Fix factor of 2 in Gamma_K17 DFE

Confirmed by @klohmueller here: #1477
popsim-consortium · Jun 13, 2023 · 5f319a5 · 5f319a5
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Showing 2 changed files with 8 additions and 2 deletions.
diff --git a/stdpopsim/catalog/HomSap/dfes.py b/stdpopsim/catalog/HomSap/dfes.py
@@ -34,6 +34,9 @@ def _KimDFE():
     Na = 12378
     gamma_scale = 875
     gamma_shape = 0.186  # shape
+    # Extra factor of 2 in mean is to account for difference between tools
+    # in how fitness is defined
+    # (1+s for homozygote in SLiM versus 1+2s in dadi)
     gamma_mean = (-gamma_shape * gamma_scale * 2) / (2 * Na)  # expected value
     h = 0.5  # dominance coefficient
     negative = stdpopsim.MutationType(
@@ -74,7 +77,10 @@ def _HuberDFE():
     ]
     neutral = stdpopsim.MutationType()
     gamma_shape = 0.19  # shape
-    gamma_mean = -0.014  # expected value
+    # Extra factor of 2 in mean is to account for difference between tools
+    # in how fitness is defined
+    # (1+s for homozygote in SLiM versus 1+2s in dadi)
+    gamma_mean = -0.014 * 2  # expected value
     h = 0.5  # dominance coefficient
     negative = stdpopsim.MutationType(
         dominance_coeff=h,

diff --git a/stdpopsim/qc/HomSap.py b/stdpopsim/qc/HomSap.py
@@ -1703,7 +1703,7 @@ def Huber2017():
     negative = stdpopsim.MutationType(
         dominance_coeff=0.5,
         distribution_type="g",  # gamma distribution
-        distribution_args=[-0.014, 0.19],
+        distribution_args=[-0.014 * 2, 0.19],
     )
 
     return stdpopsim.DFE(