Create dfes.py

stdpopsim/catalog/DroMel/dfes.py

@@ -0,0 +1,50 @@
+import stdpopsim
+
+_species = stdpopsim.get_species("DroMel")
+
+###########################################################
+#
+# DFEs
+#
+###########################################################
+
+
+def _HuberDFE():
+    id = "Gamma_H17"
+    description = "Deleterious Gamma DFE"
+    long_description = """
+    Return neutral and negative MutationType()s representing a drosophila DFE.
+    Huber et al. (2017), https://doi.org/10.1073/pnas.1619508114.
+    DFE parameters are based on the Full model described in Table S2, in which
+    singletons are excluded and a recent mutation rate estimate is used
+    (mu=3x10e-9, Keightley 2014).
+    """
+    citations = [
+        stdpopsim.Citation(
+            author="Huber et al.",
+            year=2017,
+            doi="https://doi.org/10.1073/pnas.1619508114",
+            reasons="to be defined",  # include the dfe_model reason
+        )
+    ]
+    neutral = stdpopsim.ext.MutationType()
+    gamma_shape = 0.33  # shape
+    gamma_mean = -3.96e-04  # expected value
+    h = 0.5  # dominance coefficient
+    negative = stdpopsim.ext.MutationType(
+        dominance_coeff=h,
+        distribution_type="g",  # gamma distribution
+        distribution_args=[gamma_mean, gamma_shape],
+    )
+
+    return stdpopsim.DFE(
+        id=id,
+        description=description,
+        long_description=long_description,
+        mutation_types=[neutral, negative],
+        proportions=[0.26, 0.74],  # LNS = 2.85 x LS
+        citations=citations,
+    )
+
+
+_species.add_dfe(_HuberDFE())