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Typo in documentation? #1562

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jiseonmin opened this issue May 22, 2024 · 3 comments
Closed

Typo in documentation? #1562

jiseonmin opened this issue May 22, 2024 · 3 comments

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@jiseonmin
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Hi, I was using MallardBlackDuck_2L19 model, and it looks like the migration matrix is symmetric in stdpopsim (version 0.2.0), but the documentation says the migration is 10^-6 times 0.84 (Black-Mallard) and 1.10 (Malard-Black). (https://popsim-consortium.github.io/stdpopsim-docs/stable/catalog.html#sec_catalog_AnaPla_models)

@andrewkern
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huh this isn't good. the model param csv file doesn't match the code...

@jiseonmin
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I see the source paper (https://onlinelibrary.wiley.com/doi/10.1111/mec.15343) and the code (https://github.com/popsim-consortium/stdpopsim/blob/main/stdpopsim/catalog/AnaPla/demographic_models.py) both have a symmetric migration rate (2.82 migrants per generation).

Checking the commit history, I see only one commit by @petrelharp 3 years ago (6b3d7bb)... Do you know what happened here?

@petrelharp
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Well, here's what happened: #883, #920, #921, #1021. But, my guess the reason for this discrepancy is that (a) first I had thought migration rates were forwards-time, and so needed to be scaled by modern pop sizes (and thus asymmetric); but then (b) figured out they weren't, and forgot to update the parameter table. So, I think we just need to fix the parameter table. Thanks!

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