indval {labdsv}R Documentation

Dufrene-Legendre Indicator Species Analysis

Description

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

Usage

indval(x, ...)
## Default S3 method:
indval(x,clustering,numitr=1000,...)
## S3 method for class 'stride'
indval(x,comm,numitr=1,...)
## S3 method for class 'indval'
summary(object, p=0.05, type='short', digits=2, show=p,
       sort=FALSE, too.many=100, ...)

Arguments

x

a matrix or data.frame of samples with species as columns and samples as rows, or an object of class ‘stride’ from function stride

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

comm

a data.frame with samples as rows and species as columns

object

an object of class ‘indval’

p

the maximum probability for a species to be listed in the summary

type

a switch to choose between ‘short’ and ‘long’ style summary

digits

the number of significant digits to show

show

the threshold to show values as opposed to a dot column place-holder

sort

a switch to control user-managed interactive table sorting

too.many

a threshold reduce the listing for large data sets

...

additional arguments to the summary or generic 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_{ij} = presence/absence (1/0) of species i in sample j;
x_{ij} = abundance of species i in sample j;
n_c = number of samples in cluster c;
for cluster c \in K;

f_{ic} = {\sum_{j \in c} p_{ij} \over n_c}

a_{ic} = {\sum_{j \in c} x_{ij} / n_c \over \sum_{k=1}^K (\sum_{j \in k} x_{ij} / n_k)}

d_{ic} = f_{ic} \times a_{ic}

Calculated on a ‘stride’ the function calculates the indicator values of species for each of the separate partitions in the stride.

Value

The default function returns a list of class ‘indval’ 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 stride-based function returns a data.frame with the number of clusters in the first column and the mean indicator value in the second.

The ‘summary’ function has two options. In ‘short’ mode it presents a table of indicator species whose probability is less then ‘p’, giving their indicator value and the identity of the cluster they indicate, along with the sum of probabilities for the entire data set. In ‘long’ mode, the indicator value of each species in each class is shown, with values less than ‘show’ replaced by a place-holder dot to emphasize larger values.

If ‘sort==TRUE’, a prompt is given to re-order the rows of the matrix interactively.

Note

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.

Author(s)

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

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

isamic

Examples

data(bryceveg) # returns a vegetation data.frame
data(brycesite)
clust <- cut(brycesite$elev,5,labels=FALSE)
summary(indval(bryceveg,clust))

[Package labdsv version 2.0-1 Index]