Adding Huber et al 2017 DFE for HomSap

stdpopsim/catalog/HomSap/dfes.py

@@ -45,3 +45,47 @@ def _KimDFE():
 
 
 _species.add_dfe(_KimDFE())
+
+
+def _HuberDFE():
+    id = "Gamma_H17"
+    description = "Deleterious Gamma DFE"
+    long_description = """
+    Return neutral and negative MutationType()s representing a Homo sapiens 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
+    All Data (none of the listed filters) were used.
+    """  # [this was a different filtering scheme than the Huber et al DroMel DFE ]
+    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.MutationType()
+    gamma_shape = 0.19  # shape
+    gamma_mean = -0.014  # expected value
+    h = 0.5  # dominance coefficient
+    negative = stdpopsim.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=[
+            0.3,
+            0.7,
+        ],  # [0.3 and 0.7 were used in Xin's analysis,
+        #  but I couldn't find these values in the Huber paper]
+        citations=citations,
+    )
+
+
+_species.add_dfe(_HuberDFE())