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(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, or partana
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

Note

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.

Author(s)

David W. Roberts droberts@montana.edu

References

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.

See Also

duleg

Examples

    data(bryceveg)
    dis.bc <- dsvdis(bryceveg,'bray/curtis')
    clust <- sample(1:5,nrow(bryceveg),replace=TRUE)
    isamic(bryceveg,clust)

[Package labdsv version 1.3-1 Index]