sim.msABC.sanger: Simulate summary statistics using msABC

In gehara/PipeMaster: Building and Simulating Coalescent models.

Simulate summary statistics using msABC

Description

Simulate summary statistics using msABC

Usage

sim.msABC.sanger(
  model,
  use.alpha = F,
  nsim.blocks = 5,
  path = getwd(),
  append.sims = F,
  block.size = 1000,
  msABC.call = get.msABC(),
  output.name = "model",
  ncores = 1
)

Arguments

model	A model object bult by the main.menu function.
use.alpha	Logical.If TRUE the most recent population size change will be exponential. If FALSE sudden demographic changes. Default is FALSE.
nsim.blocks	Number of blocks to simulate. The total number of simulations is: nsim.blocks x sim.block.size.
path	Path to write the output. By default outputs will be saved in the working directory.
append.sims	Logical. If TRUE simulations will be appended in the last output. Default is FALSE.
msABC.call	String. Path to the msABC executable. msABC binaries for Mac's and Linux are included in the package and should work in most computers.
output.name	String. The prefix of the output names. Defalt is "model"
sim.block.size	Simulations are performed in blocks. This argument defines the size of the block in number of simulations, i.e. how many simulations to run per block.
get.moments	Logical. If TRUE computes the four moments (mean, variance, kurtosis, skewness) of each summary statistics across loci. If False only mean is computed. Defalt is FALSE.

Value

Writes simulations and parameters to the path directory. msABC outputs a bunch of summary stats by defalt. They need to be selectd a posteriori.

Note

This function does not work on Windows systems.

Author(s)

Marcelo Gehara

References

Hudson R.R. (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics, 18, 337–338.

Pavlidis P., Laurent S., & Stephan W. (2010) msABC: A modification of Hudson’s ms to facilitate multi-locus ABC analysis. Molecular Ecology Resources, 10, 723–727.

gehara/PipeMaster documentation built on April 19, 2024, 8:14 a.m.