Larval habitat#

The following parameters determine mosquito larval development related to habitat and climate. For more information, see Larval habitat. Parameters for the vector life cycle more broadly are described in Vector life cycle.

Note

Parameters are case-sensitive. For Boolean parameters, set to 1 for true or 0 for false. Minimum, maximum, or default values of “NA” indicate that those values are not applicable for that parameter.

EMOD does not use true defaults; that is, if the dependency relationships indicate that a parameter is required, you must supply a value for it. However, many of the tools used to work with EMOD will use the default values provided below.

JSON format does not permit comments, but you can add “dummy” parameters to add contextual information to your files. Any keys that are not EMOD parameter names will be ignored by the model.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Aquatic_Arrhenius_1

float

0

1.00E+15

8.42E+10

The Arrhenius equation, \(a_1^{-a_2/T}\), with T in degrees Kelvin, parameterizes the daily rate of fractional progression of mosquito aquatic development (egg-hatching through emergence). This duration is a decreasing function of temperature. The variable a1 is a temperature-independent scale factor on development rate.

 
{
    "Vector_Species_Params": [
        {
            "Aquatic_Arrhenius_1": 9752291.727,
            "Name": "arabiensis"
        }
    ]
}

Aquatic_Arrhenius_2

float

0

1.00E+15

8328

The Arrhenius equation, \(a_1^{-a_2/T}\), with T in degrees Kelvin, parameterizes the daily rate of fractional progression of mosquito aquatic development (egg-hatching through emergence). This duration is a decreasing function of temperature. The variable a2 governs how quickly the rate changes with temperature.

 
{
    "Vector_Species_Params": [
        {
            "Aquatic_Arrhenius_2": 8328,
            "Name": "arabiensis"
        }
    ]
}

Aquatic_Mortality_Rate

float

0

1

0.1

The base aquatic mortality per day for the species before adjusting for effects of overpopulation and drying out of aquatic habitat.

 
{
    "Vector_Species_Params": [
        {
            "Aquatic_Mortality_Rate": 0.1,
            "Name": "arabiensis"
        }
    ]
}

Drought_Egg_Hatch_Delay

float

0

1

0.33

Proportion of regular egg hatching that still occurs when habitat dries up. Enable_Drought_Egg_Hatch_Delay must be set to 1.

 
{
    "Enable_Drought_Egg_Hatch_Delay": 1,
    "Drought_Egg_Hatch_Delay": 0.33
}

Egg_Arrhenius1

float

0

1.00E+10

6.16E+07

The Arrhenius equation, \(a_1^{-a_2/T}\), with T in degrees Kelvin, parameterizes the daily rate of mosquito egg hatching. This duration is a decreasing function of temperature. The variable a1 is a temperature-independent scale factor on hatching rate. Enable_Temperature_Dependent_Egg_Hatching must be set to 1.

 
{
    "Enable_Temperature_Dependent_Egg_Hatching": 1,
    "Egg_Arrhenius1": 61599956,
    "Egg_Arrhenius2": 5754
}

Egg_Arrhenius2

float

0

1.00E+10

5754.03

The Arrhenius equation, \(a_1^{-a_2/T}\), with T in degrees Kelvin, parameterizes the daily rate of mosquito egg hatching. This duration is a decreasing function of temperature. The variable a2 is a temperature-dependent scale factor on hatching rate. Enable_Temperature_Dependent_Egg_Hatching must be set to 1.

 
{
    "Enable_Temperature_Dependent_Egg_Hatching": 1,
    "Egg_Arrhenius1": 61599956,
    "Egg_Arrhenius2": 5754
}

Egg_Hatch_Density_Dependence

enum

NA

NA

NO_DENSITY_DEPENDENCE

The effect of larval density on egg hatching rate. Possible values are:

DENSITY_DEPENDENCE

Egg hatching is reduced when the habitat is nearing its carrying capacity.

NO_DENSITY_DEPENDENCE

Egg hatching is not dependent upon larval density.

 
{
    "Egg_Hatch_Density_Dependence": "NO_DENSITY_DEPENDENCE"
}

Egg_Saturation_At_Oviposition

enum

NA

NA

NO_SATURATION

If laying all eggs from ovipositing females would overflow the larval habitat capacity on a given day, the means by which the viable eggs become saturated. Possible values are:

NO_SATURATION

Egg number does not saturate; all eggs are laid.

