indspc {labdsv}R Documentation

Compositional Indicator Species Analysis

Description

Calculates the mean similarity of all plots in which a species occurs.

Usage

indspc(taxa, dis, numitr=100)
## S3 method for class 'indspc'
plot(x, ...)

Arguments

taxa

a data frame of taxa, samples as rows, species as columns

dis

an object of class ‘dist’ from dist, vegdist, or dsvdis

numitr

the number of iterations to use to establish the quantiles of the distribution

x

an object of class indspc

...

additional arguments to the plot function

Value

a list with two data.frames: vals with species name, mean similarity, and number of occurrences, and quantiles with the distribution of the quantiles

Note

One measure of the habitat specificity of a species is the degree to which a species only occurs in communities that are similar to each other. This function calculates the mean similarity of all samples in which each species occurs. The mean similarity of species which only occur once is set to 0, rather than NA.

The calculated values can be compared to random samples of plots with the same number of occurrences.

Author(s)

David W. Roberts droberts@montana.edu

References

http://ecology.msu.montana.edu/labdsv/R/labdsv

See Also

indval,isamic

Examples

data(bryceveg) # returns a vegetation data.frame
dis.bc <- dsvdis(bryceveg,'bray/curtis')
    # returns a Bray/Curtis dissimilarity matrix
indspc(bryceveg,dis.bc)

[Package labdsv version 1.4-1 Index]