fscWrite: Write fastsimcoal2 input files
In strataG: Summaries and Population Structure Analyses of Genetic Data

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

Write files necessary to run a fastsimcoal2 simulation.

fscWrite(
  demes,
  genetics,
  migration = NULL,
  events = NULL,
  est = NULL,
  def = NULL,
  label = "strataG.fsc",
  use.wd = FALSE
)

`demes`	matrix of deme sampling information created by the `fscSettingsDemes` function.
`genetics`	data.frame specifying loci to simulate created by the `fscSettingsGenetics` function.
`migration`	a list of matrices giving the migration rates between pairs of demes created by the `fscSettingsMigration` function.
`events`	matrix of historical events created by the `fscSettingsEvents` function.
`est`	list of parameter estimation definitions and rules generated by the `fscSettingsEst` function.
`def`	matrix of parameter values to substitute into the model generated by the `fscSettingsDef` function.
`label`	character string used to label output files for the simulation.
`use.wd`	use current working directory for input and output? If `FALSE` then a temporary directory in the session temporary directory. Note that this directory is deleted when the R session closed. See `tempdir` for more information.

Writes input files for fastsimcoal2 and returns a list of input parameters, input file, and input filenames. This list is the primary input to fscRun.

fastsimcoal2 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. The function fscTutorial() will open a detailed tutorial on the interface in your web browser.

Eric Archer eric.archer@noaa.gov

Excoffier, L. and Foll, M (2011) fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios Bioinformatics 27: 1332-1334.
Excoffier, L., Dupanloup, I., Huerta-Sánchez, E., Sousa, V.C., and M. Foll (2013) Robust demographic inference from genomic and SNP data. PLOS Genetics, 9(10):e1003905.
http://cmpg.unibe.ch/software/fastsimcoal2/

fsc.input, fscRun, fscRead

## Not run: 
#' # three demes with optional names
demes <- fscSettingsDemes(
  Large = fscDeme(10000, 10), 
  Small = fscDeme(2500, 10),
  Medium = fscDeme(5000, 3, 1500)
)

# four historic events
events <- fscSettingsEvents(
  fscEvent(event.time = 2000, source = 1, sink = 2, prop.migrants = 0.05),
  fscEvent(2980, 1, 1, 0, 0.04),
  fscEvent(3000, 1, 0),
  fscEvent(15000, 0, 2, new.size = 3)
 )
 
# four genetic blocks of different types on three chromosomes.  
genetics <- fscSettingsGenetics(
  fscBlock_snp(10, 1e-6, chromosome = 1),
  fscBlock_dna(10, 1e-5, chromosome = 1),
  fscBlock_microsat(3, 1e-4, chromosome = 2),
  fscBlock_standard(5, 1e-3, chromosome = 3)
)

params <- fscWrite(demes = demes, events = events, genetics = genetics)

## End(Not run)