HW_sim.R

#################################################################################################
#### This is a simulation to demonstrate how real populations reach Hardy Weinburg equilibrium
#### under random mating.
#### Author: Corey Chivers, 2011
#################################################################################################

cross<-function(parents)
{
	offspring<-c('d','d') #initiate a child object
	offspring[1]<-sample(parents[1,],1)
	offspring[2]<-sample(parents[2,],1)

	return(offspring)
}

random_mating<-function()
{
	tmp_pop<-pop
	for(n in 1:N)
	{
		parents<-sample(1:N,2)
		tmp_pop[n,]<-cross(pop[parents,])
	}
	pop<-tmp_pop
}





genotypes<-c('A','a')

p<-0.5
q<-1-p
N=200
a_freq<-c(p,q)

pop<-array(sample(genotypes,2*N,p=a_freq,replace=T),dim=c(N,2))

I<-200
num_generations=1
g_freq<-array(dim=c(I,3))
p_vec<-array(dim=I)
for(i in 1:I)
{
	p<-runif(1,0,1)
	q<-1-p
	a_freq<-c(p,q)
	
	pop[,1]<-sample(genotypes,N,p=a_freq,replace=T)
	pop[,2]<-sample(genotypes,N,p=a_freq,replace=T)

	for(g in 1:num_generations)
		random_mating()


	f_aa<-0
	f_Aa<-0
	f_AA<-0

	for(n in 1:N)
	{
		if(identical(pop[n,],c('A','A')))
			f_AA=f_AA+1
		if(identical(pop[n,],c('A','a')) || identical(pop[n,],c('a','A') ))
			f_Aa=f_Aa+1
		if(identical(pop[n,],c('a','a')))
			f_aa=f_aa+1
	
	}
	f_aa<-f_aa/N
	f_Aa<-f_Aa/N
	f_AA<-f_AA/N
	
	g_freq[i,]<-c(f_AA,f_Aa,f_aa)
	p_vec[i]<-p	
}
pdf('HW.pdf')
## Plot the sims
plot(p_vec,g_freq[,1],col='green',xlab='p, or 1-q',ylab='')
points(p_vec,g_freq[,2],col='red')
points(p_vec,g_freq[,3],col='blue')


## Theoretical Curves
curve(x^2,col='green',add=T)
curve((1-x)^2,col='blue',add=T)
curve(2*x*(1-x),col='red',add=T)
dev.off()

I represents the number of populations to simulate, each with a random fraction p. N is the size of each population. So, if you increase I, you'll simulate more populations. If you increase N, you'll increase the number of individuals in each population. The bigger the population, the closer the genotype proportions will be to those predicted by HW.