sim.meta: Simulate a meta-community (and its phylogeny)
In willpearse/pez: Phylogenetics for the Environmental Sciences

Description Usage Arguments Details Value Note Author(s) See Also

sim.meta.comm simulates species moving through a metacommunity. At each time-step each cell's next abundance for each species is env.quality - current.abundance + stochastic, and a species gets as many chances to migrate in each time-step as it has cells (the same cell could migrate multiple times). I use a Poisson for everything because I don't want half-species (these are individuals), and keeping everything in Poisson makes it easier to compare the relative rates of everything.

sim.meta.comm(size = 10, n.spp = 8, timesteps = 10,
  p.migrate = 0.05, env.lam = 10, abund.lam = 5, stoch.lam = 1)

sim.meta.phy.comm(size = 10, n.spp = 8, timesteps = 10,
  p.migrate = 0.3, env.lam = 10, abund.lam = 5, stoch.lam = 1,
  p.speciate = 0.05)

`size`	the length and width of the meta-community in grid cells
`n.spp`	number of species
`timesteps`	number of time-steps (each discrete)
`p.migrate`	probability that a group of species in each grid cell will migrate to another grid cell each timestep (i.e., 10 cells occuped by a species –> 10*`p.migrate` chance of migration)
`env.lam`	lambda value for Poisson distribution used to distribute environmental quality; essentially the carrying capacity (for each species separately) for that cell
`abund.lam`	lambda value for Poisson distribution used to distribute initial abundances and abundance after migration
`stoch.lam`	lambda value for Poisson distribution of noise added to the next step abundance calculation. With equal chance, this is taken as either a positive or a negative number (see details if you're confused as to why this is Poisson!)
`p.speciate`	probabilty that, at each timestep, a species will speciate. A species can only speciate, migrate, or reproduce if it has individuals!

sim.meta.phy.comm As above, but with a simulation of phylogeny as well - there are no additional extinction parameters, since extinction happens as a natural consequence of ecological interactions.

For sim.meta.comm a list with a species-site matrix as the first slot, and the environment as the second. Rownames of the site-species are the List with the x and y co-ordinates of the simulation grid pasted together; colnames are arbitrary species names. sim.meta.comm, a comparative.comm object (since we have now simulated a phylogeny), with the same naming convention for the site names. phylogeny.

sim.meta.phy.comm comparative.comm object that describes the data; note that the rownames of the community object refer to the row.column of the data in the simulated grid assemblages.

scape is a much more sophisticated simulation of the biogeography, but requires you to supply a phylogeny. You pays your money, you makes your choice.

Will Pearse

sim.phy scape

willpearse/pez documentation built on June 18, 2019, 9:33 p.m.