Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!
Get Started for Free

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(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 pam, partana, or slice
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)

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)
labdsv

Ordination and Multivariate Analysis for Ecology

v2.0-1
GPL (>= 2)
Authors
David W. Roberts <droberts@montana.edu>
Initial release

We don't support your browser anymore

Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.