simDrift: Simulate Drift
In steveped/driftSim: Simulate Genetic Drift

Description Usage Arguments Details Value Examples

Simulate drift across a number of populations and generations, for a single allele

1 2	simDrift(f0, N0, Nt, t, n, mig, surv, litter, pops = c("same", "flip50", "flip100", "fixed", "absent"), sd = 0, genoProbs = c(1, 1, 1), ...)

`f0`	The allele frqeuency pre-bottleneck
`N0`	The effective population size pre-bottleneck
`Nt`	The effective population size after 't' generations
`t`	The number of generations
`n`	The number of populations
`mig`	The migration rate
`surv`	The survival rate at the original population bottleneck
`litter`	The litter size at each generation
`pops`	Specify the method for generating f0 in surrounding populations. Choosing `pops = "same"` gives neighbouring populations with the same starting frequency. Choosing `pops = "flip50"` gives neighbouring populations where allele frequencies are flipped between 0.5 and 1, such that if f0 = 0.55, in neighbouring populations it will be given f0 = 0.95. Choosing `pops = "flip100"` gives neighbouring populations with allele frequencies flipped between 0 and 1, such that if f0 = 0.55, neighbouring populations will be given f0 = 0.45. Choosing either `pops = "fixed"` or `pops = "absent"` will set the alleles to be strictly fixed or absent in the neighbouring populations.
`sd`	The variability of allele frequencies in neighbouring populations around the central population.
`genoProbs`	A vector of length three indicating the selective advantage for each genotype. Should be specified as relative probabilities and defaults to the vector `c(1, 1, 1)`, giving an equal probability of selection to each genotype. By way of example, a 20% fitness increase for a homozygous reference allele could be given the vector `c(1.2, 1, 1)`.

Starting with the initial population size, which is equal across all populations, all populations are subject to the same bottleneck with survival probability as given in the argument surv. Populations are grown exponentially until reaching Nt, and despite the given litter-size, only the appropriate number will be allowed to breed at each generation.

By default, all neighbouring populations will be given the same initial frequency as the central population. These can be varied around this value on the logit scale using the parameter sd. Choosing values such as sd < 0.5 will give moderate variability around the starting frequency, whilst values near one will clearly spread the allele frequencies more widely across the entire range. Extreme values such as sd = 100 will give alleles which are effectively either fixed or absent in the neighbouring populations with equal probability.

A list with components ft and nEff. These denote the final allele frequency, and the effective populations sizes at each generation respectively.