duleg {labdsv} | R Documentation |
Calculates the indicator value (fidelity and relative abundance) of species in clusters or types.
duleg(taxa,clustering,numitr=1000) ## S3 method for class 'duleg': summary(object, p=0.05, ...)
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 optpart , slice ,
or archi |
numitr |
the number of randomizations to iterate to calculate probabilities |
object |
an object of class ‘duleg’ |
p |
the maximum probability for a species to be listed in the summary |
... |
additional arguments to the summary function |
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}
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.
Indicator value analysis was proposed by Dufrene and Legendre (1997) as a possible stopping rule 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.
David W. Roberts droberts@montana.edu http://ecology.msu.montana.edu/labdsv/R/labdsv
Dufrene, M. and Legendre, P. 1997. Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecol. Monogr. 67(3):345-366.
data(bryceveg) # returns a vegetation data.frame dis.bc <- dsvdis(bryceveg,'bray/curtis') # returns a dissimilarity matrix clust <- sample(1:5,nrow(bryceveg),replace=TRUE) duleg(bryceveg,clust)