updates to new dfe

.github/workflows/tests.yml

@@ -49,7 +49,7 @@ jobs:
         uses: actions/cache@v2
         env:
           # Increase this to reset the cache if the key hasn't changed.
-          CACHE_NUM: 4
+          CACHE_NUM: 5
         with:
           path: |
             ${{ steps.find-conda.outputs.CONDA }}/envs/${{ env.CONDA_ENV_NAME }}

stdpopsim/catalog/HomSap/dfes.py

@@ -153,13 +153,11 @@ def _KyriazisDFE():
     id = "Mixed_K23"
     description = "Deleterious Gamma DFE with additional lethals"
     long_description = """
-    The DFE estimated from human data recommended in 
-    Kyriazis et al. (2023), https://doi.org/10.1086/726736
-    for general use
+    The DFE estimated from human data recommended in Kyriazis et al.
+    (2023), https://doi.org/10.1086/726736, for general use
     This model is similar to the Kim et al. (2017) DFE based on human
-    genetic data, modified to include the dominance distribution from Henn et al. (2016).
-    One difference is an increased deleterious mutation rate per diploid of
-    0.63, informed by the analysis of 30Mb of human coding sequence.
+    genetic data, modified to include the dominance distribution from
+    Henn et al. (2016).
     The model is also augmented with an additional proportion of 0.3% of
     recessive lethals, based on the analysis of Wade et al. (2023).
     """
@@ -184,11 +182,13 @@ def _KyriazisDFE():
     )
     lethal = stdpopsim.MutationType(
         distribution_type="f",  # fixed value
-        distribution_args=[-1],  # fitness in SLiM for homozygotes is multiiplied by 1+ s
+        distribution_args=[
+            -1
+        ],  # fitness in SLiM for homozygotes is multiiplied by 1+ s
         dominance_coeff=0,
     )
-    proportion_deleterious = 0.7  # ratio 2.31:1
-    lethal_prop = proportion_deleterious * 0.003  # 0.03% lethals
+    proportion_deleterious = 2.31 / (1 + 2.31)
+    lethal_prop = proportion_deleterious * 0.003  # 0.3% lethals
     gamma_prop = proportion_deleterious - lethal_prop
     neutral_prop = 1 - proportion_deleterious
     return stdpopsim.DFE(