Description Usage Arguments Value Note
View source: R/fsc.loadScenario.R
Load skeleSim scenario parameters for fastsimcoal
1 2 3 4 5 6 7 8 | 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 |
|
migration |
a |
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 |
|
num.loci |
|
transition.rate |
dna: fraction of substitutions that are transitions. |
gsm.param |
|
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
|
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
.
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