import emod_api.config.default_from_schema_no_validation as dfs
[docs]
def species_params(manifest, species: str = None):
"""
Returns configured species parameters based on species name
Args:
manifest: file that contains path to the schema file
species: species, configuration for which, we will be adding to the simulation.
Returns:
Configured species parameters
"""
# generic
vsp = dfs.schema_to_config_subnode(manifest.schema_file, ["idmTypes", "idmType:VectorSpeciesParameters"])
vsp.parameters.Anthropophily = 0.65
vsp.parameters.Name = "gambiae"
vsp.parameters.Acquire_Modifier = 0.8
vsp.parameters.Adult_Life_Expectancy = 20
vsp.parameters.Aquatic_Arrhenius_1 = 84200000000
vsp.parameters.Aquatic_Arrhenius_2 = 8328
vsp.parameters.Aquatic_Mortality_Rate = 0.1
vsp.parameters.Days_Between_Feeds = 3
vsp.parameters.Egg_Batch_Size = 100
vsp.parameters.Immature_Duration = 2
vsp.parameters.Indoor_Feeding_Fraction = 0.95
vsp.parameters.Infected_Arrhenius_1 = 117000000000
vsp.parameters.Infected_Arrhenius_2 = 8336
vsp.parameters.Infected_Egg_Batch_Factor = 0.8
vsp.parameters.Infectious_Human_Feed_Mortality_Factor = 1.5
vsp.parameters.Male_Life_Expectancy = 10
vsp.parameters.Transmission_Rate = 0.9
vsp.parameters.Vector_Sugar_Feeding_Frequency = "VECTOR_SUGAR_FEEDING_NONE"
# adding habitats
lht = dfs.schema_to_config_subnode(manifest.schema_file, ["idmTypes", "idmType:VectorHabitat"])
lht.parameters.Habitat_Type = "WATER_VEGETATION"
lht.parameters.Max_Larval_Capacity = 20000000
# end adding larval capacity
vsp.parameters.Habitats = [lht.parameters]
builtin_species_list = ["gambiae", "arabiensis", "funestus", "fpg_gambiae", "minimus", "dirus"] # please update if more species is added
if species == "gambiae": # same as generic species
return vsp.parameters
elif species == "arabiensis":
# default arabiensis
vsp.parameters.Name = "arabiensis"
vsp.parameters.Indoor_Feeding_Fraction = 0.5
# replacing habitats
lht1 = dfs.schema_to_config_subnode(manifest.schema_file, ["idmTypes", "idmType:VectorHabitat"])
lht1.parameters.Habitat_Type = "TEMPORARY_RAINFALL"
lht1.parameters.Max_Larval_Capacity = 800000000
lht2 = dfs.schema_to_config_subnode(manifest.schema_file, ["idmTypes", "idmType:VectorHabitat"])
lht2.parameters.Habitat_Type = "CONSTANT"
lht2.parameters.Max_Larval_Capacity = 80000000
# end adding larval capacity
vsp.parameters.Habitats = [lht1.parameters, lht2.parameters]
return vsp.parameters
elif species == "funestus":
vsp.parameters.Name = "funestus"
# replacing habitats
lht1 = dfs.schema_to_config_subnode(manifest.schema_file, ["idmTypes", "idmType:VectorHabitat"])
lht1.parameters.Habitat_Type = "TEMPORARY_RAINFALL"
lht1.parameters.Max_Larval_Capacity = 800000000
lht2 = dfs.schema_to_config_subnode(manifest.schema_file, ["idmTypes", "idmType:VectorHabitat"])
lht2.parameters.Habitat_Type = "CONSTANT"
lht2.parameters.Max_Larval_Capacity = 80000000
# end adding larval capacity
vsp.parameters.Habitats = [lht1.parameters, lht2.parameters]
return vsp.parameters
