compspec {labdsv}

Compositional Specificity Analysis

Description

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

Usage

compspec(comm, dis, numitr=100, drop=FALSE, progress=FALSE)
## S3 method for class 'compspec'
plot(x,spc=NULL,pch=1,type='p',col=1,...)

Arguments

comm

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

dis

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

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 a progress bar

x

an object of class compspec

spc

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

pch

which glyph to plot for species

type

which type of plot

col

an integer or integer vector) to color the points

...

additional arguments to the plot function

Value

a list with several data.frames: ‘vals’ with species name, mean similarity, number of occurrences, and probability 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 species name.

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, and compares that value to the distribution of mean similarities for randomly generated sets of the same size. The mean similarity of species which only occur once is set to 0, rather than NA.

If drop=TRUE each species is deleted in turn and a new dissimilarity matrix minus that species is calculated for the analysis. This eliminates the bias that part of the similarity of communities being analyzed is due to the known joint occurrence of the species being analyzed.

Author(s)

David W. Roberts [e-mail]

See Also

indval,isamic

Examples

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