Configuration parameters

The parameters described in this reference section can be added to the JavaScript Object Notation (JSON) formatted configuration file to determine the core behavior of a simulation including the computing environment, functionality to enable, additional files to use, and characteristics of the disease being modeled. This file contains mostly a flat list of JSON key:value pairs. For more information on how to use these files, see Create a configuration file.

The tables below contain only parameters available when using the tuberculosis simulation type. Some parameters may appear in multiple categories.

Note

Parameters are case-sensitive. For Boolean parameters, set to 1 for true or 0 for false. JSON does not permit comments, but you can add “dummy” parameters to add contextual information to your files.

Disease progression

The following parameters determine the characteristics of tuberculosis progression, such as incubation, latency, activation, and whether progression is fast or slow.

Parameter Data type Minimum Maximum Default Description Example
TB_Active_Cure_Rate float 0 1 0 The mean rate at which active symptomatic individuals progress to a cured (uninfected) state. In the absence of treatment, this rate is added to TB_Inactivation_Rate and TB_Active_Mortality_Rate to determine the total rate of the active smear-positive state, then the ratio of TB_Active_Cure_Rate to total rate determines the probability that an actively infected individual will go to a cured state after a mean duration of 1 / total rate.
{
    "TB_Active_Cure_Rate": 1e-09
}
TB_Active_Period_Distribution enum NA NA NOT_INITIALIZED

Distribution for duration of active disease. For all possible values, the mean is defined by total rate, which is the sum of TB_Inactivation_Rate and TB_Active_Mortality_Rate corrected for smear status. Possible values are:

NOT_INITIALIZED
No distribution set.
FIXED_DURATION
A constant duration incubation period.
UNIFORM_DURATION
A uniform random draw for the duration of the incubation period.
GAUSSIAN_DURATION
Duration of the active period is defined by the mean and standard deviation (defined by TB_Active_Period_Std_Dev) of the Gaussian distribution. Negative values are truncated at zero.
EXPONENTIAL_DURATION
The active period is the mean of the exponential random draw.
POISSON_DURATION
The active period is the mean of the random Poisson draw.
LOG_NORMAL_DURATION
The active period is a log normal distribution defined by a mean and log width.
BIMODAL_DURATION
The distribution is bimodal, the duration is a fraction of the active period for a specified period of time and equal to the active period otherwise.
PIECEWISE_CONSTANT
The distribution is specified with a list of years and a matching list of values. The duration at a given year is that specified for the nearest previous year.
PIECEWISE_LINEAR
The distribution is specified with a list of years and matching list of values. The duration at a given year is a linear interpolation of the specified values.
WEIBULL_DURATION
The duration is a Weibull distribution with a given scale and shape.
DUAL_TIMESCALE_DURATION
The duration is two exponential distributions with given means.
{
    "TB_Active_Period_Distribution": "EXPONENTIAL_DURATION"
}
TB_Active_Period_Std_Dev float 0 3.40E+38 1 The standard deviation for the distribution of the duration of active TB. Used when TB_Active_Period_Distribution is set to GAUSSIAN_DURATION.
{
    "TB_Active_Period_Std_Dev": 200
}
TB_Active_Presymptomatic_Infectivity_Multiplier float 0 1 0.0274 The scale factor for Base_Infectivity to give the infectiousness of active presymptomatic individuals.
{
    "TB_Active_Presymptomatic_Infectivity_Multiplier": 0.19999999999999998
}
TB_Extrapulmonary_Fraction_Adult float 0 1 0 The fraction of active cases in adults (age 15 or over) that are extrapulmonary. The sum of this and TB_Smear_Positive_Fraction_Adult must be less than or equal to 1.
{
    "TB_Extrapulmonary_Fraction_Adult": 0.33
}	

TB_Extrapulmonary_Fraction_Child float 0 1 0 The fraction of active cases in children (under age 15) that are extrapulmonary. The sum of this and TB_Smear_Positive_Fraction_Child must be less than or equal to 1.
{
    "TB_Extrapulmonary_Fraction_Child": 0.33
}

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.
{
    "TB_Extrapulmonary_Mortality_Multiplier": 1
}
TB_Fast_Progressor_Fraction_Adult float 0 1 1 The fraction of adults (age 15 or over) that are fast progressors.
{
    "TB_Fast_Progressor_Fraction_Adult": 0.5
}
TB_Fast_Progressor_Fraction_Child float 0 1 1 The fraction of children (under age 15) that are fast progressors.
{
    "TB_Fast_Progressor_Fraction_Child": 0.5
}
TB_Fast_Progressor_Rate float 0 1 4.11E-05 The mean rate at which individuals who are fast progressors progress from a latently infected state to an active presymptomatic state. This rate is added to the TB_Latent_Cure_Rate to determine the total rate of the latently infected state, then the ratio of TB_Fast_Progressor_Rate to the total rate is calculated. This ratio determines the probability that a latently infected fast progressor will go to an active presymptomatic state after a mean duration of 1 / total rate.
{
    "TB_Fast_Progressor_Rate": 0.02
}

