Functions to create pop.info, locus.params, and
hist.ev input matrices for fastsimcoal function.
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)
a vector giving size of each populaiton.
a vector giving the number of samples to take from each population.
a vector giving the number of generations in the past at which samples are taken.
a vector giving the growth rate of each population.
a character representation of what type of marker to simulate. Can be "dna", "msat", or "snp".
dna: number of DNA base pairs to use.
msat, snp: number of loci to simulate.
dna, msat: per base pair or locus mutation rate.
dna: fraction of substitutions that are transitions. Set to 1 (all transitions) for SNPs.
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).
msat: Range constraint (number of different
alleles allowed). A value of 0 means no range constraint.
recombination rate between adjacent markers. No effect for SNPs.
number or character identifying which chromosome the marker is on.
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 will cause the value in chromosome.
positive integer giving the ploidy of the marker type to be simulated.
Number of generations, t, before present at which the historical event happened.
Source deme (the first listed deme has index 0)
Sink deme
Expected proportion of migrants to move from source to sink.
New size for the sink deme, relative to its size at generation t.
New growth rate for the sink deme.
New migration matrix to be used further back in time.
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/