strataG (version 1.0.3)

fastsimcoal: Run fastsimcoal

Description

Run a fastsimcoal simulation and load results into a gtypes object.

Usage

fastsimcoal(pop.info, locus.params, mig.rates = NULL, hist.ev = NULL,
  label = NULL, quiet = TRUE, delete.files = TRUE, exec = "fsc252",
  num.cores = NULL)

Arguments

pop.info

matrix of population sampling information created by the fscPopInfo function.

locus.params

data.frame specifying loci to simulate created by the fscLocusParams function.

mig.rates

a matrix or list of matrices giving the migration rates between pairs of populations.

hist.ev

matrix of historical events created by the fscHistEv function.

label

character string to label files with.

quiet

logical. Run quietly?

delete.files

logical. Delete files when done?

exec

name of fastsimcoal executable.

num.cores

number of cores to use.

References

Excoffier, L. and Foll, M (2011) fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios Bioinformatics 27: 1332-1334. http://cmpg.unibe.ch/software/fastsimcoal2/