GSImulate: Simulate baseline and mixture files into the current working...
In eriqande/GSImulator:

This is a wrapper around ms2geno that should make it much easier to use

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GSImulate(refsizes, mixsizes, num_loci, num_sets, variability_string,
  marker_pars, M_num = NULL, M_matrix = NULL, repunits = character(0),
  ploidy = 2, write_012 = FALSE)

`refsizes`	integer vector of sample sizes for the reference samples from each collection (population)
`mixsizes`	integer vector of samples sizes of individuals that go into the mixture data set.
`num_loci`	the number of loci to simulate
`num_sets`	desired number of data sets.
`variability_string`	the command to pass to ms to influence the number of segregating sites. Either something like "-s 20" for fixed number of segsites, or "-t 8" to set the value of theta to 8.
`marker_pars`	a string that gives all the command line arguments needed for either microsatellites or SNPs (but not both!) to be simulated. See the documentation for ms2geno.
`M_num`	a number for 4Nem to be passed to ms to make a symmetrical island model. Gets overridden by M_matrix if M_matrix is present (i.e. non-NULL). Set this to NA if you want to simulate a single panmictic population that is masquerading as multiple populations using ms2geno's –ms-pop-override option.
`M_matrix`	a full migration matrix if you want to pass one in. Will override M_num if present. By default it will be NULL.
`repunits`	optional vector that must be the same length as refsizes and which gives the reporting units to which each collection belongs (NOT IMPLEMENTED)
`ploidy`	the ploidy of the organisms to be simulated.
`write_012`	logical. If TRUE, writes Basefile and Mixfile as sets of 012 files to be read by, for example, genoscapeRtools::read_012. Default is FALSE

# microsatellites
GSImulate(
   refsizes = c(200, 200, 150, 100),
   mixsizes = c(25, 25, 10, 30),
   num_loci = 20,
   num_sets = 5,
   variability_string = "-t 2.4",
   marker_pars = "-u .15 3",
   M_num = 5)

# microsatellites using --ms-pop-override
GSImulate(
   refsizes = c(200, 200, 150, 100),
   mixsizes = c(25, 25, 10, 30),
   num_loci = 20,
   num_sets = 5,
   variability_string = "-t 2.4",
   marker_pars = "-u .15 3",
   M_num = NA)

# SNPs ascertained from 8 individuals from each population
# and taken if all three genotypes are seen
GSImulate(
   refsizes = c(200, 200, 150, 100),
   mixsizes = c(25, 25, 10, 30),
   num_loci = 20,
   num_sets = 5,
   variability_string = "-t 2.4",
   marker_pars = "-s 1 8 -2 -s 2 8 -2 -s 3 8 -2 -s 4 8 -2 --all-pops-geno-asc",
   M_num = 5)