add dog demographic model

docs/parameter_tables/CanFam/EarlyWolfAdmixture_7F14.csv

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+Population size,"1000",Boxer pop. size
+Population size,"2,639",Basenji pop. size
+Population size,"1,914",Dingo pop. size
+Population size,"26,092",Chinese wolf pop. size
+Population size,"11,427",Israeli wolf pop. size
+Population size,"5,426",Croatian wolf pop. size
+Population size,"19,446",Golden jackal pop. size
+Population size,"793",Ancestral Boxer and Basenji pop. size
+Population size,"1,999",Ancestral Boxer-Basenji and Dingo pop. size
+Population size,"1,393",Ancestral Israeli and Croatian wolf pop. size
+Population size,"12,627",Ancestral Israeli-Croatian and Chinese wolf pop. size
+Population size,"44,993",Ancestral dog and wolf pop. size
+Population size,"18,169",Ancestral dog, wolf, and jackal pop. size
+Migration rate,0.84,Israeli wolf -> Basenji migration rate
+Migration rate,0.07,Basenji -> Israeli wolf migration rate
+Migration rate,0.03,Chinese wolf -> Dingo migration rate
+Migration rate,0.04,Dingo -> Chinese wolf migration rate
+Migration rate,0,Golden jackal -> Israeli wolf migration rate
+Migration rate,0.05,Israeli wolf -> Golden jackal migration rate
+Migration rate,0.02,Golden jackal -> ancestral dog and wolf migration rate
+Migration rate,0.99,ancestral dog and wolf -> Golden jackal migration rate
+Time (gen.),"12,102",Boxer/Basenji split time
+Time (gen.),"12,795",Ancestral Boxer and Basenji/Dingo split time
+Time (gen.),"13,389",Israeli wolf/Croatian wolf split time
+Time (gen.),"13,455",Ancestral Israeli and Croatian wolf/Chinese wolf split time
+Time (gen.),"14,874",dog/wolf split time
+Time (gen.),"398,262",dog and wolf/Golden jackal split time
+Generation time (yrs.),3,Generation time
+Mutation rate,1e-8,Mutation rate

