simpson

0th

Percentile

Simpson's diversity index

Simpson's diversity index

Keywords
math
Usage
simpson(x, with.replacement=FALSE)
Arguments
x
Ecosystem vector; coerced to class count
with.replacement
Boolean, with default FALSE meaning to sample without replacement; see details section
Details

Returns the Simpson index $D$: the probability that two randomly sampled individuals belong to different species. There is some confusion as to the precise definition: some authors specify that the two individuals are necessarily distinct (ie sampling without replacement), and some do not.

Simpson (1949) assumed sampling without replacement and gave

$$1-\frac{\sum_{i=1}^Sn_i\left(n_i-1\right)}{J(J-1)}$$ in our notation.

He and Hu (2005) assumed sampling with replacement: $$1-\frac{\sum_{i=1}^Sn_i^2}{J^2}.$$

The difference is largely academic but is most pronounced when many species occur with low counts (ie close to 1).

References

  • S. P. Hubbell 2001.The Unified Neutral Theory of Biodiversity. Princeton University Press.
  • F. He and X.-S. Hu 2005.Hubbell's Fundamental Biodiversity Parameter and the Simpson Diversity Index. Ecology Letters, volume 8, pp386-390. doi:10.1111/j.1461-0248.2005.00729.x
  • E. H. Simpson 1949.Measurement of diversity,Nature, volume 163, p688

See Also

preston

Aliases
  • simpson
Examples
data(butterflies)

D <- simpson(butterflies)
theta <- optimal.prob(butterflies)*2*no.of.ind(butterflies)

# compare theta with D/(1-D) (should be roughly equal; see He & Hu 2005):
theta
D/(1-D)


# Second argument pedantic in practice.

# Mostly, the difference is small:
simpson(butterflies,FALSE) - simpson(butterflies,TRUE)

# Most extreme example:
x <- count(c(1,1))
simpson(x,TRUE)
simpson(x,FALSE)
Documentation reproduced from package untb, version 1.6-5, License: GPL

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