SATURATION_AT_OVIPOSITION

Eggs are saturated at oviposition; habitat is filled to capacity and excess eggs are discarded.

SIGMOIDAL_SATURATION

Eggs are saturated along a sigmoidal curve; proportionately fewer eggs are laid depending on how oversubscribed the habitat would be.

 
{
    "Egg_Saturation_At_Oviposition": "SATURATION_AT_OVIPOSITION"
}

Enable_Drought_Egg_Hatch_Delay

boolean

0

1

0

Controls whether or not eggs hatch at delayed rates, set by Drought_Egg_Hatch_Delay, when the habitat dries up completely.

 
{
    "Enable_Drought_Egg_Hatch_Delay": 1,
    "Drought_Egg_Hatch_Delay": 0.33
}

Enable_Egg_Mortality

boolean

0

1

0

Controls whether or not to include a daily mortality rate on the egg population, which is independent of climatic factors.

 
{
    "Enable_Egg_Mortality": 1
}

Enable_Temperature_Dependent_Egg_Hatching

boolean

0

1

0

Controls whether or not temperature has an effect on egg hatching, defined by Egg_Arrhenius_1 and Egg_Arrhenius_2.

 
{
    "Enable_Temperature_Dependent_Egg_Hatching": 1,
    "Egg_Arrhenius1": 61599956.864,
    "Egg_Arrhenius2": 5754.033
}

Habitats

array of json objects

NA

NA

NA

A measure of the habitat type and scale factors used to estimate larval population. This parameter is an array of JSON objects where each object specifies scale factor for a given habitat type or, for LINEAR_SPLINE, with a more detailed configuration for scaling. The numeric scaling value represents larval density with the number of larvae in a 1x1-degree area. The factor multiplicatively scales the resulting weather or population-dependent functional form. See Larval habitat for more information. Possible habitat values are:

CONSTANT

Larval carrying capacity is constant throughout the year and does not depend on weather. However, mosquito abundance will exhibit a seasonal signal due to the effects of temperature on aquatic developmental rates.

TEMPORARY_RAINFALL

This habitat type corresponds to temporary puddles which are replenished by rainfall and drained through evaporation and infiltration. Habitat availability is proportional to temperature and humidity, and decays over time as configured by the parameter Temporary_Habitat_Decay_Factor.

WATER_VEGATATION

This habitat type corresponds to semi-permanent habitats, such as developing vegetation on the edges of small water sources such as swamps or rice cultivation settings. Development of habitat lags behind rainfall, and typically peaks near the end of the rainy season. Habitat decays daily, as specified by the parameter Semipermanent_Habitat_Decay_Rate.

HUMAN_POPULATION

This habitat type scales with correlates of human development, such as available water in pots in urban areas. It is configured by multiplying the number of people in a node’s population times the capacity value set for this parameter, and is not climate-dependent.

BRACKISH_SWAMP

This habitat type deals with the dynamics of how rain fills brackish swamps, how this habitat availability decays, and includes a rainfall-driven mortality threshold. Habitat decay rate is specified by the parameter Semipermanent_Habitat_Decay_Rate.

LINEAR_SPLINE

The LINEAR_SPLINE configuration specifies the day of year, larval value, and larval capacity scaling number. The model linearly interpolates the values to estimate the habitat availability for each vector species without requiring climatological data.

ALL_HABITATS

Scale equally across all habitat types.

The values set here can be scaled per node using LarvalHabitatMultiplier in the demographics file (see NodeAttributes) or per intervention using Larval_Habitat_Multiplier in the campaign file (see ScaleLarvalHabitat).

The following example shows how to specify larval habitat using LINEAR_SPLINE.

{
    "Vector_Species_Params": [
        {
            "name": "funestus",
            "Habitats": [
                {
                    "Habitat_Type": "LINEAR_SPLINE",
                    "Capacity_Distribution_Number_Of_Years": 2,
                    "Capacity_Distribution_Over_Time": {
                        "Times": [
                            0,
                            30.417,
                            60.833,
                            91.25,
                            121.667,
                            152.083,
                            182.5,
                            212.917,
                            243.333,
                            273.75,
                            304.167,
                            334.583,
                            365,
                            395.417,
                            425.833,
                            456.25,
                            486.667,
                            517.083,
                            547.5,
                            577.917,
                            608.333,
                            638.75,
                            669.167,
                            699.583
                        ],
                        "Values": [
                            0,
                            0,
                            0,
                            0,
                            0.2,
                            1,
                            1,
                            1,
                            0.5,
                            0.2,
                            0,
                            0,
                            0,
                            0,
                            0,
                            0,
                            0.2,
                            1,
                            1,
                            1,
                            0.5,
                            0.2,
                            0,
                            0
                        ]
                    },
                    "Max_Larval_Capacity": 10000000000
                }
            ]
        }
    ]
}

The following example shows how to specify the larval habitat using climatological habitat types (you may use one or more for each vector species).

