PopGenome (version 1.2.6)

test.params-class: Set parameter for Coalescent Simulation.

Description

This object can be passed to the function MS after having set parameter values. This class eases the process of passing on all necessary values to the MS function.

Arguments

theta

mutation parameter theta (4Nmu), where N is the diplod population size and mu the mutation rate per locus. It needs to be provided as vector of length n.regions

seeds

specify 3 random number seeds. a vector of length 3 with positive values is expected

fixedSegsites

usually the number of segregating sites varies in each iteration. Please provide a single numeric value if the number of segregating sites needs to be fixed.

recombination

provide a vector of format: c(p, nsites), p = cross over parameter rate, nsites is the number of sites between recombination occurs

geneConv

in addition to recombination intra-locus non-cross-over exchange gene conversion can be included in simulation, expected format is c(f, gamma), f denote the ratio, g/r, where r is the probability per generation of crossing-over between adjacent sites. (

growth

population size is measured by $N(t) = N0 exp^{alpha*t}$. provide alpha as integer value. negative values indicate that population was larger in the past than present

migration

specify the migration rate between popualtions. Please provide a single numeric value.

demography

vector of length 3 or 4 with first value denoted as 'type' valid 'types' for vectors of length 3 are as following: - 1 to set a growth rate change alpha at a certain time t: c(1, t, alpha) - 2 set all subpop to size $x * N_{0}

See Also

MS

Examples

# params           <- new("test.params")
# params@theta     <- rep(5,n.regions)
# params@migration <- 3