compute.frequency.evolution.until.convergence: Compute the evolution of the frequency of the genotypes until...
In frederic-michaud/hapex: FRequency Evolution Simulator of Sex-linked Alleles

Description Usage Arguments Details Value Examples

Given a genome, this function simulate the evolution of the frequency of all the possible genotype that exist until convergence has been reach.

1
2
3

compute.frequency.evolution.until.convergence(genome,
  initial.frequency = NULL, min.generations = 25, max.generations = 1e+05,
  criteria = 1e-08, keep.all.generation = TRUE)

`genome`	A S4 object of the type genome
`initial.frequency`	The initial frequency of the various genotype. If NULL is given the initial frequencies will all be set to the same value
`min.generations`	The minimum number of generation to be computed
`max.generations`	The maximum number of generation to be computed. If the convergence is not reached in this time, iteration stop and a warning is emited. A value of zero indicate no limit.
`criteria`	If the sum of the slope of the evolution of the genotype frequency is under this number, the simulation stop (if the other criteria are also met)
`keep.all.generation`	tell wether to give only the value of the last three generations or all of them. Kepping only the last generations improve computation time. Default value = TRUE

Convergence is evaluated in the following way. First, a few generation are perform (warmup) without measuring the criteria since they might be oscillation due to male/female proportion effect. Then, at each generation, the total slope \abs(\vec({_t}-\vec{x_{t-1}}) and the total curvature \abs(\vec({_t}-\vec{x_{t-1}})

A matrix containing the frequencies of each genotype at each generation

locus1 = data.frame(allele1=c(1,1),allele2 = c(1,2),sd = c(0,1),fitness.male=c(1,1),fitness.female=c(1,1))
locus2 = data.frame(allele1=  c(1,1,2),allele2 = c(1,2,2),fitness.female = c(1,0.9,0.8),fitness.male = c(0.6,0.8,1))
genome = create.genome(locus1,locus2)
freqs <- compute.frequency.evolution.until.convergence(genome)