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)
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!
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.
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.