Using ploidy option versus number of individuals * ploidy

[isinaltinkaya]

Hi,

I have run bunch of simulations aiming to simulate diploid individuals using number_of_individuals * 2 as sample size. I just noticed that there is also a ploidy option. Are there any difference between using ploidy=2 and ploidy=default; sample_size=size*2 to simulate diploid samples? I would assume not since these would be haplotype counts, but I could not be sure if this would affect the calculation of any other parameters like recombination rate rho or theta.

Thanks!

[benjeffery]

There's more detail about ploidy here if you missed it: https://tskit.dev/msprime/docs/stable/ancestry.html#sec-ancestry-ploidy
In addition to storing the individuals correctly in the tree sequence this argument also affects the time scale on which coalescence occurs.
If you have further questions please ask, I'm converting this issue to a discussion.