mutmodel: Mutation model logic

In fwsim: Fisher-Wright Population Simulation

Description

Functions for mutation model logic, e.g. probability of downwards and upwards mutations etc.

Usage

mutmodel_not_mut(mutmodel, locus, alleles)
mutmodel_dw_mut(mutmodel, locus, alleles)
mutmodel_up_mut(mutmodel, locus, alleles)
approx_stationary_dist(mutmodel, alleles)

Arguments

mutmodel	a mutmodel object created with init_mutmodel.
locus	the locus of interest (integer, remember postfix L).
alleles	vector of integers (remember postfix L) of the alleles of interest.

Value

Mutation probabilities for locus locus in mutation model mutmodel at alleleles alleles.

Author(s)

Mikkel Meyer Andersen <[e-mail]> and Poul Svante Eriksen

Examples

mutpars.locus1 <- c(0.149,   2.08,    18.3,   0.149,   0.374,   27.4) # DYS19
mutpars.locus2 <- c(0.500,   1.18,    18.0,   0.500,   0.0183,  349)  # DYS389I
mutpars.locus3 <- c(0.0163,  17.7,    11.1,   0.0163,  0.592,   14.1)  # DYS391
mutpars <- matrix(c(mutpars.locus1, mutpars.locus2, mutpars.locus3), ncol = 3)
colnames(mutpars) <- c("DYS19", "DYS389I", "DYS391")
mutmodel <- init_mutmodel(modeltype = 2L, mutpars = mutpars)

mutmodel_not_mut(mutmodel, locus = 1L, alleles = 10L:20L)
mutmodel_dw_mut(mutmodel, locus = 1L, alleles = 10L:20L)
mutmodel_up_mut(mutmodel, locus = 1L, alleles = 10L:20L)

statdists <- approx_stationary_dist(mutmodel, alleles = 5L:20L)
bp <- barplot(statdists, beside = TRUE)
text(bp, 0.02, round(statdists, 1), cex = 1, pos = 3) 
text(bp, 0, rep(rownames(statdists), ncol(mutmodel$mutpars)), cex = 1, pos = 3)


mutpars <- matrix(c(c(0.003, 0.001), rep(0.004, 2), rep(0.001, 2)), ncol = 3)
colnames(mutpars) <- c("DYS19", "DYS389I", "DYS391")
mutmodel <- init_mutmodel(modeltype = 1L, mutpars = mutpars)
mutmodel
statdists <- approx_stationary_dist(mutmodel, alleles = 5L:20L)
statdists

bp <- barplot(statdists, beside = TRUE)
text(bp, 0.02, round(statdists, 1), cex = 1, pos = 3) 
text(bp, 0, rep(rownames(statdists), ncol(mutmodel$mutpars)), cex = 1, pos = 3)

fwsim documentation built on May 2, 2019, 8:33 a.m.