cmd2pops: Create SCRM command line for a model with two populations

Description

This function creates a command line tailored for an isolation with migration model with two populations. The command line can then be fed to the scrm package to run the model.

Usage

cmd2pops(parameters, nSites, nLoci, nDip, mutrate, extra = FALSE)

Value

a character vector with two entries. The first entry is the scrm command line for the loci without any barriers against migration, while the second entry is the scrm command line for the loci without migration between divergent ecotypes.

Arguments

parameters: A vector where each entry corresponds to a different parameter, e.g. one entry is the size of the reference population, another is the time of recent split, etc. Please note that this functions depends on the ordering of the parameters in the vector and thus, it should only be used with a vector created with the createParams function.
nSites: An integer representing the number of base pairs that each locus should have.
nLoci: An integer that represents how many independent loci should be simulated.
nDip: An integer representing the total number of diploid individuals to simulate. Note that scrm actually simulates haplotypes, so the number of simulated haplotypes is double of this. Also note that this is the total number of diploid individuals and this function will distribute the individuals equally by the two populations.
mutrate: A number representing the mutation rate assumed for the simulations.
extra: is a logical value indicating whether the required number of loci should be enforced. The default is FALSE but, if set to TRUE, then additional loci will be simulated. These additional loci are simulated to try to have sufficient loci to keep the required number of loci after filtering.

Examples

Run this code

# create a vector with parameter values for a two populations model
params <- createParams(Nref = c(25000, 25000), ratio = c(0.1, 3), pool = c(5, 250),
seq = c(0.0001, 0.001), split = c(0, 3), CW = c(1e-13, 1e-3), WC = c(1e-13, 1e-3),
bT = c(0, 0.2), model = "2pops")

# create the command line for the scrm package
cmd2pops(parameters = params, nSites = 2000, nLoci = 100, nDip = 100, mutrate = 2e-8)

Run the code above in your browser using DataLab