adding DFE for Arabidopsis

stdpopsim/catalog/AraTha/dfes.py

@@ -0,0 +1,52 @@
+import stdpopsim
+
+_species = stdpopsim.get_species("AraTha")
+
+###########################################################
+#
+# DFEs
+#
+###########################################################
+
+
+def _HuberDFE():
+    id = "Gamma_H18"
+    description = "Deleterious Gamma DFE"
+    long_description = """
+    Return neutral and negative MutationType()s representing an Arabidopsis DFE.
+    From Huber et al. (2018), https://doi.org/10.1038/s41467-018-05281-7.
+    Gamma parameters are based on the additive-only model for A. thaliana described in
+    Supplementary Table 4.
+    """
+    citations = [
+        stdpopsim.Citation(
+            author="Huber et al.",
+            year=2018,
+            doi="https://doi.org/10.1038/s41467-018-05281-7",
+            reasons="to be defined",  # include the dfe_model reason
+        )
+    ]
+    neutral = stdpopsim.MutationType()
+    gamma_shape = 0.27  # shape
+    gamma_mean = -0.0004  # 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,
+            1.0,
+        ],
+        citations=citations,
+    )
+
+
+_species.add_dfe(_HuberDFE())