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String polish and few errors spotted in QC fixed
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gregorgorjanc committed Dec 24, 2024
1 parent 562596c commit cb347ab
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28 changes: 28 additions & 0 deletions docs/parameter_tables/CanFam/EarlyWolfAdmixture_6F14.csv
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Population size,"2,639",Basenji pop. size
Population size,"1,914",Dingo pop. size
Population size,"26,092",Israeli wolf pop. size
Population size,"11,427",Croatian wolf pop. size
Population size,"5,426",Chinese wolf pop. size
Population size,"19,446",Golden jackal pop. size
Population size,"793",Ancestral Basenji pop. size
Population size,"1,999",Ancestral Basenji-Dingo pop. size
Population size,"1,393",Ancestral Israeli-Croatian wolf pop. size
Population size,"12,627",Ancestral (Israeli-Croatian)-Chinese wolf pop. size
Population size,"44,993",Ancestral dog-wolf pop. size
Population size,"18,169",Ancestral (dog-wolf)-golden jackal (root) pop. size
Migration rate,0.18,Israeli wolf -> Basenji migration rate
Migration rate,0.07,Basenji -> Israeli wolf migration rate
Migration rate,0.03,Chinese wolf -> Dingo migration rate
Migration rate,0.04,Dingo -> Chinese wolf migration rate
Migration rate,0.00,Golden jackal -> Israeli wolf migration rate
Migration rate,0.05,Israeli wolf -> Golden jackal migration rate
Migration rate,0.02,Golden jackal -> Ancestral dog-wolf migration rate
Migration rate,0.99,Ancestral dog-wolf -> Golden jackal migration rate
Time (gen.),"12,102",Ancestral Basenji split time
Time (gen.),"12,795",Ancestral Basenji-Dingo split time
Time (gen.),"13,389",Ancestral Israeli-Croatian wolf split time
Time (gen.),"13,455",Ancestral (Israeli-Croatian)-Chinese wolf split time
Time (gen.),"14,874",Ancestral dog-wolf split time
Time (gen.),"398,262",Ancestral (dog-wolf)-golden jackal split time
Generation time (yrs.),3,Generation time
Mutation rate,1e-8,Mutation rate
27 changes: 0 additions & 27 deletions docs/parameter_tables/CanFam/EarlyWolfAdmixture_7F14.csv

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13 changes: 7 additions & 6 deletions stdpopsim/catalog/CanFam/demographic_models.py
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Expand Up @@ -32,7 +32,8 @@ def _dog_wolf_admixture():
end times of the two populations that define it (section S9.2.3 in S9).
While Boxer reference genome was used, no Boxer-specific parameters
were estimated in the model, hence Boxer was removed from this model
implementation.
implementation. Boxer coalesced with Basenji, so Ancestral Basenji
population here is ancestral population to Boxer and Basenji.
"""
citations = [

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stdpopsim.Citation(
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model.add_population(

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initial_size=N_ancDOG,
name="ancDOG",
description="Ancestral Basenji and Dingo",
description="Ancestral Basenji-Dingo",
)
model.add_population(

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initial_size=N_ancWLF1,
name="ancWLF1",
description="Ancestral Israeli and Croatian wolf",
description="Ancestral Israeli-Croatian wolf",
)
model.add_population(

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initial_size=N_ancWLF,
name="ancWLF",
description="Ancestral Israeli-Croatian and Chinese wolf",
description="Ancestral (Israeli-Croatian)-Chinese wolf",
)
model.add_population(

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initial_size=N_ancDW,
name="ancDW",
description="Ancestral dog and wolf",
description="Ancestral dog-wolf",
)
model.add_population(

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initial_size=N_root,
name="root",
description="Ancestral root of dog, wolf, and jackal",
description="Ancestral (dog-wolf)-golden jackal (root)",
)

model.set_migration_rate(rate=m_ISW_BSJ, source="BSJ", dest="ISW")
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