emodpy_malaria.vector_config module¶
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emodpy_malaria.vector_config.
set_team_defaults
(config, mani)¶ Set configuration defaults using team-wide values, including drugs and vector species.
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emodpy_malaria.vector_config.
set_team_vs_params
(config, mani)¶
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emodpy_malaria.vector_config.
get_species_params
(cb, species)¶
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emodpy_malaria.vector_config.
set_species
(config, species_to_select)¶ Use this function to specify which mosquito species to use in the simulation.
- Parameters
config – schema-backed config smart dict
species_to_list – list of 1 or more strings.
- Returns
None
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emodpy_malaria.vector_config.
set_resistances
(config)¶ Use this function after you’re done calling add_resistance. config is the input and the output
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emodpy_malaria.vector_config.
add_alleles
(allele_names_in, allele_inits_in)¶ This is public API function for user to add alleles. User specifies the list of alleles and corresponding initial distribution.
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emodpy_malaria.vector_config.
add_mutation
(from_allele, to_allele, rate)¶ Public API function for user to add mutations as part of vector genetics configuration. A mutation is specified with a source allele, a destination allele, and a rate
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emodpy_malaria.vector_config.
add_trait
(manifest, allele_combo, trait_name, trait_value)¶ Use this function to add traits as part of vector genetics configuration. Should produce something like:
{ "Allele_Combinations": [["X", "X"],["a0", "a1"]], "Trait_Modifiers": {"INFECTED_BY_HUMAN": 0} },
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emodpy_malaria.vector_config.
add_resistance
(manifest, insecticide_name, species, combo, blocking=1.0, killing=1.0, repelling=1.0, larval_killing=1.0)¶ Use this function to add insecticide resistances. An insecticide can have a list of resistances. Add each resistance separately with the same name:
Insecticides = [ { "Name": "pyrethroid", "Resistances": [ { "Allele_Combinations": [ [ "a1", "a1" ] ], "Blocking_Modifier": 1.0, "Killing_Modifier": pyrethroid_killing, "Species": "gambiae" } ] },
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emodpy_malaria.vector_config.
set_genetics
(vsp, manifest)¶ Don’t need to pass these anymore since they are module variables. But actually need to try with more than one set and see where I end up in terms of design.