Hi Hinda Haned!
I was wondering if anyone had experience simulating non-random mating human populations with R.
I want to simulate the evolution of disease susceptibility loci under certain evolutionary scenarios and under specific non-random mating schemes. For example, at each generation, p% of the matings occur between first cousins, offspring from such unions (must) have on average 1/16 of their genome autozygous. I've been exploring simulation softwares for a while , but they offer limited mating schemes, mainly because relationships between individuals can not be extracted.
I guess there is plenty of programs that can simulate various scenarious. However, each simulation has a likely different scope and therefore the implenetations differ. I guess you could write your own simulator quite easily with few lines of R code - various r* functions can be of great help. If I understand your question concerning the relationship take a look at a function kinship() or relationshipAdditive() in the GeneticsPed package. As has been pointed out by Thibaut, the package is not ready for use. However, you can see how kinship or additive genetic relationship coefficients can be computed. There is also a package kinship() that also has some similar functions. Gregor