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strataG (version 1.0.3)

fastsimcoal.input: Input functions for fastsimcoal parameters

Description

Functions to create pop.info, locus.params, and hist.ev input matrices for fastsimcoal function.

Usage

fscPopInfo(pop.size, sample.size, sample.times = 0, growth.rate = 0)
fscLocusParams(locus.type = c("dna", "msat", "snp"), sequence.length = NULL,
  num.loci = NULL, mut.rate = NULL, transition.rate = 1/3,
  gsm.param = 0, range.constraint = 0, recomb.rate = 0,
  chromosome = NULL, num.chrom = NULL, ploidy = 2)
fscHistEv(num.gen = 0, source.deme = 0, sink.deme = 0,
  prop.migrants = 1, new.sink.size = 1, new.sink.growth = 0,
  new.mig.mat = 0)

Arguments

pop.size
a vector giving size of each populaiton.
sample.size
a vector giving the number of samples to take from 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.
mut.rate
dna, msat: per base pair or locus mutation rate.
transition.rate
dna: fraction of substitutions that are transitions. Set to 1 (all transitions) for SNPs.
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
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. No effect for SNPs.
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. Any non-NULL integer w
ploidy
positive integer giving the ploidy of the marker type to be simulated.
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.

References

Excoffier, L. and Foll, M (2011) fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios Bioinformatics 27: 1332-1334. http://cmpg.unibe.ch/software/fastsimcoal2/

See Also

fastsimcoal