proportion neutral

popsim-consortium · May 16, 2023 · 7d657ad · 7d657ad
1 parent 5f109bc
commit 7d657ad
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Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/stdpopsim/qc/AraTha.py b/stdpopsim/qc/AraTha.py
@@ -223,13 +223,16 @@ def Huber2018DFE():
         # (1+s for homozygote in SLiM versus 1+2s in dadi)
         distribution_args=[-2 * gamma_shape * gamma_scale, gamma_shape],  # mean, shape
     )
+    # proportion of single-nuc changes that are synonymous,
+    # from counting the codon table
+    prop_neutral = 330 / 1728
 
     return stdpopsim.DFE(
         id=id,
         description=id,
         long_description=id,
         mutation_types=[neutral, negative],
-        proportions=[0.3, 0.7],
+        proportions=[prop_neutral, 1 - prop_neutral],
     )
 
 

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, 0.19],  # mean, shape
     )
 
     return stdpopsim.DFE(