{
    "Vector_Species_Params": [
        {
            "Name": "arabiensis",
            "Habitats": [
                {
                    "Habitat_Type": "BRACKISH_SWAMP",
                    "Max_Larval_Capacity": 30000000
                },
                {
                    "Habitat_Type": "TEMPORARY_RAINFALL",
                    "Max_Larval_Capacity": 11250000000
                },
                {
                    "Habitat_Type": "WATER_VEGETATION",
                    "Max_Larval_Capacity": 6000000000
                }
            ]
        }
    ]
}

Larval_Density_Dependence

enum

NA

NA

UNIFORM_WHEN_OVERPOPULATION

The functional form of mortality and growth delay for mosquito larvae based on population density. Possible values are:

UNIFORM_WHEN_OVERPOPULATION

Mortality is uniformly applied to all larvae when the population exceeds the specified carrying capacity for that habitat.

GRADUAL_INSTAR_SPECIFIC

Mortality and delayed growth are instar-specific, where the younger larvae are more susceptible to predation and competition from older larvae.

LARVAL_AGE_DENSITY_DEPENDENT_MORTALITY_ONLY

Mortality is based only on larval age.

DENSITY_DELAYED_GROWTH_NOT_MORTALITY

There is no mortality, only delayed growth in larvae.

NO_DENSITY_DEPENDENCE

There is no additional larval density-dependent mortality factor.

 
{
    "Larval_Density_Dependence": "GRADUAL_INSTAR_SPECIFIC"
}

Larval_Rainfall_Mortality_Threshold

float

0.01

1000

100

The threshold value on daily rainfall in millimeters, above which larval mortality is applied when Vector_Larval_Rainfall_Mortality is set to either SIGMOID or SIGMOID_HABITAT_SHIFTING.

 
{
    "Larval_Rainfall_Mortality_Threshold": 30.0
}

Rainfall_In_mm_To_Fill_Swamp

float

1

10000

1000

Millimeters of rain to fill larval habitat to capacity. This is only used for vector species with Habitats set to BRACKISH_SWAMP.

 
{
    "Rainfall_In_mm_To_Fill_Swamp": 1000.0
}

Semipermanent_Habitat_Decay_Rate

float

0.0001

100

0.01

Daily rate of larval habitat loss for semi-permanent habitats with Habitats parameter value of WATER_VEGETATION or BRACKISH_SWAMP.

 
{
    "Semipermanent_Habitat_Decay_Rate": 0.01
}

Temporary_Habitat_Decay_Factor

float

0.001

100

0.05

The factor to convert raw evaporation rate (ignoring boundary layer effects) to the daily rate of larval habitat loss for temporary habitats (Habitats set to TEMPORARY_RAINFALL). Units are (larval carrying capacity per day) / (kg per square meter per second).

 
{
    "Temporary_Habitat_Decay_Factor": 0.05
}

Vector_Larval_Rainfall_Mortality

enum

NA

NA

NONE

The type of vector larval mortality function due to rainfall. Possible values are:

NONE

No larval mortality due to rainfall.

SIGMOID

The mortality rate grows linearly from 0 at the threshold to 1 at twice the threshold value.

SIGMOID_HABITAT_SHIFTING

The threshold value is reduced by a factor proportional to how full the larval habitat is.

 
{
    "Vector_Larval_Rainfall_Mortality": "SIGMOID"
}

Vector_Migration_Habitat_Modifier

float

0

3.40E+38

0

The preference of a vector to migrate toward a node with more habitat. Only used when Vector_Sampling_Type is set to TRACK_ALL_VECTORS. Enable_Vector_Migration must be set to 1.

 
{
    "Vector_Migration_Habitat_Modifier": 1.0
}

x_Temporary_Larval_Habitat

float

0

10000

1

Scale factor for the habitat size for all mosquito populations.

 
{
    "x_Temporary_Larval_Habitat": 1
}