poolABC (version 1.0.0)

runSCRM: Run scrm and obtain genotypes

Description

This function will run the scrm package, according to the command line supplied as input. It will also combine haplotypes into genotypes and re-organize the output if the simulations were performed under a single origin scenario. This is to ensure that the output of the four-population models will always follow the same order: the two divergent ecotypes in the first location, followed by the two divergent ecotypes in the second location.

Usage

runSCRM(commands, nDip, nPops, model)

Value

a list with the simulated genotypes. Each entry is a different locus and, for each locus, different rows represent different individuals and each column is a different site.

Arguments

commands

A character string containing the commands for the scrm package. This string can be created using the cmd2pops, the cmdSingle or the cmdParallel functions.

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.

nPops

An integer that informs of how many populations exist on the model you are trying to run.

model

Either "2pops", "Single" or "Parallel" indicating which model should be simulated.

Examples

# 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
cmds <- cmd2pops(parameters = params, nSites = 2000, nLoci = 10, nDip = 100, mutrate = 2e-8)

# run SCRM and obtain the genotypes
runSCRM(commands = cmds, nDip = 100, nPops = 2, model = "2pops")