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