labdsv (version 1.8-0)

compspec: Compositional Specificity Analysis

Description

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

Usage

compspec(taxa, dis, numitr=100, drop=FALSE, progress=FALSE)
# S3 method for compspec
plot(x,spc=NULL,…)

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

drop

a switch to determine whether to drop species out when calculating their compspec value

progress

a switch to control printing out progress

x

an object of class compspec

spc

an integer code to specify exactly which species drop-out to plot

…

additional arguments to the plot function

Value

a list with several data.frames: ‘vals’ with species name, mean similarity, number of occurrences, and probaability of observing as high a mean similarity as observed, and ‘quantiles’ with the distribution of the quantiles of mean similarity for given numbers of occurrences. If drop=TRUE, results specific to dropping out each species in turn are added to the list by taxon name.

References

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

See Also

indval,isamic

Examples

# NOT RUN {
data(bryceveg) # returns a vegetation data.frame
dis.bc <- dsvdis(bryceveg,'bray/curtis')
    # returns a Bray/Curtis dissimilarity matrix
compspec(bryceveg,dis.bc)
# }