fsc.loadScenario: Load skeleSim scenario parameters for fastsimcoal
In skeleSim: Genetic Simulation Engine

Load skeleSim scenario parameters for fastsimcoal

fsc.loadScenario(num.pops, pop.size, sample.size, mut.rate, migration = NULL,
  sample.times = NULL, growth.rate = NULL, locus.type = c("dna", "msat",
  "snp"), sequence.length = NULL, num.loci = NULL, transition.rate = NULL,
  gsm.param = NULL, range.constraint = NULL, recomb.rate = NULL,
  chromosome = NULL, num.chrom = NULL, num.gen = NULL,
  source.deme = NULL, sink.deme = NULL, prop.migrants = NULL,
  new.sink.size = NULL, new.sink.growth = NULL, new.mig.mat = NULL,
  fastsimcoal.exec = "fsc252")

`num.pops`	number of populations.
`pop.size`	a vector giving size of each populaiton.
`sample.size`	a vector giving the number of samples to take from each population.
`mut.rate`	`dna, msat`: per base pair or locus mutation rate.
`migration`	a `num.pop` x `num.pop` matrix or list of matrices giving the migration rates between each population.
`sample.times`	a vector giving the number of generations in the past at which samples are taken.
`growth.rate`	a vector giving the growth rate of each population.
`locus.type`	a character representation of what type of marker to simulate. Can be "dna", "msat", or "snp".
`sequence.length`	`dna`: number of DNA base pairs to use.
`num.loci`	`msat, snp`: number of loci to simulate.
`transition.rate`	dna: fraction of substitutions that are transitions.
`gsm.param`	`msat`: Value of the geometric parameter for a Generalized Stepwise Mutation (GSM) model. This value represents the proportion of mutations that will change the allele size by more than one step. Values between 0 and 1 are required. A value of 0 is for a strict Stepwise Mutation Model (SMM).
`range.constraint`	`msat`: Range constraint (number of different alleles allowed). A value of 0 means no range constraint.
`recomb.rate`	recombination rate between adjacent markers.
`chromosome`	number or character identifying which chromosome the marker is on.
`num.chrom`	a value giving the number of chromosomes that the `locus.params` marker specifications should be copied for. If `NULL`, then chromosome assignment is taken from the `chromosome` column in `locus.params`. Any non-`NULL` integer will cause the `chromosome` column to be ignored.
`num.gen`	Number of generations, t, before present at which the historical event happened.
`source.deme`	Source deme (the first listed deme has index 0)
`sink.deme`	Sink deme
`prop.migrants`	Expected proportion of migrants to move from source to sink.
`new.sink.size`	New size for the sink deme, relative to its size at generation t.
`new.sink.growth`	New growth rate for the sink deme.
`new.mig.mat`	New migration matrix to be used further back in time.
`fastsimcoal.exec`	executable

a scenario.params object to be loaded into a list in the scenarios slot of a skeleSim.params object.

Vectors for pop.size, sample.size, sample.times, and growth.rate will be expanded/recycled to ensure they are as long as num.pops.

Depending on the choice of locus.type, values for some arguments may be ignored. See argument list above for which arguments are applicable to which locus.type.

skeleSim documentation built on May 2, 2019, 5:16 a.m.