Yesterday I updated my little population genetic simulation & numerical analysis package PopGen so that users can overlay the change in allele frequency through time on the same plot.
To install PopGen I would recommend first installing devtools from CRAN after which it can easily be installed directly from GitHub as follows:
Load the package:
Now let's use the function
selection to plot changes in allele frequency through time under a
simple biallelic selection model.
The funciont takes as arguments:
## function (p0 = 0.01, w = c(1, 0.9, 0.8), time = 100, show = "p", ## pause = 0, ...) ## NULL
which includes the initial frequency of allele A (
p), the fitnesses of the homozygote
(AA), heterozygote (Aa), and homozygote (aa), in that order (
w), and some
First, let's try to run the model under its default conditions:
We can modify the argument values of the function. The default conditions show co-dominance for fitness. Let's run a co-dominance, recessive, and dominance for fitness models as follows:
## co-dominance for fitness selection(time=600) ## dominance for fitness selection(w=c(1,1,0.8),time=600,color="blue",add=TRUE) ## recessive for fitness selection(w=c(1,0.8,0.8),time=600,color="red",add=TRUE) legend(x="bottomright",legend=c("co-dominance","dominance","recessive"), col=c("black","blue","red"),lty=1)
selection can also show other things - such as the fitness surface, and δp as a
function of p. Here's what I mean, in this case using a severe overdominance model:
par(mfrow=c(3,1)) w<-c(0.6,1,0.4) selection(p0=0.001,w=w,time=50) selection(w=w,show="surface") selection(p0=0.001,w=w,show="cobweb",time=50) title(main="cobweb plot of p(t+1)~p(t)")
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