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import msprime | ||
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import stdpopsim | ||
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_species = stdpopsim.get_species("PhoSin") | ||
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def Robinson2022_TwoEpoch(): | ||
id = "QC-Vaquita2Epoch_1R22" | ||
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populations = [ | ||
stdpopsim.Population(id="Vaquita", description=""), | ||
] | ||
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# Time of second epoch | ||
T_2 = 2162 | ||
# population sizes | ||
N_ANC = 4485 | ||
N_2 = 2807 | ||
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return stdpopsim.DemographicModel( | ||
id=id, | ||
description=id, | ||
long_description=id, | ||
generation_time=_species.generation_time, | ||
mutation_rate=5.83e-9, | ||
populations=populations, | ||
population_configurations=[ | ||
msprime.PopulationConfiguration( | ||
initial_size=N_2, metadata=populations[0].asdict() | ||
), | ||
], | ||
demographic_events=[ | ||
msprime.PopulationParametersChange( | ||
time=T_2, initial_size=N_ANC, population_id=0 | ||
), | ||
], | ||
population_id_map=[{"Vaquita": 0}] * 2, | ||
) | ||
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_species.get_demographic_model("Vaquita2Epoch_1R22").register_qc( | ||
Robinson2022_TwoEpoch() | ||
) | ||
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def Robinson2022(): | ||
""" | ||
Gamma DFE from Robinson et al. 2022 Science. | ||
""" | ||
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id = "Robinson2022_gamma_dfe" | ||
neutral = stdpopsim.MutationType() | ||
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negative = stdpopsim.MutationType( | ||
dominance_coeff_list=[0.0, 0.01, 0.1, 0.4], | ||
dominance_coeff_breaks=[-0.1, -0.01, -0.001], | ||
distribution_type="g", # gamma distribution | ||
distribution_args=[-0.0257, 0.131], | ||
) | ||
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return stdpopsim.DFE( | ||
id=id, | ||
description=id, | ||
long_description=id, | ||
mutation_types=[neutral, negative], | ||
proportions=[0.3, 0.7], | ||
) | ||
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_species.get_dfe("Gamma_R22").register_qc(Robinson2022()) |