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Mallard demographic model #883

Merged
merged 1 commit into from
Apr 15, 2021
Merged

Mallard demographic model #883

merged 1 commit into from
Apr 15, 2021

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petrelharp
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@petrelharp petrelharp commented Apr 9, 2021 •
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Here's a demographic model for AnaPla from Lavretsky et al.!

@jeromekelleher
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Can you rebase please @petrelharp, #826 has been merged.

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codecov bot commented Apr 9, 2021 •
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Codecov Report

Merging #883 (6b3d7bb) into main (8e3f9df) will increase coverage by 0.00%.
The diff coverage is 100.00%.

Impacted file tree graph

@@           Coverage Diff           @@
##             main     #883   +/-   ##
=======================================
  Coverage   99.21%   99.21%           
=======================================
  Files          80       81    +1     
  Lines        2537     2558   +21     
  Branches      290      290           
=======================================
+ Hits         2517     2538   +21     
  Misses         10       10           
  Partials       10       10
Impacted Files Coverage Δ
stdpopsim/catalog/AnaPla/__init__.py 100.00% <100.00%> (ø)
stdpopsim/catalog/AnaPla/demographic_models.py 100.00% <100.00%> (ø)

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@petrelharp
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This isn't ready for review because we don't actually have the correct ancestral pop size, but it should be a good example for how to do a demographic model PR.

@petrelharp petrelharp force-pushed the mallard_demog branch 2 times, most recently from 7715866 to 1bac5bb Compare April 14, 2021 03:53
@petrelharp petrelharp marked this pull request as ready for review April 14, 2021 03:53
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I got the missing number from the authors - I think this is ready to go.

jeromekelleher
jeromekelleher approved these changes Apr 14, 2021
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LGTM!

apragsdale
apragsdale reviewed Apr 14, 2021
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Looks great! Just the commented out mutation rate, as the PR to handle that has been merged

stdpopsim/catalog/AnaPla/demographic_models.py Outdated
],
generation_time=4,
model=model,
# mutation_rate=4.83e-9,
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This could be uncommented now, I think - and will be checked in QC!

@petrelharp petrelharp merged commit 64854db into popsim-consortium:main Apr 15, 2021
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Argh, I forgot to update the parameter table.

This was referenced Apr 15, 2021
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@petrelharp petrelharp mentioned this pull request May 28, 2024
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@apragsdale apragsdale apragsdale left review comments

@jeromekelleher jeromekelleher jeromekelleher approved these changes

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@petrelharp @jeromekelleher @apragsdale