cmdSingle: Create SCRM command line for a single origin scenario

Description

This function creates a command line tailored for a scenario of single origin to explain ecotype formation. The command line can then be fed to the scrm package to run the model.

Usage

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

Value

a character vector with four entries. The first entry is the scrm command line for the loci without any barriers against migration. The second entry is the command line for the loci without migration from the C towards the W ecotype. The third entry is command line for the loci without migration from the W towards the C ecotype and the last 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.

Details

For convenience, imagine we have two divergent ecotypes, named C and W. This model assumes that the first population corresponds to the C ecotype at the first location, the second population to the C ecotype in the second location, the third population to the W ecotype in the first location and the fourth population to the W ecotype in the second location.

Examples

Run this code

# create a vector with parameter values for the single origin scenario
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),
CC =  c(1e-13, 1e-3), WW = c(1e-13, 1e-3), ANC = c(1e-13, 1e-3), bT = c(0, 0.2),
bCW = c(0, 0.5), bWC = c(0, 0.5), model = "Single")

# create the command line for the scrm package
cmdSingle(parameters = params, nSites = 2000, nLoci = 100, nDip = 400, mutrate = 2-8)

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