fix #262, switch recipes to sim_ancestry()

MesserLab · Feb 12, 2022 · 42b9aad · 42b9aad
1 parent 4220d59
commit 42b9aad
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Showing 5 changed files with 9 additions and 8 deletions.
diff --git a/...M/recipes/Recipe 17.8 - Starting a hermaphroditic WF model with a coalescent history I.py b/...M/recipes/Recipe 17.8 - Starting a hermaphroditic WF model with a coalescent history I.py
@@ -2,7 +2,7 @@
 
 import msprime, pyslim
 
-ts = msprime.simulate(sample_size=10000, Ne=5000, length=1e8,
-    mutation_rate=0.0, recombination_rate=1e-8)
+ts = msprime.sim_ancestry(samples=5000, population_size=5000,
+    sequence_length=1e8, recombination_rate=1e-8)
 slim_ts = pyslim.annotate_defaults(ts, model_type="WF", slim_generation=1)
 slim_ts.dump("recipe_17.8.trees")
diff --git a/QtSLiM/recipes/Recipe 17.9 - Starting a sexual nonWF model with a coalescent history I.py b/QtSLiM/recipes/Recipe 17.9 - Starting a sexual nonWF model with a coalescent history I.py
@@ -3,8 +3,8 @@
 import msprime, pyslim, random
 import numpy as np
 
-ts = msprime.simulate(sample_size=10000, Ne=5000, length=1e8,
-    mutation_rate=0.0, recombination_rate=1e-8)
+ts = msprime.sim_ancestry(samples=5000, population_size=5000,
+    sequence_length=1e8, recombination_rate=1e-8)
 
 tables = ts.dump_tables()
 pyslim.annotate_defaults_tables(tables, model_type="nonWF", slim_generation=1)

diff --git a/...i/Recipes/Recipe 17.8 - Starting a hermaphroditic WF model with a coalescent history I.py b/...i/Recipes/Recipe 17.8 - Starting a hermaphroditic WF model with a coalescent history I.py
@@ -2,7 +2,7 @@
 
 import msprime, pyslim
 
-ts = msprime.simulate(sample_size=10000, Ne=5000, length=1e8,
-    mutation_rate=0.0, recombination_rate=1e-8)
+ts = msprime.sim_ancestry(samples=5000, population_size=5000,
+    sequence_length=1e8, recombination_rate=1e-8)
 slim_ts = pyslim.annotate_defaults(ts, model_type="WF", slim_generation=1)
 slim_ts.dump("recipe_17.8.trees")
diff --git a/SLiMgui/Recipes/Recipe 17.9 - Starting a sexual nonWF model with a coalescent history I.py b/SLiMgui/Recipes/Recipe 17.9 - Starting a sexual nonWF model with a coalescent history I.py
@@ -3,8 +3,8 @@
 import msprime, pyslim, random
 import numpy as np
 
-ts = msprime.simulate(sample_size=10000, Ne=5000, length=1e8,
-    mutation_rate=0.0, recombination_rate=1e-8)
+ts = msprime.sim_ancestry(samples=5000, population_size=5000,
+    sequence_length=1e8, recombination_rate=1e-8)
 
 tables = ts.dump_tables()
 pyslim.annotate_defaults_tables(tables, model_type="nonWF", slim_generation=1)

diff --git a/VERSIONS b/VERSIONS
@@ -15,6 +15,7 @@ development head:
 	get rid of a spurious self-test error that happened occasionally due to changed to relatedness(); the test itself was wrong (#269)
 	fix the appearance of SLiMgui profile output when in dark mode (#270)
 	advance copyrights to 2022
+	fix recipes 17.8 and 17.9 to use sim_ancestry() instead of simulate()
 
 
 version 3.7 (Eidos version 2.7)