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This is a new page. I will gradually move some frequently-asked questions from the mailing list to here.
1. Applicability
1.1 Can simuPOP simulate XX individuals with XX loci?
Please see http://simupop.sourceforge.net/cookbook/pmwiki.php/Main/MiscScripts for a discussion of this topic.
2. Mating scheme
2.1 Can I generate populations with different inbreeding coefficient (or effective population size)?
simuPOP simulates random and well-defined non-random mating schemes. Because statistics such as effective population size and inbreeding coefficient can be calculated or estimated in different ways, they are considered as observations and cannot be used to direct mating scheme. On the other hand, because different mating schemes can lead to the same statistic, it is not always clear what is an appropriate mating scheme to simulate a population with desired property.
In the case of inbreeding, any of the following mating schemes can introduce inbreeding, and even be tweaked to demonstrate similar levels of inbreeding:
- a small population size that mimics a large family so that everyone is more or less related.
- a large population consists of small subpopulations within which inbreeding exists.
- a large population in which most people outbreed but some people inbreed.
- a large population where everyone has a probability to breed with his or her close relative.
If you choose a particular mating scheme, it would be possible to calculate theoretical inbreeding coefficients from simulation parameters, and vise versa. The easiest one can perhaps be defined as a probability p to mate with his/her cousin (sibling?), and 1-p to mate randomly. If you can derive p from inbreeding coefficient f in this case, a mating scheme can be easily (with some pitfalls that I can help you get around) defined.
