| runSCRM {poolABC} | R Documentation |
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)
Arguments
commands |
A character string containing the commands for the scrm
package. This string can be created using the |
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. |
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.
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")