From f3ac5669397cdd81544f3c4c31da28c9ad005cf6 Mon Sep 17 00:00:00 2001
From: peter <petrel.harp@gmail.com>
Date: Sat, 18 Jan 2025 20:37:58 -0800
Subject: [PATCH] positive selection for HomSap

---
 stdpopsim/catalog/HomSap/dfes.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/stdpopsim/catalog/HomSap/dfes.py b/stdpopsim/catalog/HomSap/dfes.py
index 66e918230..448e4195f 100644
--- a/stdpopsim/catalog/HomSap/dfes.py
+++ b/stdpopsim/catalog/HomSap/dfes.py
@@ -234,6 +234,10 @@ def _ZhenDFE():
         distribution_type="g",  # gamma distribution
         distribution_args=[gamma_mean, gamma_shape],
     )
+    # p. 2 in supplement says that the total sequence length of synonymous sites LS
+    # related to the total sequence length LNS by LNS = 2.31 * LS
+    prop_synonymous = 1 / (1 + 2.31)
+
     sel_coeff = 10 ** (-3.949)
     prop_beneficial = 1.55e-2
     positive = stdpopsim.MutationType(
@@ -248,10 +252,10 @@ def _ZhenDFE():
         long_description=long_description,
         mutation_types=[neutral, negative, positive],
         proportions=[
-            0.3,
-            0.7 * (1 - prop_beneficial),
-            0.7 * prop_beneficial,
-        ],  # [0.3 and 0.7 are from Gamma_H17
+            prop_synonymous,
+            (1 - prop_synonymous) * (1 - prop_beneficial),
+            (1 - prop_synonymous) * prop_beneficial,
+        ],
         citations=citations,
     )