elif species == "fpg_gambiae": # from Jon Russel's sims, still called "gambiae"
vsp.parameters.Acquire_Modifier = 0.8
vsp.parameters.Indoor_Feeding_Fraction = 0.5
vsp.parameters.Vector_Sugar_Feeding_Frequency = "VECTOR_SUGAR_FEEDING_EVERY_DAY"
# replacing habitats
lht = dfs.schema_to_config_subnode(manifest.schema_file, ["idmTypes", "idmType:VectorHabitat"])
lht.parameters.Habitat_Type = "LINEAR_SPLINE"
lht.parameters.Max_Larval_Capacity = 316227766.01683795
lht.parameters.Capacity_Distribution_Number_Of_Years = 1
# adding larval capacity
cdot = dfs.schema_to_config_subnode(manifest.schema_file, ["idmTypes", "idmType:InterpolatedValueMap"])
cdot.parameters.Times = [0, 30.417, 60.833, 91.25, 121.667, 152.083, 182.5, 212.917, 243.333, 273.75, 304.167,
334.583]
cdot.parameters.Values = [3, 0.8, 1.25, 0.1, 2.7, 8, 4, 35, 6.8, 6.5, 2.6, 2.1]
lht.parameters.Capacity_Distribution_Over_Time = cdot.parameters
# end adding larval capacity
vsp.parameters.Habitats = [lht.parameters]
return vsp.parameters
elif species == "minimus": # from Monique Ambrose's sims
vsp.parameters.Anthropophily = 0.5
vsp.parameters.Name = "minimus"
vsp.parameters.Acquire_Modifier = 0.8
vsp.parameters.Adult_Life_Expectancy = 25
vsp.parameters.Egg_Batch_Size = 70
vsp.parameters.Indoor_Feeding_Fraction = 0.6
vsp.parameters.Transmission_Rate = 0.8
# adding habitats
lht1 = dfs.schema_to_config_subnode(manifest.schema_file, ["idmTypes", "idmType:VectorHabitat"])
lht1.parameters.Habitat_Type = "WATER_VEGETATION"
lht1.parameters.Max_Larval_Capacity = 2e7
lht2 = dfs.schema_to_config_subnode(manifest.schema_file, ["idmTypes", "idmType:VectorHabitat"])
lht2.parameters.Habitat_Type = "LINEAR_SPLINE"
lht2.parameters.Max_Larval_Capacity = 3e7
lht2.parameters.Capacity_Distribution_Number_Of_Years = 1
# adding larval capacity
cdot = dfs.schema_to_config_subnode(manifest.schema_file, ["idmTypes", "idmType:InterpolatedValueMap"])
cdot.parameters.Times = [0, 1, 245, 275, 364]
cdot.parameters.Values = [0.2, 0.2, 0.7, 3, 3]
lht2.parameters.Capacity_Distribution_Over_Time = cdot.parameters
# end adding larval capacity
vsp.parameters.Habitats = [lht1.parameters, lht2.parameters]
return vsp.parameters
elif species == "dirus": # dirus for Monique Ambrose's sims
vsp.parameters.Anthropophily = 0.5
vsp.parameters.Name = "dirus"
vsp.parameters.Adult_Life_Expectancy = 30
vsp.parameters.Egg_Batch_Size = 70
vsp.parameters.Indoor_Feeding_Fraction = 0.01
vsp.parameters.Transmission_Rate = 0.8
# adding habitats
lht1 = dfs.schema_to_config_subnode(manifest.schema_file, ["idmTypes", "idmType:VectorHabitat"])
lht1.parameters.Habitat_Type = "CONSTANT"
lht1.parameters.Max_Larval_Capacity = 1e7
lht2 = dfs.schema_to_config_subnode(manifest.schema_file, ["idmTypes", "idmType:VectorHabitat"])
lht2.parameters.Habitat_Type = "TEMPORARY_RAINFALL"
lht2.parameters.Max_Larval_Capacity = 7e7
# end adding larval capacity
vsp.parameters.Habitats = [lht1.parameters, lht2.parameters]
return vsp.parameters
else:
return builtin_species_list