TB_Inactivation_Rate float 0 1 0.00041096 The mean rate at which active symptomatic (smear-positive, smear-negative, and extrapulmonary) individuals progress to an inactivated (latently infected) state. In the absence of treatment, this rate is added to TB_Active_Cure_Rate and TB_Active_Mortality_Rate to determine the total rate of the active symptomatic state, then the ratio of TB_Active_Cure_Rate to total rate determines the probability that an active syptomatic individual will go to a latently infected state after a mean duration of 1 / total rate.
{
    "TB_Inactivation_Rate": 0.05
}

TB_Latent_Cure_Rate float 0 1 0.0005479 The mean rate at which individuals progress from a latently infected state to a cured (uninfected) state. This rate is added to either the TB_Fast_Progressor_Rate or the TB_Slow_Progressor_Rate to determine the total rate of the latently infected state (depending on whether the individual is a fast progressor or slow progressor, respectively), then the ratio of TB_Latent_Cure_Rate to total rate is calculated. This ratio determines the probability that a latently infected individual will go to a cured state.
{
    "TB_Latent_Cure_Rate": 0.1
}
TB_Presymptomatic_Cure_Rate float 0 1 0.0274 The mean rate at which active presymptomatic individuals progress to a cured (uninfected) state. This rate is added to TB_Presymptomatic_Rate to determine the total rate of the active presymptomatic state, then the ratio of TB_Presymptomatic_Cure_Rate to total rate is calculated. This ratio determines the probability that an active presymptomatic individual will go to a cured state after a mean duration of 1 / total rate.
{
    "TB_Presymptomatic_Cure_Rate": 0.05
}

TB_Presymptomatic_Rate float 0 1 0.0274 The mean rate at which active presymptomatic individuals progress to an active symptomatic state. This rate is added to TB_Presymptomatic_Cure_Rate to determine the total rate of the active presymptomatic state, then the ratio of TB_Presymptomatic_Rate to total rate is calculated. This ratio determines the probability that an active presymptomatic individual will go to active symptomatic disease after a mean duration of 1 / total rate.
{
    "TB_Presymptomatic_Rate": 0.0333
}
TB_Relapsed_to_Active_Rate float 0 1 4.11E-05 The mean rate at which relapsed individuals progress to an active symptomatic state.
{
    "TB_Relapsed_to_Active_Rate": 0.01
}
TB_Slow_Progressor_Rate float 0 1 2.05E-06 The mean rate at which individuals who are slow progressors progress from a latently infected state to an active presymptomatic state. This rate is added to the TB_Latent_Cure_Rate to determine the total rate of the latently infected state, then the ratio of TB_Slow_Progressor_Rate to the total rate is calculated. This ratio determines the probability that a latently infected fast progressor will go to an active presymptomatic state after a mean duration of 1 / total rate.
{
    "TB_Slow_Progressor_Rate": 0.02
}

TB_Smear_Positive_Fraction_Adult float 0 1 1 The fraction of active cases in adults (age 15 and over) that are smear-positive. The sum of TB_Smear_Positive_Fraction_Adult and TB_Extrapulmonary_Fraction_Adult must be less than or equal to 1. This sum plus the fraction of smear-negative adults is equal to 1.
{
    "TB_Smear_Positive_Fraction_Adult": 1
}
TB_Smear_Positive_Fraction_Child float 0 1 1 The fraction of active cases in children (under age 15) that are smear-positive. The sum of TB_Smear_Positive_Fraction_Child and TB_Extrapulmonary_Fraction_Child must be less than or equal to 1. This sum plus the fraction of smear-negative children is equal to 1.
{
    "TB_Smear_Positive_Fraction_Child": 1
}

Drugs and treatments

The following parameters determine the efficacy of drugs and other treatments.

Parameter Data type Minimum Maximum Default Description Example
TB_Drug_Clearance_Rate float 0 1 1 The daily rate at which treatment with an anti-TB drug causes disease clearance. This parameter, TB_Drug_Inactivation_Rate, TB_Drug_Mortality_Rate, and TB_Drug_Relapse_Rate specify the daily probability of a change in the TB disease state during the course of treatment. The sum of these rates and the total duration of treatment specify the probability that any event occurs. If no event occurs, the individual fails drug treatment.
{	
    "TB_Drug_Params": {
        "BurninDrug": {
            "TB_Drug_Clearance_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_Efficacy_Multiplier_Failed float 0 1 1 The scale factor for drug efficacy parameters (TB_Drug_Inactivation_Rate and TB_Drug_Clearance_Rate) to give the efficacy of first-line drugs when given to individuals who have failed treatment.
{
    "TB_Drug_Efficacy_Multiplier_Failed": 1.0
}

TB_Drug_Efficacy_Multiplier_MDR float 0 1 1 The scale factor for drug efficacy parameters (TB_Drug_Inactivation_Rate and TB_Drug_Clearance_Rate) to give the efficacy of first-line drugs when given to individuals with MDR-TB.
{
    "TB_Drug_Efficacy_Multiplier_MDR": 1.0
}

