rarefaction.overlap: Rarefaction Overlap

In EricArcher/sprex: Species Richness and Extrapolation

Rarefaction Overlap

Description

Calculate the percent of overlap between two species estimate distributions where the larger sample size has been rarefied to match the smaller sample size.

Usage

rarefaction.overlap(x, y, f0.func, n.rare = NULL, ...)

Arguments

x, y	two vectors of species frequencies where the i-th element is the number of species represented by only i samples.
f0.func	function to use to calculate f0. Can be Chao1, ACE, jack1, jack2, iChao1, or Swor1.
n.rare	sample size to rarefy both populations to. Must be <= the minimum sample size. If NULL, the minimum sample size is used.
...	other arguments to f0.func.

Details

Calculates the expected number of species and the standard deviation for the smaller sample size of x and y using the frequency distributions of each. The function then fits a gamma distribution to each of these estimates, and returns the percent of overlap as the integral of the mininum value of the PDF for the two distributions. Integration takes place from 0 to the largest quantile representing 0.99999 of either distribution.

Value

a vector with the percent of overlap between the two distributions, the sample size, and species estimates for the x and y vectors.

Author(s)

Eric Archer [e-mail]

References

Colwell, R.K., A. Chao, N.J. Gotelli, S.-Y. Lin, C.X. Mao, R.L. Chazdon, and J.T. Longino. 2012. Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages. Journal of Plant Ecology 5(1):3-21.

See Also

discovery.curve

Examples

data(osa.old.growth)
data(osa.second.growth)
x <- expand.freqs(osa.old.growth)
y <- expand.freqs(osa.second.growth)
rarefaction.overlap(x, y, Chao1)

EricArcher/sprex documentation built on Sept. 4, 2023, 8:35 a.m.