Added QC for duck/mallard (AnaPla) #1021
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@@ Coverage Diff @@
## main #1021 +/- ##
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+ Coverage 98.62% 98.63% +0.01%
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Files 85 86 +1
Lines 2845 2867 +22
Branches 341 341
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+ Hits 2806 2828 +22
Misses 31 31
Partials 8 8
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grahamgower
approved these changes
Oct 4, 2021
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Late to the party here, but: awesome, thanks @igronau! |
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The Demographic model implemented for Black duck and Mallard. See Original Model QC Issue #921
I reviewed the demographic parameters reported by Lavretsky et al. (2019) (Figure 6), and added the ancestral population size reported to @petrelharp in personal communication. I used these values to implement a demographic model and ran the unit tests. All seems good.
Regarding @petrelharp 's comment about the migration rate, I'm pretty sure that the rate we use in the model is consistent with what Lavretsky and colleagues infer using dadi. The raw dadi estimates (after scaled by N_anc) should be equivalent to the per-generation rate used by the coalescent simulator of msprime. To confirm this with 100%, one may wish to generate data using this model and run dadi on the data to see if the expected values are indeed inferred.