AlphaSimR: runMacs2 – R documentation

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runMacs2

Alternative wrapper for MaCS

Description

A wrapper function for runMacs. This wrapper is designed to be easier to use than supply custom comands to manualCommand in runMacs. It effectively automates the creation of an appropriate manualCommand using user supplied variables, but only deals with a subset of the possibilities. The defaults were chosen to match species="GENERIC" in runMacs.

Usage

runMacs2(
  nInd,
  nChr = 1,
  segSites = NULL,
  Ne = 100,
  bp = 1e+08,
  genLen = 1,
  mutRate = 2.5e-08,
  histNe = c(500, 1500, 6000, 12000, 1e+05),
  histGen = c(100, 1000, 10000, 1e+05, 1e+06),
  inbred = FALSE,
  split = NULL,
  ploidy = 2L,
  returnCommand = FALSE,
  nThreads = NULL
)

Arguments

`nInd`	number of individuals to simulate
`nChr`	number of chromosomes to simulate
`segSites`	number of segregating sites to keep per chromosome
`Ne`	effective population size
`bp`	base pair length of chromosome
`genLen`	genetic length of chromosome in Morgans
`mutRate`	per base pair mutation rate
`histNe`	effective population size in previous generations
`histGen`	number of generations ago for effective population sizes given in histNe
`inbred`	should founder individuals be inbred
`split`	an optional historic population split in terms of generations ago
`ploidy`	ploidy level of organism
`returnCommand`	should the command passed to manualCommand in `runMacs` be returned. If TRUE, MaCS will not be called and the command is returned instead.
`nThreads`	if OpenMP is available, this will allow for simulating chromosomes in parallel. If the value is NULL, the number of threads is automatically detected.

Value

an object of MapPop-class or if returnCommand is true a string giving the MaCS command passed to the manualCommand argument of runMacs.

Examples

# Creates a populations of 10 outbred individuals
# Their genome consists of 1 chromosome and 100 segregating sites
# The command is equivalent to using species="GENERIC" in runMacs
founderPop = runMacs2(nInd=10,nChr=1,segSites=100)

AlphaSimR

Breeding Program Simulations

v0.13.0

MIT + file LICENSE

Authors

Chris Gaynor [aut, cre] (<https://orcid.org/0000-0003-0558-6656>), Gregor Gorjanc [aut] (<https://orcid.org/0000-0001-8008-2787>), John Hickey [aut] (<https://orcid.org/0000-0001-5675-3974>), Daniel Money [ctb] (<https://orcid.org/0000-0001-5151-3648>), David Wilson [ctb]

Initial release

2020-10-20