genepop: Run GENEPOP

In EricArcher/strataG: Summaries and Population Structure Analyses of Genetic Data

Run GENEPOP

Description

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

Usage

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)

Arguments

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

Value

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.

Note

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.

Author(s)

Eric Archer [e-mail]

References

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

See Also

hweTest, LDgenepop

Examples

## 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)

EricArcher/strataG documentation built on Feb. 12, 2023, 4:11 a.m.