Diversity indices {wiqid}

Biodiversity indices

Description

Common indices of biodiversity, expressed as the number of common species.

Usage

biodSimpson(abVec, correct = TRUE)
biodShannon(abVec)
biodBerger(abVec)
biodBrillouin(cntVec)

Arguments

abVec

a vector of measures of abundance, eg. counts of individuals or biomass, one element per species; or a corresponding matrix or data frame, which will be converted to a vector with rowSums.

cntVec

a vector (or matrix or data frame) of counts of individuals, one element per species. Non-integers will be rounded without warning.

correct

if TRUE, a small sample correction is applied, and in that case abVec should have count data (non-integers will be silently rounded).

Details

biodSimpson

Inverse of Simpson's (1949) index of dominance. If correct = TRUE, a small-sample correction is applied, giving Hurlbert's (1971) diversity index. Otherwise, the result is equivalent to Hill's (1973) N_2.

biodShannon

Exponential form of Shannon's (1948) entropy measure, equivalent to Hill's (1973) N_1.

biodBerger

Inverse of Berger & Parker's (1970) index of dominance, equivalent to Hill's (1973) N_Inf.

biodBrillouin

Exponential form of Brillouin's index: for small, completely censused populations, Brillouin's index is a more appropriate measure of entropy than Shannon's measure (Maurer & McGill 2011:61).

Value

The relevant index.

Warning

It is important that the proportions of each species in the sample represent those in the population from which it is drawn. This will not be the case if probability of inclusion varies among species, as often occurs when samples are collected in the field.

Author(s)

Mike Meredith

References

Berger, W H; F L Parker. 1970. Diversity of planktonic Foramenifera in deep sea sediments. Science 168:1345-1347.

Hill, M O. 1973. Diversity and evenness: a unifying notation and its consequences. Ecology 54:427-431.

Hurlbert, S H. 1971. The nonconcept of species diversity: A critique and alternative parameters. Ecology 52:577-586.

Maurer, B A; B J McGill. 2011. Measurement of species diversity. 55-64 in Magurran, A E, and B J McGill, editors. Biological diversity: frontiers in measurement and assessment. Oxford University Press, Oxford, New York NY

Shannon, C E. 1948. A mathematical theory of communication. Bell System Technical Journal 27:379-423

Simpson, E H. 1949. Measurement of diversity. Nature 163:688.

See Also

richSobs and Species richness estimators for alternatives to indices.

Examples

data(KillarneyBirds)
apply(KillarneyBirds, 2, biodSimpson)