Mortality and survival¶
The following parameter determine mortality and survival characteristics of the disease being modeled and the population in general (nondisease mortality).
Note
Parameters are casesensitive. 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 onART HIVcaused 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, nondisease causes. Enable_Natural_Mortality must be set to 1. Possible values are:
Properties, rates, and bin sizes can be set for nondisease 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 (nondisease) 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 mortalityblocking immunity decays after the mortalityblocking 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:

{
"Mortality_Time_Course": "MORTALITY_AFTER_INFECTIOUS"
}

TB_Active_Mortality_Rate 
float 
0 
1 
0.0009589 
The mean rate at which active smearpositive 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 smearpositive state, then the ratio of TB_Active_Mortality_Rate to total rate determines the probability that an active smearpositive individual will die from TB disease after a mean duration of 1 / total rate. 
{
"TB_Active_Mortality_Rate": 5e08
}

TB_Drug_Mortality_Rate 
float 
0 
1 
0 
The daily rate at which treatment with an antiTB drug causes death in an individual with drugsensitive 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": 1e09,
"TB_Drug_Inactivation_Rate_HIV": 1e09,
"TB_Drug_Inactivation_Rate_MDR": 1e09,
"TB_Drug_Mortality_Rate": 1e09,
"TB_Drug_Mortality_Rate_HIV": 1e09,
"TB_Drug_Mortality_Rate_MDR": 1e09,
"TB_Drug_Primary_Decay_Time_Constant": 179,
"TB_Drug_Relapse_Rate": 1e09,
"TB_Drug_Relapse_Rate_HIV": 1e09,
"TB_Drug_Relapse_Rate_MDR": 1e09,
"TB_Drug_Resistance_Rate": 1e09,
"TB_Drug_Resistance_Rate_HIV": 1e09,
"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": 1e09,
"TB_Drug_Inactivation_Rate_HIV": 1e09,
"TB_Drug_Inactivation_Rate_MDR": 1e09,
"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 noninfectious. 
{
"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 smearnegative 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 smearnegative state, then the ratio of the aforementioned product to total rate determines the probability that an active smearnegative 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
}
