Clarification of the Ne vs initial_size vs population_size parameters

[David-Peede]

Hello All! I am working on converting msprime code written in 0.X to 1.X and I have seemed to confuse myself and would appreciate some clarification. In msprime versions 0.Xs in the simulate() function you can pass the reference effective population size by using the Ne parameter, however, this is overwritten if you use initial_size parameter in the PopulationConfiguration function. In msprime 1.Xs the population_size parameter in the sim_ancestry function is analogous to the old Ne parameter with the exception that it cannot be used in tandem with the initial_size parameter in the add_population function. Is this interpretation correct? I apologize upfront if this is a simple question, but I have been doing mental gymnastics all morning and thought it would be best to seek clarification straight from the source!

Thanks in advance for any and all help!

-Dave

[jeromekelleher]

Hi @David-Peede 👋

A lot of mental gymnastics has been done on this issue 😉

Yes, you have it right. One thing we realised while doing the refactoring for msprime 1.0 is there is no "reference population size", it's just the sizes of the populations at various times. I had just confused myself into thinking there was.