Mortality and survival#

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

ART_CD4_at_Initiation_Saturating_Reduction_in_Mortality

float

0

3.40E+38

350

The duration from ART enrollment to on-ART HIV-caused death increases with CD4 at ART initiation up to a threshold determined by this parameter value.

 
{
    "ART_CD4_at_Initiation_Saturating_Reduction_in_Mortality": 350
}

Base_Mortality

float

0

1000

0.001

The base mortality of the infection before accounting for individual immune modification factors. Depending on the setting of Mortality_Time_Course, this is either the daily probability of the disease being fatal (DAILY_MORTALITY) or the probability of death at the end of the infection duration (MORTALITY_AFTER_INFECTIOUS). Enable_Disease_Mortality must be set to 1 (true).

 
{
    "Enable_Vital_Dynamics": 1,
    "Mortality_Time_Course": "DAILY_MORTALITY",
    "Base_Mortality": 0.01
}

Days_Between_Symptomatic_And_Death_Weibull_Heterogeneity

float

0.1

10

1

The time between the onset of AIDS symptoms and death is sampled from a Weibull distribution; this parameter governs the heterogeneity (inverse shape) of the Weibull.

 
{
    "Days_Between_Symptomatic_And_Death_Weibull_Heterogeneity": 0.5
}

Days_Between_Symptomatic_And_Death_Weibull_Scale

float

1

3650

183

The time between the onset of AIDS symptoms and death is sampled from a Weibull distribution; this parameter governs the scale of the Weibull.

 
{
    "Days_Between_Symptomatic_And_Death_Weibull_Scale": 618.3
}

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_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
}

HIV_Adult_Survival_Scale_Parameter_Intercept

float

0.001

1000

21.182

This parameter determines the intercept of the scale parameter, ?, for the Weibull distribution used to determine HIV survival time.

Survival time with untreated HIV infection depends on the age of the individual at the time of infection, and is drawn from a Weibull distribution with shape parameter (see HIV_Adult_Survival_Shape_Parameter) and scale parameter, ?. The scale parameter is allowed to vary linearly with age as follows:

\(\lambda\) = HIV_Adult_Survival_Scale_Parameter_Intercept + HIV_Adult_Survival_Scale_ Parameter_Slope * Age (in years).

 
{
    "HIV_Adult_Survival_Scale_Parameter_Intercept": 21.182,
    "HIV_Adult_Survival_Scale_Parameter_Slope": -0.2717,
    "HIV_Adult_Survival_Shape_Parameter": 2.0,
    "HIV_Age_Max_for_Adult_Age_Dependent_Survival": 50.0
}

HIV_Adult_Survival_Scale_Parameter_Slope

float

-1000

1000

-0.2717

This parameter determines the slope of the scale parameter, ?, for the Weibull distribution used to determine HIV survival time.

Survival time with untreated HIV infection depends on the age of the individual at the time of infection, and is drawn from a Weibull distribution with shape parameter (see HIV_Adult_Survival_Shape_Parameter) and scale parameter, ?. The scale parameter is allowed to vary linearly with age as follows:

\(\lambda\) = HIV_Adult_Survival_Scale_Parameter_Intercept + HIV_Adult_Survival_Scale_ Parameter_Slope * Age (in years).

Because survival time with HIV becomes shorter with increasing age, HIV_Adult_Survival_Scale_ Parameter_Slope should be set to a negative number.

 
{
    "HIV_Adult_Survival_Scale_Parameter_Intercept": 21.182,
    "HIV_Adult_Survival_Scale_Parameter_Slope": -0.2717,
    "HIV_Adult_Survival_Shape_Parameter": 2.0,
    "HIV_Age_Max_for_Adult_Age_Dependent_Survival": 50.0
}

HIV_Adult_Survival_Shape_Parameter

float

0.001

1000

2

This parameter determines the shape of the Weibull distribution used to determine age-dependent survival time for individuals infected with HIV.

 
{
    "HIV_Adult_Survival_Scale_Parameter_Intercept": 21.182,
    "HIV_Adult_Survival_Scale_Parameter_Slope": -0.2717,
    "HIV_Adult_Survival_Shape_Parameter": 2.0,
    "HIV_Age_Max_for_Adult_Age_Dependent_Survival": 50.0
}

HIV_Age_Max_for_Adult_Age_Dependent_Survival

float

0

75

70

Survival time with untreated HIV infection depends on the age of the individual at the time of infection, and is drawn from a Weibull distribution with shape parameter and scale parameter, ?. See HIV_Adult_Survival_Scale_Parameter_Intercept, HIV_Adult_Survival_Scale_ Parameter_Slope, and HIV_Adult_Survival_Shape_Parameter.

Although the scale parameter for survival time declines with age, it cannot become negative. To avoid negative survival times at older ages, this parameter, HIV_Age_Max_for_Adult_Age_Dependent_Survival, determines the age beyond which HIV survival is no longer affected by further aging.

 
{
    "HIV_Adult_Survival_Scale_Parameter_Intercept": 21.182,
    "HIV_Adult_Survival_Scale_Parameter_Slope": -0.2717,
    "HIV_Adult_Survival_Shape_Parameter": 2.0,
    "HIV_Age_Max_for_Adult_Age_Dependent_Survival": 50.0
}

HIV_Age_Max_for_Child_Survival_Function

float

0

75

15

The maximum age at which an individual’s survival will be fit to the child survival function. If the value of this parameter falls between zero and the age of sexual debut, model results are not sensitive to this parameter as there is no mechanism for children to become infected between infancy and sexual debut.

 
{
    "HIV_Adult_Survival_Scale_Parameter_Intercept": 21.182,
    "HIV_Adult_Survival_Scale_Parameter_Slope": -0.2717,
    "HIV_Adult_Survival_Shape_Parameter": 2.0,
    "HIV_Age_Max_for_Adult_Age_Dependent_Survival": 50.0,
    "HIV_Age_Max_for_Child_Survival_Function": 15.0
}

HIV_Child_Survival_Rapid_Progressor_Fraction

float

0

1

0.57

The proportion of HIV-infected children who are rapid HIV progressors.

 
{
    "HIV_Child_Survival_Rapid_Progressor_Fraction": 0.57,
    "HIV_Child_Survival_Rapid_Progressor_Rate": 1.52
}

HIV_Child_Survival_Rapid_Progressor_Rate

float

0

1000

1.52

The exponential decay rate, in years, describing the distribution of HIV survival for children who are rapid progressors.

 
{
    "HIV_Child_Survival_Rapid_Progressor_Fraction": 0.57,
    "HIV_Child_Survival_Rapid_Progressor_Rate": 1.52
}

HIV_Child_Survival_Slow_Progressor_Scale

float

0.001

1000

16

The Weibull scale parameter describing the distribution of HIV survival for children who are slower progressors.

 
{
    "HIV_Child_Survival_Slow_Progressor_Scale": 16.0,
    "HIV_Child_Survival_Slow_Progressor_Shape": 2.7
}

HIV_Child_Survival_Slow_Progressor_Shape

float

0.001

1000

2.7

The Weibull shape parameter describing the distribution of HIV survival for children who are slower progressors.

 
{
    "HIV_Child_Survival_Slow_Progressor_Scale": 16.0,
    "HIV_Child_Survival_Slow_Progressor_Shape": 2.7
}

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
}