Simulate a Metapopulation System

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Description

Function metacycle runs simulation of a metapopulation system.

Usage

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metacycle(steps = 1, d, A, p = rep(1, length(A)), y = 1, x = 1, e = min(A), alpha = 1, locations = NULL, ...)

Arguments

steps

Number of time steps

d

Distances among patches

A

Areas of patches

p

Initial occupancies of the patches, must be 0 or 1.

y, x, e

Parameters of the metapopulation models

alpha

Exponential decay rate in connectivity

locations

Coordinates of the patches

...

Other parameters of the model

Details

For details of the model see the pdf document in the doc folder of the packages: Chapter 4 explains simulation, and Chapter 3 describes the estimeatin of the parameters.

Function metastep performs one simulation step. It is a lower level function and trickier to parametrize. See the code for its working, or consult the pdf file in doc folder.

Value

Function metacycle returns an object of class "metacycle" with following items.

p

Occupancy matrix with a row for each location and column for each step

d

connectivity from the exponenential decay model.

A

Sizes of patches

y, x, e, alpha

Input parameters of the model

locations

Coordinates of the patches, found from cmdscale if not given.

J.obs

Observed incidences for each patch.

P.obs

Observed number of occupied site for each step.

J.pot, S.pot, C.pot

Expected incidence and parameters S and C.

Author(s)

Jari Oksanen

References

Hanski, I. 1999. Metapopulation Ecology. Oxford UP.

See Also

nothing yet

Examples

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## Parameters similar to a Melitae cinxia network
data(fritty)
d <- with(fritty, dist(cbind(x.crd, y.crd)))
sim <- with(fritty, metacycle(100, d, A, p, x = 0.42, e = 0.061, y = 15.2))
plot(sim$P.obs,   type = "l", col = "blue", lwd = 2,
 xlab = "Time", ylab = "Population Size")
plot(sim$J.pot, sim$J.obs, xlab="Expected incidence", ylab="Simulated incidence")

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