 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(taxa,clustering,sort=FALSE)

Arguments

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 pam, partana, or slice

sort

if TRUE, return in order of highest value to lowest rather than input order

Value

a data.frame of species indicator values

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).

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. In press.

See Also

indval

Examples

# NOT RUN {
    data(bryceveg)
    dis.bc <- dsvdis(bryceveg,'bray/curtis')
    clust <- sample(1:5,nrow(bryceveg),replace=TRUE)
    isamic(bryceveg,clust)
# }