An R package for simulating a pedigree with genetic merits and phenotypes, starting from a base population (generation 0). The pedigree depth and design can be chosen by the values provided to the arguments of the simulation function.
Starting from a base population with equal number of males and females,
next generations are simulated for a user-defined number of generations.
The size of the base population is defined by the user.
No selection (natural or artificial) and non-random mating is applied to this population.
Natural (mortality) and artificial selection are applied to the next generations.
Different selection patterns can be applied to males and females, including
different proportion of selected individuals from selection candidates (after applying mortality) as parents of the next generation,
random or merit-based selection, and generation overlap.
Selected individuals are mated randomly using function simulatePed,
or mated assortatively/disassortatively using function assortative.
In assortative/disassortative mating, males and females are sorted for mating based on the criteria for which they have been selected for
(can be different between males and females).
Further choices, such as litter size, and avoiding fullsib matings and parent-progeny matings are provided.
Performance and genetic merit of individuals are simulated using the basic rules of quantitative genetics.
The performance (P) of an individual is influenced by genetic (A) and environmental (E) effects.
Thus, P = A + E, and Var(P) = Var(A) + Var(E).
The additive genetic merit (A) of an individual is the average of its parents' additive genetic merits
'(PA = (A + A)/2)
plus the Mendelian Sampling term due to the sampling of alleles passed from the parent to the offspring.
The Mendelian Sampling variance is half of Var(A) in the base population.
Because there is no provided information for environmental effects, the environment effect is
assigned to individuals from a normal distribution of random numbers (E ~ N(0, IVar(E))).