mutation.selection: Gene frequencies over time under mutation-selection balance

In learnPopGen: Population Genetic Simulations & Numerical Analysis

Description

This function performs numerical analysis of mutation-selection balance with mutation from A to a and selection against (either or both of) Aa and aa.

Usage

	mutation.selection(p0=1.0, w=c(1,0), u=0.001, time=100, show="q", pause=0, 
		ylim=c(0,1))

Arguments

p0	Starting frequency for the A allele.
w	Fitnesses of the heterozygote (Aa) and homozygote deleterious (aa) genotypes. The fitness of genotype AA is assumed to be 1.0.
u	Rate at which A alleles are converted to a alleles by mutation.
time	Number of generations to run the analysis.
show	Two options for plotting. "q" shows the frequency of a through time; "fitness" plots the mean fitness over time. The default is show="q".
pause	Pause between generations. pause=0.01 (for instance) might smooth animation.
ylim	Limits on the y-axis for plotting.

Value

The function creates one of three possible plots, depending on the value of show.

The function also invisibly returns the frequency of the A allele through time and the mean population fitness as an object of class "mutation.selection" that can be printed or re-plotted with associated print and plot methods, respectively. The plot method also permits user control over various attributes of the appearance of the plot, such as the color of the plotted lines (color), the line widths (lwd), the limits of the y-axis (ylim), and the type of line (e.g., "l" vs. "s", via the argument type).

Author(s)

Liam Revell [e-mail]

See Also

genetic.drift, selection

Examples

	mutation.selection(w=c(1,0),time=100,ylim=c(0,0.1))

Example output

learnPopGen documentation built on May 21, 2019, 1 a.m.