metacycle: Simulate a Metapopulation System
In metapop: Metapopulations and Incidence Functions

Description Usage Arguments Details Value Author(s) References See Also Examples

Function metacycle runs simulation of a metapopulation system.

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

`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

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.

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.

Jari Oksanen

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

nothing yet

## 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")