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
}

ART_Reactivation_Factor

float

0

1

1

Factor for ART reducing reactivation in HIV+.

 
{
    "ART_Reactivation_Factor": 0.95
}

CoInfection_Mortality_Rate_Off_ART

float

0

3.40282e+38

0

The daily rate of death in excess to TB when coinfected with HIV off ART.

 
{
    "CoInfection_Mortality_Rate_On_ART": 0.01
}

CoInfection_Mortality_Rate_On_ART

float

0

3.40282e+38

0

The daily rate of death in excess to TB when coinfected with HIV on ART.

 
{
    "CoInfection_Mortality_Rate_On_ART": 0.003
}

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_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
}

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"
}

TB_Active_Mortality_Rate

float

0

1

0.0009589

The mean rate at which active smear-positive individuals die from TB disease. This is an exponential rate.

In the absence of treatment, this rate is added to TB_Active_Cure_Rate and TB_Inactivation_Rate to determine the total rate of the active smear-positive state, then the ratio of TB_Active_Mortality_Rate to total rate determines the probability that an active smear-positive individual will die from TB disease after a mean duration of 1 / total rate.

 
{
    "TB_Active_Mortality_Rate": 5e-08
}

TB_Drug_Mortality_Rate

float

0

1

0

The daily rate at which treatment with an anti-TB drug causes death in an individual with drug-sensitive TB.

 
{
    "TB_Drug_Params": {
        "BurninDrug": {
            "TB_Drug_Cure_Rate": 0.0111,
            "TB_Drug_Inactivation_Rate": 0,
            "TB_Drug_Mortality_Rate": 0.00162,
            "TB_Drug_Relapse_Rate": 0.00223,
            "TB_Drug_Resistance_Rate": 0
        }
    }
}

TB_Drug_Mortality_Rate_HIV

float

0

1

0

The daily probability of death for HIV+ individual with drug sensitive active infection under drug treatment.

 
{
    "TBHIV_Drug_Params": {
        "ACFDOTS": {
            "TB_Drug_Cure_Rate": 0.25,
            "TB_Drug_Inactivation_Rate": 1e-09,
            "TB_Drug_Inactivation_Rate_HIV": 1e-09,
            "TB_Drug_Inactivation_Rate_MDR": 1e-09,
            "TB_Drug_Mortality_Rate": 1e-09,
            "TB_Drug_Mortality_Rate_HIV": 1e-09,
            "TB_Drug_Mortality_Rate_MDR": 1e-09,
            "TB_Drug_Primary_Decay_Time_Constant": 179,
            "TB_Drug_Relapse_Rate": 1e-09,
            "TB_Drug_Relapse_Rate_HIV": 1e-09,
            "TB_Drug_Relapse_Rate_MDR": 1e-09,
            "TB_Drug_Resistance_Rate": 1e-09,
            "TB_Drug_Resistance_Rate_HIV": 1e-09,
            "TB_Reduced_Acquire": 1,
            "TB_Reduced_Transmit": 1,
            "TB_Drug_Cure_Rate_HIV": 0,
            "TB_Drug_Cure_Rate_MDR": 0
        },
        "DOTSHQ": {
            "TB_Drug_Cure_Rate": 0.008,
            "TB_Drug_Inactivation_Rate": 1e-09,
            "TB_Drug_Inactivation_Rate_HIV": 1e-09,
            "TB_Drug_Inactivation_Rate_MDR": 1e-09,
            "TB_Drug_Mortality_Rate": 0.00038,
            "TB_Drug_Mortality_Rate_HIV": 0.00038,
            "TB_Drug_Mortality_Rate_MDR": 0.0008,
            "TB_Drug_Primary_Decay_Time_Constant": 179,
            "TB_Drug_Relapse_Rate": 0.00089,
            "TB_Drug_Relapse_Rate_HIV": 0.00089,
            "TB_Drug_Relapse_Rate_MDR": 0.001,
            "TB_Drug_Resistance_Rate": 0.0001,
            "TB_Drug_Resistance_Rate_HIV": 0.0001,
            "TB_Reduced_Acquire": 1,
            "TB_Reduced_Transmit": 0.5,
            "TB_Drug_Cure_Rate_HIV": 0.0004,
            "TB_Drug_Cure_Rate_MDR": 0.0004
        }
    }
}

TB_Drug_Mortality_Rate_MDR

float

0

1

0

The daily probability of death for individual with MDR active infection under drug treatment.

 
{
    "TB_Drug_Mortality_Rate_MDR": 0
}

TB_Extrapulmonary_Mortality_Multiplier

float

0

1

0.4

The scale factor for TB_Active_Mortality_Rate to give the mortality rate of active extrapulmonary individuals. In the absence of treatment, the product is added to TB_Active_Cure_Rate and TB_Inactivation_Rate to determine the total rate of the active extrapulmonary state, then the ratio of the aforementioned product to total rate determines the probability that an active extrapulmonary individual will die from TB disease after mean duration of 1 / total rate. Extrapulmonary individuals are considered non-infectious.

 
{
    "TB_Extrapulmonary_Mortality_Multiplier": 1
}

TB_Smear_Negative_Mortality_Multiplier

float

0

1

0.4

The scale factor to increase the mortality rate set by TB_Active_Mortality_Rate for individuals with smear-negative TB. In the absence of treatment, the product is added to TB_Active_Cure_Rate and TB_Inactivation_Rate to determine the total rate of the active smear-negative state, then the ratio of the aforementioned product to total rate determines the probability that an active smear-negative individual will die from TB disease after mean duration of 1 / total rate.

 
{
    "TB_Smear_Negative_Mortality_Multiplier": 1
}

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
}