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add mus mus domesticus demographic model #1485

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merged 13 commits into from
Oct 17, 2023
Merged

add mus mus domesticus demographic model #1485

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f90f788
add mus mus dom model
peter-d-fields May 20, 2023
a38619f
small mod to syntax
peter-d-fields May 21, 2023
20d0430
add mus musculus musculus demographic model
peter-d-fields May 28, 2023
6ab7bc7
fix odd vscode related file naming
peter-d-fields May 28, 2023
5ccf682
fix first name, add parameter table
peter-d-fields Jun 3, 2023
b496de4
add second parameter table
peter-d-fields Jun 3, 2023
6f9822d
add castaneous demographic model and parameter table
peter-d-fields Jun 3, 2023
14d28c9
added information about source of model data
peter-d-fields Jun 3, 2023
abc45cb
fix time intervals in history and parameter table files
peter-d-fields Jun 17, 2023
51386ba
Merge branch 'popsim-consortium:main' into mus_mus_dem_history
peterdfields Oct 9, 2023
0cf42b0
fix time, size intervals based on Ilan's suggestions
peter-d-fields Oct 9, 2023
408af33
Merge branch 'popsim-consortium:main' into mus_mus_dem_history
peterdfields Oct 16, 2023
6720d15
add table values to match published demographic models
peter-d-fields Oct 16, 2023
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116 changes: 116 additions & 0 deletions docs/parameter_tables/MusMus/DomesticusEurope_1F22.csv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,116 @@
Population size,133912,Ancestral population size
Population size,133912,Pop. size during 1st time interval
Population size,133912,Pop. size during 2nd time interval
Population size,98811,Pop. size during 3rd time interval
Population size,98811,Pop. size during 4th time interval
Population size,131050,Pop. size during 5th time interval
Population size,173594,Pop. size during 6th time interval
Population size,227037,Pop. size during 7th time interval
Population size,279833,Pop. size during 8th time interval
Population size,316861,Pop. size during 9th time interval
Population size,327217,Pop. size during 10th time interval
Population size,309961,Pop. size during 11th time interval
Population size,271935,Pop. size during 12th time interval
Population size,222951,Pop. size during 13th time interval
Population size,173264,Pop. size during 14th time interval
Population size,131392,Pop. size during 15th time interval
Population size,101471,Pop. size during 16th time interval
Population size,82953,Pop. size during 17th time interval
Population size,73097,Pop. size during 18th time interval
Population size,69317,Pop. size during 19th time interval
Population size,69939,Pop. size during 20th time interval
Population size,74185,Pop. size during 21th time interval
Population size,81892,Pop. size during 22th time interval
Population size,93046,Pop. size during 23th time interval
Population size,107067,Pop. size during 24th time interval
Population size,121751,Pop. size during 25th time interval
Population size,132063,Pop. size during 26th time interval
Population size,131016,Pop. size during 27th time interval
Population size,115426,Pop. size during 28th time interval
Population size,90926,Pop. size during 29th time interval
Population size,67337,Pop. size during 30th time interval
Population size,50557,Pop. size during 31th time interval
Population size,41195,Pop. size during 32th time interval
Population size,36886,Pop. size during 33th time interval
Population size,34163,Pop. size during 34th time interval
Population size,29931,Pop. size during 35th time interval
Population size,23419,Pop. size during 36th time interval
Population size,16490,Pop. size during 37th time interval
Population size,11240,Pop. size during 38th time interval
Population size,8332,Pop. size during 39th time interval
Population size,7480,Pop. size during 40th time interval
Population size,8463,Pop. size during 41th time interval
Population size,11758,Pop. size during 42th time interval
Population size,18939,Pop. size during 43th time interval
Population size,33028,Pop. size during 44th time interval
Population size,58488,Pop. size during 45th time interval
Population size,97250,Pop. size during 46th time interval
Population size,136620,Pop. size during 47th time interval
Population size,159142,Pop. size during 48th time interval
Population size,147212,Pop. size during 49th time interval
Population size,115399,Pop. size during 50th time interval
