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move PhoSin QC where it should go #1561

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May 8, 2024
Merged

move PhoSin QC where it should go #1561

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11a2719
put PhoSin qc where it should go
petrelharp May 7, 2024
c1d44ca
fixup of coefficient
petrelharp May 8, 2024
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72 changes: 0 additions & 72 deletions qc/PhoSin.py
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2 changes: 1 addition & 1 deletion stdpopsim/catalog/PhoSin/dfes.py
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Expand Up @@ -48,7 +48,7 @@ def _RobinsonDFE():
# is defined in fitDadi and in SLiM ]
# Since the inferred value of Na is not reported in the supplement, we use
# here the value of the mean as reported in the supp info
gamma_mean = -0.00971 # mean of gamma (see bottom of page 12 in supp)
gamma_mean = -0.0257 # mean of gamma (see bottom of page 12 in supp)
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Yes, this is correct. Thanks, @petrelharp for fixing this.


# dominance coefficient assumed in fitDadi inference was fully additive (h=0.5).
# However, in the simulations described by Robinson et al. (2022), they used
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27 changes: 27 additions & 0 deletions stdpopsim/qc/PhoSin.py
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Expand Up @@ -43,3 +43,30 @@ def Robinson2022_TwoEpoch():
_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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