From 9f959e23b9ea53d38a9cbd1a94bd9c0de309512a Mon Sep 17 00:00:00 2001
From: vcaudill <viccaud@gmail.com>
Date: Fri, 9 Apr 2021 16:11:49 -0700
Subject: [PATCH] started Anole demographic model not complete yet

---
 docs/parameter_tables/AnoCar/Anole_5B19.csv   |  6 ++
 stdpopsim/catalog/AnoCar/__init__.py          |  1 +
 .../catalog/AnoCar/demographic_models.py      | 75 +++++++++++++++++++
 3 files changed, 82 insertions(+)
 create mode 100644 docs/parameter_tables/AnoCar/Anole_5B19.csv
 create mode 100644 stdpopsim/catalog/AnoCar/demographic_models.py

diff --git a/docs/parameter_tables/AnoCar/Anole_5B19.csv b/docs/parameter_tables/AnoCar/Anole_5B19.csv
new file mode 100644
index 000000000..070293ac1
--- /dev/null
+++ b/docs/parameter_tables/AnoCar/Anole_5B19.csv
@@ -0,0 +1,6 @@
+Population size,"6,755,470",Eastern Florda (EF) pop. size
+Migration rate, 2.36E-07,GA-EF migration rate
+Migration rate, 1.93E-07,EF-GA migration rate
+Epoch Time (gen.),"2023869",GA/EF split time
+Generation time (yrs.),1.5,Generation time
+Mutation rate (subst/1yr),2.1e-10,Mutation rate
diff --git a/stdpopsim/catalog/AnoCar/__init__.py b/stdpopsim/catalog/AnoCar/__init__.py
index 30cbab0fd..302ca5e48 100644
--- a/stdpopsim/catalog/AnoCar/__init__.py
+++ b/stdpopsim/catalog/AnoCar/__init__.py
@@ -2,3 +2,4 @@
 Catalog definitions for AnoCar (Ensembl ID='anolis_carolinensis')
 """
 from . import species  # noqa: F401
+from . import demographic_models  # noqa: F401
diff --git a/stdpopsim/catalog/AnoCar/demographic_models.py b/stdpopsim/catalog/AnoCar/demographic_models.py
new file mode 100644
index 000000000..2a126bd1a
--- /dev/null
+++ b/stdpopsim/catalog/AnoCar/demographic_models.py
@@ -0,0 +1,75 @@
+import msprime
+
+import stdpopsim
+
+_species = stdpopsim.get_species("AnoCar")
+
+
+def _GA_vs_EF_IMex():
+    id = "Anoli_5B19"
+    description = "Anoli GA-EK split"
+    long_description = """
+        This is a model fit to whole genomes of Anolis carolinesis
+        using five populations and fitting a model of
+        isolation with constant migration and no interruption
+        of gene flow.
+        See Figure 3 and table 2 Bourgeois et al 2019.
+    """
+    T = 1  # in generations
+    N_GulfAtlantic = 364329
+    N_EasternFlorida = 6755470
+    N_Anc = 2156641
+    # the migration rate
+    m_ge = 2.36e-07
+    m_eg = 1.93e-07
+    # Tsc, time during which stable populations stay connected
+    # Tscg, time since population size change (with gene flow)
+    # Tsc = 61217
+    # Tscg = 1962652
+    # after inital split initial populations have a population
+    # size of N_GulfAtlantic_a and N_EasternFlorida_a
+    # N_GulfAtlantic_a = 5971380
+    # N_EasternFlorida_a = 2137291
+
+    model = msprime.Demography()
+    model.add_population(
+        initial_size=N_GulfAtlantic,
+        name="Gulf_Atlantic",
+        description="Anoles from Gulf Atlantic",
+    )
+    model.add_population(
+        initial_size=N_EasternFlorida,
+        name="Eastern_Florida",
+        description="Anoles from Eastern Florida",
+    )
+    model.add_population(
+        initial_size=N_Anc,
+        name="Ancestral",
+        description="Ancestral population",
+    )
+    model.set_migration_rate(rate=m_ge, source="Gulf_Atlantic", dest="Eastern_Florida")
+    model.set_migration_rate(rate=m_eg, source="Eastern_Florida", dest="Gulf_Atlantic")
+
+    model.add_population_split(
+        time=T, derived=["Gulf_Atlantic", "Eastern_Florida"], ancestral="Ancestral"
+    )
+
+    return stdpopsim.DemographicModel(
+        id=id,
+        description=description,
+        long_description=long_description,
+        citations=[
+            stdpopsim.Citation(
+                author="Bourgeois et al.",
+                year=2019,
+                doi="https://doi.org/10.1093/gbe/evz110",
+                reasons={stdpopsim.CiteReason.DEM_MODEL},
+            )
+        ],
+        generation_time=1.5,
+        model=model,
+        # mutation_rate=2.1e-10,
+    )
+
+
+_species.add_demographic_model(_GA_vs_EF_IMex)