stdpopsim/catalog/CanFam/demographic_models.py

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+import msprime
+import stdpopsim
+
+_species = stdpopsim.get_species("CanFam")
+
+
+###########################################################
+#
+# Demographic models
+#
+###########################################################
+
+
+def _dog_wolf_admixture():
+    id = "EarlyWolfAdmixture_7F14"
+    description = "Dog domestication with wolf and jackal"
+    long_description = """
+    Demographic model of dog domestication with the Boxer reference
+    genome, two basal dog breeds, three wolves, and a golden jackal.
+    The topology was based on the neighbor-joining tree constructed
+    from genome-wide pairwise divergence. The parameters of the model
+    were inferred using the Generalized Phylogenetic Coalescent Sampler
+    (G-PhoCS) (Gronau et al. 2011) on neutral autosomal loci from
+    whole genome sequences. See Figure 5A in Freedman et al. 2014.
+    Note that Freedman et al. 2014 calibrated the parameters with a
+    mutation rate of 1e-8.
+    """
+    citations = [
+        stdpopsim.Citation(
+            author="Freedman et al.",
+            year="2014",
+            doi="https://doi.org/10.1371/journal.pgen.1004016",
+            reasons={stdpopsim.CiteReason.DEM_MODEL},
+        )
+    ]
+
+    generation_time = 3
+
+    #  parameter value definitions based on published values
+
+    # Estimated (calibrated) effective population sizes, from Table S12
+    # ******Not correct - putting in for flake8
+    N_BOX = 1000  # Have not found this value yet
+    # ******Not correct
+
+    N_BSJ = 2639
+    N_DNG = 1914
+    N_ISW = 26092
+    N_CRW = 11427
+    N_CHW = 5426
+    N_GLJ = 19446
+    N_ancDOG1 = 793
+    N_ancDOG = 1999
+    N_ancWLF1 = 1393
+    N_ancWLF = 12627
+    N_ancDW = 44993
+    N_root = 18169
+
+    # Estimated (calibrated) divergence times, from Table S12
+    T_ancDOG1 = 12102
+    T_ancDOG = 12795
+    T_ancWLF1 = 13389
+    T_ancWLF = 13455
+    T_ancDW = 14874
+    T_ancroot = 398262
+
+    # Migration rates, from Table S12
+    # migration is constant continuous geneflow from the start and end times of
+    # the two populations that define it. See section S9.2.3 in S9.
+    m_ISW_BSJ = 0.18
+    m_BSJ_ISW = 0.07
+    m_CHW_DNG = 0.03
+    m_DNG_CHW = 0.04
+    m_GLJ_ISW = 0
+    m_ISW_GLJ = 0.05
+    m_GLJ_ancDW = 0.02
+    m_ancDW_GLJ = 0.99
+
+    model = msprime.Demography()
+    model.add_population(
+        initial_size=N_BOX,
+        name="BOX",
+        description="Boxer",
+    )
+    model.add_population(
+        initial_size=N_BSJ,
+        name="BSJ",
+        description="Basenji",
+    )
+    model.add_population(
+        initial_size=N_DNG,
+        name="DNG",
+        description="Dingo",
+    )
+    model.add_population(
+        initial_size=N_CHW,
+        name="CHW",
+        description="Chinese wolf",
+    )
+    model.add_population(
+        initial_size=N_ISW,
+        name="ISW",
+        description="Israeli wolf",
+    )
+    model.add_population(
+        initial_size=N_CRW,
+        name="CRW",
+        description="Croatian wolf",
+    )
+    model.add_population(
+        initial_size=N_GLJ,
+        name="GLJ",
+        description="Golden jackal",
+    )
+    model.add_population(
+        initial_size=N_ancDOG1,
+        name="ancDOG1",
+        description="Ancestral Boxer and Basenji",
+    )
+    model.add_population(
+        initial_size=N_ancDOG,
+        name="ancDOG",
+        description="Ancestral Boxer-Basenji and Dingo",
+    )
+    model.add_population(
+        initial_size=N_ancWLF1,
+        name="ancWLF1",
+        description="Ancestral Israeli and Croatian wolf",
+    )
+    model.add_population(
+        initial_size=N_ancWLF,
+        name="ancWLF",
+        description="Ancestral Israeli-Croatian and Chinese wolf",
+    )
+    model.add_population(
+        initial_size=N_ancDW,
+        name="ancDW",
+        description="Ancestral dog and wolf",
+    )
+    model.add_population(
+        initial_size=N_root,
+        name="root",
+        description="Ancestral root of dog, wolf, and jackal",
+    )
+
+    model.set_migration_rate(rate=m_ISW_BSJ, source="BSJ", dest="ISW")
+    model.set_migration_rate(rate=m_BSJ_ISW, source="ISW", dest="BSJ")
+    model.set_migration_rate(rate=m_CHW_DNG, source="DNG", dest="CHW")
+    model.set_migration_rate(rate=m_DNG_CHW, source="CHW", dest="DNG")
+    model.set_migration_rate(rate=m_GLJ_ISW, source="ISW", dest="GLJ")
+    model.set_migration_rate(rate=m_ISW_BSJ, source="BSJ", dest="ISW")
+    model.set_migration_rate(rate=m_ISW_GLJ, source="GLJ", dest="ISW")
+    model.set_migration_rate(rate=m_GLJ_ancDW, source="ancDW", dest="GLJ")
+    model.set_migration_rate(rate=m_ancDW_GLJ, source="GLJ", dest="ancDW")
+
+    model.add_population_split(
+        time=T_ancDOG1, derived=["BOX", "BSJ"], ancestral="ancDOG1"
+    )
+    model.add_population_split(
+        time=T_ancDOG, derived=["ancDOG1", "DNG"], ancestral="ancDOG"
+    )
+    model.add_population_split(
+        time=T_ancWLF1, derived=["ISW", "CRW"], ancestral="ancWLF1"
+    )
+    model.add_population_split(
+        time=T_ancWLF, derived=["ancWLF1", "CHW"], ancestral="ancWLF"
+    )
+    model.add_population_split(
+        time=T_ancDW, derived=["ancDOG", "ancWLF"], ancestral="ancDW"
+    )
+    model.add_population_split(
+        time=T_ancroot, derived=["ancDW", "GLJ"], ancestral="root"
+    )
+
+    return stdpopsim.DemographicModel(
+        id=id,
+        description=description,
+        long_description=long_description,
+        citations=citations,
+        generation_time=generation_time,
+        model=model,
+    )
+
+
+_species.add_demographic_model(_dog_wolf_admixture())