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labdsv (version 1.2-0)

duleg: 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, \dots)

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 randomizations to iterate to calculate probabilities
object
an object of class duleg
...
additional arguments to the summary function

Value

  • a list with components:
  • relfrqrelative frequency of species in classes
  • relaburelative abundance of species in classes
  • indvalthe indicator value for each species
  • maxclsthe class each species has maximum indicator value for
  • indclsthe indicator value for each species to its maximum class
  • pvalthe 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.

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 $K$; $$f_{i,c} = {\sum_{j \in c} p_{i,j} \over n_c}$$ $$a_{i,c} = {(\sum_{j \in c} x_{i,j}) / n_c \over \sum_{k=1}^K ((\sum_{j \in k} x_{i,j}) / n_k)}$$ $$d_{i,c} = f_{i,c} \times a_{i,c}$$

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

Run this code
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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