Mortality and survival

The following parameter determine mortality and survival characteristics of the disease being modeled and the population in general (non-disease mortality).

See Severe disease and mortality for more information about how fever, anemia, and parasite counts lead to severe malaria and mortality.

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

Anemia_Mortality_Inverse_Width

float

0.1

1000000

10

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the inverse width relative to threshold value of severe disease turn-on around threshold for anemia.

 
{
    "Anemia_Mortality_Inverse_Width": 150
}

Anemia_Mortality_Threshold

double

NA

NA

3

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the inverse width relative to threshold value of mortality turn-on around threshold for hemoglobin count in grams per deciliter (g/dL) at which 50% of individuals die per day.

 
{
    "Anemia_Mortality_Threshold": 1.5
}

Anemia_Severe_Inverse_Width

float

0.1

1000000

10

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the inverse width relative to threshold value of severe disease turn-on around threshold for anemia.

 
{
    "Anemia_Severe_Inverse_Width": 20
}

Anemia_Severe_Threshold

float

0

100

5

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the severe disease threshold level for anemia. Threshold units are in grams per deciliter (g/dL).

 
{
    "Anemia_Severe_Threshold": 3.0
}

Death_Rate_Dependence

enum

NA

NA

NOT_INITIALIZED

Determines how likely individuals are to die from natural, non-disease causes. Enable_Natural_Mortality must be set to 1. Possible values are:

NOT_INITIALIZED

The daily mortality rate is 0, and no one dies from non-disease related causes.

NONDISEASE_MORTALITY_BY_AGE_AND_GENDER

The individual’s age and gender are taken into account to determine the daily mortality rate.

NONDISEASE_MORTALITY_BY_YEAR_AND_AGE_FOR_EACH_GENDER

Gender, age, and year, are all taken into account to determine the daily mortality rate.

Properties, rates, and bin sizes can be set for non-disease mortality for each gender in the demographics file (see Complex distributions parameters).

 
{
    "Death_Rate_Dependence": "NONDISEASE_MORTALITY_BY_AGE_AND_GENDER"
}

Enable_Disease_Mortality

boolean

0

1

1

Controls whether or not individuals are removed from the simulation due to disease deaths.

 
{
    "Enable_Disease_Mortality": 1
}

Enable_Natural_Mortality

boolean

0

1

0

Controls whether or not individuals are removed from the simulation due to natural (non-disease) deaths. Enable_Vital_Dynamics must be set to 1 (true). Use Death_Rate_Dependence to set the natural death rate.

 
{
    "Enable_Natural_Mortality": 1,
    "Enable_Vital_Dynamics": 1
}

Fever_Mortality_Inverse_Width

float

0.1

1000000

10

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the inverse width relative to threshold value of mortality turn-on around threshold for fever.

 
{
    "Fever_Mortality_Inverse_Width": 1000
}

Fever_Mortality_Threshold

double

NA

NA

3

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the fever mortality threshold, in units of degrees Celsius above normal body temperature (defined as 37 C).

 
{
    "Fever_Mortality_Threshold": 10
}

Mortality_Blocking_Immunity_Decay_Rate

float

0

1

0.001

The rate at which mortality-blocking immunity decays after the mortality-blocking immunity offset period. Enable_Immune_Decay must be set to 1.

 
{
    "Mortality_Blocking_Immunity_Decay_Rate": 0.1
}

Mortality_Time_Course

enum

NA

NA

DAILY_MORTALITY

The method used to calculate disease deaths. Enable_Disease_Mortality must be set to 1.

Possible values are:

DAILY_MORTALITY

Calculated at every time step.

MORTALITY_AFTER_INFECTIOUS

Calculated once at the end of the disease duration.

 
{
    "Mortality_Time_Course": "MORTALITY_AFTER_INFECTIOUS"
}

x_Other_Mortality

float

0

3.40E+38

1

Scale factor for mortality from causes other than the disease being simulated. Base mortality is provided by the demographics file (see Complex distributions parameters). Enable_Natural_Mortality must be set to 1.

 
{
    "x_Other_Mortality": 1
}