sim.metapopgen.coral: Function to simulate metapopulation genetics of coral...

In MarcoAndrello/MetaPopGen_0.0.8: Simulation of metapopulation genetics

Description

This function is built upon sim.metapopgen.monoecious to simulate the genetics of coral metapopulations. Each coral colony is considered as an individual.
There are five stage-classes, corresponding to age 0+, age 1+, age 2+, age 3+ and dead individuals. Individuals can persist in the 3+ class. Individuals in the "dead" class are coral skeletons. The "survival" probability of the dead class indicates whether a coral skeleton persists or is destroyed. Recruitment is dependent on the total number of individuals in the deme, including dead individuals, because they occupy space.
The parameter kappa0 is the maximum number of individuals in the deme (carrying capacity).

Usage

sim.metapopgen.coral(N1, sigma, phi_F, phi_M, kappa0, ...)

Arguments

N1	Number of individuals at the beginning of the simulation. 3-D array giving the number of individuals of each genotype in each deme and each of the five stage-classes (0+, 1+, 2+, 3+ and dead) at the beginning of the simulation. The first dimension is the genotype, the second dimension is the deme and the third dimension is the stage-class. To be used when input.type = "array".
sigma, phi_F, phi_M	They have the same meaning as in sim.metapopgen.monoecious, the only difference being the meaning of the fifth stage class (dead individuals). The "survival" probability of the dead class, sigma[i,j,5], indicates whether a coral skeleton persists or is destroyed: for example, if sigma[i,j,5] = 0.85, coral skeletons are destroyed with a 0.15 probability each time-step. The fecundities of the fifth stage class (dead individuals) must be set to 0.
kappa0	2-D array of length c(n,T_max). Carrying capacity used to calculate the density-dependent settler survival probabilities. kappa0[i,t] is the maximum number of individuals allowed for deme i at time t. If the total number of individuals Ntot(i,t) present in a deme (including dead individuals: coral skeletons) is larger than kappa0[i,t], then recruitment probability is set to 0. Otherwise, recruitment probability is set to [kappa0[i,t] - Ntot(i,t)] / Stot(i,t), where Stot(i,t) is the total number of settlers in deme i at time t. kappa0 can also be a 1-D array of length n: this will be interpreted as a carrying capacity constant in time.
...	All the other parameters to be passed to the function, as in sim.metapopgen.monoecious

Value

The same as in sim.metapopgen.monoecious.

Examples

# Simple example with 2 demes, 2 alleles and 5 years of simulations
data(Dataset.coral)
sim.metapopgen.coral(input.type="array", N1= N1, sigma = sigma, phi_M = phi_M, phi_F = phi_F, mu = mu, delta = delta, kappa0 = kappa0, T_max = T_max, save.res = save.res)

MarcoAndrello/MetaPopGen_0.0.8 documentation built on May 25, 2019, 12:23 p.m.