Malaria or vector configuration tips

The following tips are useful for the initial configuration of the vector or malaria model. Configuration tips for a specific microsolver in the model will be found on their respective component pages. For more information on using the software, or configuring input files, see How to use the software.

Simulation configuration help

There are several options for running a vector-based model. To run a basic model that functions as an enhanced SEIRS model, you will need to set the parameter Simulation_Type to the value “VECTOR_SIM”. However, to add complexity and include the full system of microsolvers for within- host parasite dynamics and other immune system interactions, set the parameter Simulation_Type to the value “MALARIA_SIM”.

To select between the cohort model versus individual mosquito model, set the Vector_Sampling_Type parameter. For the cohort model, the possible values are “VECTOR_COMPARTMENTS_NUMBER” or “VECTOR_COMPARTMENTS_PERCENT”. For the individual mosquito model, the values are “TRACK_ALL_VECTORS” or “SAMPLE_IND_VECTORS”.

Basic species configuration

The simulation configuration file has a field Vector_Species_Names which specifies the vector species that will be present in the simulation. For example, the following specifies that Anopheles arabiensis, An. funestus, and An. gambiae will be added to the simulation:

{
    "Vector_Species_Names": [
        "arabiensis",
        "funestus",
        "gambiae"
    ]
}

For each species listed, a “VectorPopulation” object will be added to the simulation at each node. Each species will be defined by parameters in the simulation configuration file for the vector ecology and behavior of the species. This allows for a mechanistic description of vector abundances and behavior through the effects of climate and weather on different preferred larval habitats.

The following example shows the syntax for configuring species parameters for Anopheles arabiensis. Note that you would also need to configure parameters for An. fuenstus and An. gambiae, if you are using a three species model as from the above example.

{
    "Vector_Species_Params": {
        "arabiensis": {
            "Acquire_Modifier": 0.2,
            "Adult_Life_Expectancy": 10,
            "Anthropophily": 0.95,
            "Aquatic_Arrhenius_1": 84200000000,
            "Aquatic_Arrhenius_2": 8328,
            "Aquatic_Mortality_Rate": 0.1,
            "Days_Between_Feeds": 3,
            "Egg_Batch_Size": 100,
            "Immature_Duration": 2,
            "Indoor_Feeding_Fraction": 1,
            "Infected_Arrhenius_1": 117000000000,
            "Infected_Arrhenius_2": 8336,
            "Infected_Egg_Batch_Factor": 0.8,
            "Infectious_Human_Feed_Mortality_Factor": 1.5,
            "Larval_Habitat_Types": {
                "TEMPORARY_RAINFALL": 11250000000
            },
            "Transmission_Rate": 0.5
        }
    }
}

While the above example shows the mosquito residing in one habitat, it is worth noting that mosquitoes can reside in multiple habitat types. This linear-combination of habitat types allows for greater control over local vector ecology (especially during dry seasons as habitat availability may be drastically different). The following example demonstrates the syntax to include several habitat types.

{
    "Vector_Species_Params": {
        "arabiensis": {
            "Acquire_Modifier": 0.2,
            "Adult_Life_Expectancy": 10,
            "Anthropophily": 0.95,
            "Aquatic_Arrhenius_1": 84200000000,
            "Aquatic_Arrhenius_2": 8328,
            "Aquatic_Mortality_Rate": 0.1,
            "Days_Between_Feeds": 3,
            "Egg_Batch_Size": 100,
            "Immature_Duration": 2,
            "Indoor_Feeding_Fraction": 1,
            "Infected_Arrhenius_1": 117000000000,
            "Infected_Arrhenius_2": 8336,
            "Infected_Egg_Batch_Factor": 0.8,
            "Infectious_Human_Feed_Mortality_Factor": 1.5,
            "Larval_Habitat_Types": {
                "TEMPORARY_RAINFALL": 11250000000,
                "WATER_VEGETATION": 6000000000
            },
            "Transmission_Rate": 0.5
        }
    }
}

Example scenarios with configuration and campaign files

There are example configuration and campaign files available to run the vector and malaria models. To download these files, go to the Vector and Malaria Scenarios. You can download the executable file to run these configuration and campaign files here: Quickstart.

Descriptions of the scenarios these files simulate can be found in the Vector and malaria tutorials.