[R-sig-eco] unbiased estimator of Simpson's index
Emili Garcia-Berthou
emili.garcia at udg.edu
Tue Aug 31 20:31:50 CEST 2010
Dear list:
I'll give a question and the answer this time, just in case it helps to
anybody in the future :-)
The standard formulae of Simpson's index of diversity (and other indices)
are available with the diversity function of the vegan package. For some
time, I wished to compute the unbiased estimator of Simpson's index (see
e.g. equation 5 in Hurlbert 1971 Ecology 52: 577-586 or page 115 of Magurran
2004's book "Measuring Biological Diversity")). I thought this was not
readily available in R and found no hints on mailing lists but Jari Oksanen
just suggested to me that it can be computed with something like
rarefy(x, 2) - 1
(You should take care of zero-richness samples, though).
I discovered afterwards at
vignette("diversity-vegan")
"the rarefied richness for two individuals is a finite sample variant of
Simpson's diversity index (or, more precisely of D1 + 1)"
Thanks to Jari (and the other vegan authors) for the answer and such a
useful package.
Cheers,
Emili GARCÍA-BERTHOU, Professor of Ecology
Institut d'Ecologia Aquàtica & Dept. Ciències Ambientals
Universitat de Girona, E-17071 GIRONA (Catalonia, Spain)
Tel.: +34 650 640 914 (dins UdG: 9221); Fax: +34 972 418 150
Personal web page: http://invasiber.org/EGarcia/
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