adding DFE for Arabidopsis

stdpopsim/catalog/AraTha/__init__.py

@@ -4,4 +4,5 @@
 from . import species  # noqa: F401
 from . import genetic_maps  # noqa: F401
 from . import demographic_models  # noqa: F401
+from . import dfes  # noqa: F401
 from . import annotations  # noqa: F401

stdpopsim/catalog/AraTha/dfes.py

@@ -0,0 +1,58 @@
+import stdpopsim
+
+_species = stdpopsim.get_species("AraTha")
+
+###########################################################
+#
+# DFEs
+#
+###########################################################
+
+
+def _HuberDFE():
+    id = "Gamma_H18"
+    description = "Deleterious Gamma DFE"
+    long_description = """
+    Return negative (no neutral, in this case) MutationType()s
+    representing an Arabidopsis DFE. From Huber et al. (2018).
+    Gamma parameters are based on Supplementary Table 4,
+    the genome-wide, additive-only model for A. LYRATA- due to
+    challenges with simulating with selfing for A. thaliana.
+    The Supplementary Table 4 DFEs are not noted to contain
+    any neutral mutations (in contrast, Supplementary Table 3
+    notes neutral proportions for two other DFEs), and in the
+    main text including neutral mutations seems like a
+    supplementary analysis rather than the main strategy.
+    """
+    citations = [
+        stdpopsim.Citation(
+            author="Huber et al.",
+            year=2018,
+            doi="https://doi.org/10.1038/s41467-018-05281-7",
+            reasons=stdpopsim.CiteReason.DFE,
+        )
+    ]
+    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())

stdpopsim/catalog/HomSap/dfes.py

@@ -68,7 +68,7 @@ def _HuberDFE():
             author="Huber et al.",
             year=2017,
             doi="https://doi.org/10.1073/pnas.1619508114",
-            reasons="to be defined",  # include the dfe_model reason
+            reasons=stdpopsim.CiteReason.DFE,
         )
     ]
     neutral = stdpopsim.MutationType()