duleg {unknown}R Documentation

Dufrene-Legendre Indicator Species Analysis

Description

Calculates the indicator value (fidelity and relative abundance) of species in clusters or types.

Usage

duleg(taxa,clustering,numitr=1000)
## S3 method for class 'duleg':
summary(object, ...)

Arguments

taxa a matrix or data.frame of samples with species as columns and samples as rows
clustering a vector of numeric cluster memberships for samples, or a classification object returned from pam, or partana
numitr the number of ramdomizations to iterate to calculate probabilities
object an object of class ‘duleg’
... additional arguments to the summary function

Details

Calculates the indicator value $d$ of species as the product of the relative frequency and relative average abundance in clusters. Specifically,

where:
p_{i,j} = presence/absence (1/0) of species $i$ in sample $j$;
x_{i,j} = abundance of species $i$ in sample j;
n_c = $ number of samples in cluster c;
for cluster c in set K;

f_{i,c} = {sum_{j in c} p_{i,j} over n_c}


a_{i,c} = {(sum_{j in c} x_{i,j}) / n_c over sum_{k=1}^K ((sum_{j in k} x_{i,j}) / n_k)}


d_{i,c} = f_{i,c} times a_{i,c}


Value

a list with components:

relfrq relative frequency of species in classes
relabu relative abundance of species in classes
indval the indicator value for each species
maxcls the class each species has maximum indicator value for
indcls the indicator value for each species to its maximum class
pval the probability of obtaining as high an indicator values as observed over the specified iterations


The ‘summary’ function simply returns the sum of probabilities for the species.

Note

Indicator value analysis was proposed by Dufrene and Legendre (1997) as a source of possible stopping rules for clustering, but has been used by ecologists for a variety of analyses. Dufrene and Legendre's nomenclature in the paper is somewhat ambiguous, but the equations above are taken from the worked example in the paper, not the equations on page 350 which appear to be in error. Dufrene and Legendre, however, multiply $d$ by 100; this function does not.

Author(s)

David W. Roberts droberts@montana.edu http://ecology.msu.montana.edu/labdsv

References

Dufrene, M. and Legendre, P. 1997. Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecol. Monogr. 67(3):345-366.

See Also

duarm

Examples

    data(bryceveg) # returns a vegetation dataframe
    dis.bc <- dsvdis(bryceveg,'bray/curtis') # returns a dissimilarity matrix
    clust <- sample(1:5,nrow(bryceveg),replace=TRUE)
    duleg(bryceveg,clust)

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