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
)
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.
the length and width of the meta-community in grid cells
number of species
number of time-steps (each discrete)
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)
lambda value for Poisson distribution used to distribute environmental quality; essentially the carrying capacity (for each species separately) for that cell
lambda value for Poisson distribution used to distribute initial abundances and abundance after migration
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!)
probabilty that, at each timestep, a species will speciate. A species can only speciate, migrate, or reproduce if it has individuals!
Will Pearse
Will Pearse
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.
sim.phy scape