Population size,111242,Pop. size during 51th time interval
Population size,145603,Pop. size during 52th time interval
Population size,90428,Pop. size during 53th time interval
Population size,3844,Pop. size during 54th time interval
Population size,2040,Pop. size during 55th time interval
Population size,2040,Pop. size during 56th time interval
Time (yrs.),1915544,Begining of 1st time interval
Time (yrs.),1654653,Begining of 2nd time interval
Time (yrs.),1429281,Begining of 3rd time interval
Time (yrs.),1234595,Begining of 4th time interval
Time (yrs.),1066418,Begining of 5th time interval
Time (yrs.),921140,Begining of 6th time interval
Time (yrs.),795646,Begining of 7th time interval
Time (yrs.),687237,Begining of 8th time interval
Time (yrs.),593589,Begining of 9th time interval
Time (yrs.),512693,Begining of 10th time interval
Time (yrs.),442812,Begining of 11th time interval
Time (yrs.),382446,Begining of 12th time interval
Time (yrs.),330300,Begining of 13th time interval
Time (yrs.),285254,Begining of 14th time interval
Time (yrs.),246340,Begining of 15th time interval
Time (yrs.),212726,Begining of 16th time interval
Time (yrs.),183689,Begining of 17th time interval
Time (yrs.),158606,Begining of 18th time interval
Time (yrs.),136938,Begining of 19th time interval
Time (yrs.),118221,Begining of 20th time interval
Time (yrs.),102052,Begining of 21th time interval
Time (yrs.),88084,Begining of 22th time interval
Time (yrs.),76019,Begining of 23th time interval
Time (yrs.),65596,Begining of 24th time interval
Time (yrs.),56592,Begining of 25th time interval
Time (yrs.),48815,Begining of 26th time interval
Time (yrs.),42096,Begining of 27th time interval
Time (yrs.),36292,Begining of 28th time interval
Time (yrs.),31279,Begining of 29th time interval
Time (yrs.),26948,Begining of 30th time interval
Time (yrs.),23207,Begining of 31th time interval
Time (yrs.),19975,Begining of 32th time interval
Time (yrs.),17183,Begining of 33th time interval
Time (yrs.),14772,Begining of 34th time interval
Time (yrs.),12688,Begining of 35th time interval
Time (yrs.),10889,Begining of 36th time interval
Time (yrs.),9334,Begining of 37th time interval
Time (yrs.),7991,Begining of 38th time interval
Time (yrs.),6831,Begining of 39th time interval
Time (yrs.),5829,Begining of 40th time interval
Time (yrs.),4964,Begining of 41th time interval
Time (yrs.),4216,Begining of 42th time interval
Time (yrs.),3570,Begining of 43th time interval
Time (yrs.),3012,Begining of 44th time interval
Time (yrs.),2530,Begining of 45th time interval
Time (yrs.),2114,Begining of 46th time interval
Time (yrs.),1754,Begining of 47th time interval
Time (yrs.),1443,Begining of 48th time interval
Time (yrs.),1175,Begining of 49th time interval
Time (yrs.),943,Begining of 50th time interval
Time (yrs.),743,Begining of 51th time interval
Time (yrs.),570,Begining of 52th time interval
Time (yrs.),420,Begining of 53th time interval
Time (yrs.),291,Begining of 54th time interval
Time (yrs.),180,Begining of 55th time interval
Time (yrs.),83,Begining of 56th time interval
Time (yrs.),0,Begining of 57th time interval
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Parameter table looks okay. I think that the standard is to have one more entry in the list of Nes than in the list of times. This should correspond to the Ne before the first time interval (the ancestral Ne). Other Nes should map to time intervals. This also relates to my comment on the "shift" in the demographic model

Generation time (yrs.),1,Average generation interval
Mutation rate,5.7e-9,Per-base per-generation mutation rate
2 changes: 1 addition & 1 deletion stdpopsim/catalog/MusMus/demographic_models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -145,7 +145,7 @@ def _dom_1pop():
]

return stdpopsim.DemographicModel(
id="M_musculus_domesticus_Europe",
id="DomesticusEurope_1F22",
description="M. musculus domesticus piecewise constant size",
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We have certain conventions for the demographic model ids. You can find them described here. According to these conventions, I would suggest something like DomesticusEurope_1F22

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Done. I also added similar names for the other demographic models.

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Looks good.

long_description="""
This model comes from MSMC using four randomly sampled
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