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")
number of populations.
a vector giving size of each populaiton.
a vector giving the number of samples to take from each population.
dna, msat
: per base pair or locus mutation rate.
a num.pop
x num.pop
matrix or list of matrices
giving the migration rates between 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: fraction of substitutions that are transitions.
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.
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 in locus.params
. Any non-NULL
integer will cause the chromosome
column to be ignored.
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.
executable
a '>scenario.params object to be loaded into a list in the
scenarios
slot of a '>skeleSim.params object.