genepop: Run GENEPOP
In strataG: Summaries and Population Structure Analyses of Genetic Data

Description Usage Arguments Value Note Author(s) References See Also Examples

Format output files and run GENEPOP. Filenames used are returned so that output files can be viewed or read and parsed into R.

genepop(
  g,
  output.ext = "",
  show.output = F,
  label = "genepop.run",
  dem = 10000,
  batches = 100,
  iter = 5000,
  other.settings = "",
  input.fname = "loc_data.txt",
  exec = "Genepop"
)

genepopWrite(g, label = NULL)

`g`	a `gtypes` object.
`output.ext`	character string to use as extension for output files.
`show.output`	logical. Show GENEPOP output on console?
`label`	character string to use to label GENEPOP input and output files.
`dem`	integer giving the number of MCMC dememorisation or burnin steps.
`batches`	integer giving number of MCMC batches.
`iter`	integer giving number of MCMC iterations.
`other.settings`	character string of optional GENEPOP command line arguments.
`input.fname`	character string to use for input file name.
`exec`	name of Genepop executable

genepop: a list with a vector of the locus names and a vector of the input and output filenames.
genepopWrite: a list with the filename written and a vector mapping locus names in the file to the original locus names.

GENEPOP is not included with strataG and must be downloaded separately. Additionally, it must be installed such that it can be run from the command line in the current working directory. See the vignette for external.programs for installation instructions.

Eric Archer eric.archer@noaa.gov

GENEPOP 4.3 (08 July 2014; Rousset, 2008)
http://kimura.univ-montp2.fr/~rousset/Genepop.htm

hweTest, LDgenepop

## Not run: 
# Estimate Nm for the microsatellite data
data(msats.g)
# Run Genepop for Option 4
results <- genepop(msats.g, output.ext = ".PRI", other.settings = "MenuOptions=4")
# Locus name mapping and files
results
# Show contents of output file
file.show(results$files["output.fname"])

## End(Not run)