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added QC for vaquita DFE
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Christopher Kyriazis authored and petrelharp committed May 7, 2024
1 parent 5f56d36 commit 1213dc1
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72 changes: 72 additions & 0 deletions qc/PhoSin.py
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import msprime

import stdpopsim


_species = stdpopsim.get_species("PhoSin")


def Robinson2022_TwoEpoch():
id = "QC-Vaquita2Epoch_1R22"

populations = [
stdpopsim.Population(id="Vaquita", description=""),
]

# Time of second epoch
T_2 = 2162
# population sizes
N_ANC = 4485
N_2 = 2807

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,
)


_species.get_demographic_model("Vaquita2Epoch_1R22").register_qc(
Robinson2022_TwoEpoch()
)


def Robinson2022():
"""
Gamma DFE from Robinson et al. 2022 Science.
"""

id = "Robinson2022_gamma_dfe"
neutral = stdpopsim.MutationType()

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],
)

return stdpopsim.DFE(
id=id,
description=id,
long_description=id,
mutation_types=[neutral, negative],
proportions=[0.3, 0.7],
)


_species.get_dfe("Gamma_R22").register_qc(Robinson2022())

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