fsc.multiple.estimate: Run fsc over multiple models

In carlopacioni/amplicR: An R package to process amplicon data

Run fsc over multiple models

Description

This function expects one or more folders within dir.in, where in each directory there are all the files needed to run fsc.estimate, which is run iteratively

Usage

fsc.multiple.estimate(
  dir.in,
  n = 5e+05,
  L = 100,
  maf = TRUE,
  ncpu = 0,
  nBatches = NULL,
  fsc.cmd = "fsc2702",
  fsc.path = "path"
)

Arguments

dir.in	The path where to run fsc
n	The number of coalescent simulations to approximate the expected SFS (-n option). This should be larger than 100,000.
L	The number of optimization cycles (-L option). It should be >50
maf	Whether a MAF SFS (default) or a derived SFS is provided (if FALSE)
ncpu	The number of CPU (threads) to use in the analysis. Automatically handle if ncpu=0 (default)
nBatches	The number of batches (-B option)
fsc.cmd	The command to use to call fsc (that may be different depending on the version installed)
fsc.path	The path where fsc is installed or "path" if it is in the PATH (that means that it can be called regardless of the working directory)

carlopacioni/amplicR documentation built on Aug. 19, 2023, 7:59 p.m.