rand.neutral

From untb v1.6-5 by Robin K S Hankin

Random neutral ecosystem

Given the size of the metacommunity $J$, and the fundamental biodiversity number $\theta$, generate an object of class count using a stochcastic mechanism consistent with the neutral theory.

Keywords: math

Usage

rand.neutral(J, theta=NULL, prob.of.mutate=NULL, string = NULL, pad = FALSE)

Arguments

J: Size of metacommunity
theta: Fundamental biodiversity number $\theta$. User must supply exactly one of theta and prob.of.mutate.
prob.of.mutate: Probability of mutation $\nu$: $\theta=2J\nu$.
string: String to add to species names. By default (ie string being NULL), species are named 1, 2,$\ldots$. Argument string supplies a prefix for these species names; a good o
pad: Boolean, with default FALSE meaning to return a count object having only extant species, and TRUE meaning to pad the count with extinct species to J species. Use this when a vector of length

Details

Uses the simulation method on page 289 of Hubbell (2001).

Note

If pad is TRUE, and you set string to extinct, things will break.

References

S. P. Hubbell 2001. The Unified Neutral Theory of Biodiversity. Princeton University Press.

Examples

rand.neutral(1000, 9)
rand.neutral(1000, 9, string="spp.")

data(butterflies)
rand.neutral(no.of.ind(butterflies), optimal.theta(butterflies),string="spp.")


# what is the distribution of abundance of the second ranked species if
# J=10, theta=0.7?
plot(table(replicate(100,rand.neutral(10,theta=0.7,pad=TRUE)[2])))

Documentation reproduced from package untb, version 1.6-5, License: GPL

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