Indicator species analysis (IndVal)

An alternative to SIMPER for identifying species indicative of given groups of sites (Dufrene & Legendre 1997). Requires abundances (counts) with samples (sites) in rows, taxa in columns. Also a group column with at least two groups specified.

For each species i in group j, define the specificity as

Aij = Nij / Ni

where Nij is the mean number of individuals of species i across sites in group j, and Ni is the sum of the mean numbers of individuals of species i over all groups.

Similarly, define the fidelity as

Bij = Nsitesij / Nsitesj

where Nsitesij is the number of sites in group j where species i is present, and Nsitesj is the total number of sites in group j.

The indicator value of species i in group j is then a value from 0 to 100 (percentage):

INDVALij = 100 Aij Bij.

The statistical significances (p values) of the indicator values are estimated by 9999 random reassignments (permutations) of sites across groups. The p values can optionally be Bonferroni corrected (multiplied with the total number of indicator values, this is highly conservative).


Dufrene, M. & P. Legendre. 1997. Species assemblages and indicator species: The need for a flexible asymmetrical approach. Ecological Monographs 67:345-366.