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petrelharp / ftprime_ms

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typo: rho or r? #79

Closed petrelharp closed 6 years ago

petrelharp commented 6 years ago

On this line we say that delterious muts are introduced at rate $\rho/100$, where $\rho = 4Nr$ and $r$ is the per-gamete recombination rate; but (a) that seems wrong, I think it should be $r/100$, and (b) I don't think that's what the simulations are actually doing.

attn: @molpopgen

molpopgen commented 6 years ago

It is correct as written. The scaled rate at which mutation enter is pdelrho. The per-gamete rate at which they enter is pdelr. In our sims, theta=rho, which is why the code matches the description.

I'd have preferred writing this in terms of theta=4Nu, but we aren't simulating neutral mutations, and so we thought it would be confusing.

petrelharp commented 6 years ago

Hah, of course. =) Sorry about that.

petrelharp commented 6 years ago

Although that line could be clarified to say that it refers to the total introduction rate, rather than per-individual.