TB_Drug_Efficacy_Multiplier_Relapsed float 0 1 1 The scale factor for drug efficacy parameters (TB_Drug_Inactivation_Rate and TB_Drug_Clearance_Rate) to give the efficacy of first-line drugs when given to individuals who have relapsed after treatment.
{
    "TB_Drug_Efficacy_Multiplier_Relapsed": 1.0
}

TB_Drug_Inactivation_Rate float 0 1 1 The daily rate at which treatment with an anti-TB drug causes inactivation. This parameter, TB_Drug_Clearance_Rate, TB_Drug_Mortality_Rate, and TB_Drug_Relapse_Rate specify the daily probability of a change in the TB disease state during the course of treatment. The sum of these rates and the total duration of treatment specify the probability that any event occurs. If no event occurs, the individual fails drug treatment.
{	
    "TB_Drug_Params": {
        "BurninDrug": {
            "TB_Drug_Clearance_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 float 0 1 0 The daily rate at which treatment with an anti-TB drug causes death. This parameter, TB_Drug_Inactivation_Rate, TB_Drug_Relapse_Rate, and TB_Drug_Clearance_Rate specify the daily probability of a change in the TB disease state during the course of treatment. The sum of these rates and the total duration of treatment specify the probability that any event occurs. If no event occurs, the individual fails drug treatment.
{	
    "TB_Drug_Params": {
        "BurninDrug": {
            "TB_Drug_Clearance_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_Params JSON object NA NA NA This JSON structure contains the names of anti-tuberculosis drugs and the parameters that define them.
{
    "TB_Drug_Params":{
        "CDCDrug":{
            "TB_Drug_Clearance_Rate":0.1,
            "TB_Drug_Inactivation_Rate":1e-09,
            "TB_Drug_Mortality_Rate":1e-09,
            "TB_Drug_Primary_Decay_Time_Constant":180.0,
            "TB_Drug_Relapse_Rate":1e-09,
            "TB_Drug_Resistance_Rate":1e-09
        },
        "CDCDrugMDR":{
            "TB_Drug_Clearance_Rate":1e-09,
            "TB_Drug_Inactivation_Rate":1e-09,
            "TB_Drug_Mortality_Rate":1e-09,
            "TB_Drug_Primary_Decay_Time_Constant":180.0,
            "TB_Drug_Relapse_Rate":1e-09,
            "TB_Drug_Resistance_Rate":1e-09
        }
    }
}
TB_Drug_Primary_Decay_Time_Constant float 0 100000 0 The number of days before the efficacy of a specific anti-TB drug begins to decay.
{
    "TB_Drug_Params": {
        "CDCDrug": {
            "TB_Drug_Clearance_Rate": 0.1,
            "TB_Drug_Inactivation_Rate": 1e-09,
            "TB_Drug_Mortality_Rate": 1e-09,
            "TB_Drug_Primary_Decay_Time_Constant": 180.0,
            "TB_Drug_Relapse_Rate": 1e-09,
            "TB_Drug_Resistance_Rate": 1e-09
        }
    }
}
TB_Drug_Relapse_Rate float 0 1 0 The daily rate at which treatment with an anti-TB drug causes disease relapse. This parameter, TB_Drug_Inactivation_Rate, TB_Drug_Mortality_Rate, and TB_Drug_Clearance_Rate specify the daily probability of a change in the TB disease state during the course of treatment. The sum of these rates and the total duration of treatment specify the probability that any event occurs. If no event occurs, the individual fails drug treatment.
{
    "TB_Drug_Params": {
        "CDCDrug": {
            "TB_Drug_Clearance_Rate": 0.1, 
            "TB_Drug_Inactivation_Rate": 1e-09, 
            "TB_Drug_Mortality_Rate": 1e-09, 
            "TB_Drug_Primary_Decay_Time_Constant": 180.0, 
            "TB_Drug_Relapse_Rate": 1e-09, 
            "TB_Drug_Resistance_Rate": 1e-09
        }	
    }
}	
TB_Drug_Resistance_Rate float 0 1 0 The daily probability that an individual with drug-sensitive TB will acquire MDR-TB. Only individuals who return to the latent state or fail can acquire MDR-TB.
{
    "TB_Drug_Params": {
        "CDCDrug": {
            "TB_Drug_Clearance_Rate": 0.1, 
            "TB_Drug_Inactivation_Rate": 1e-09, 
            "TB_Drug_Mortality_Rate": 1e-09, 
            "TB_Drug_Primary_Decay_Time_Constant": 180.0, 
            "TB_Drug_Relapse_Rate": 1e-09, 
            "TB_Drug_Resistance_Rate": 1e-09
        }	
    }
}	
TB_Drug_Types_For_This_Sim array of strings NA NA [] The list of drug types that will be used with the AntiTBPropDep intervention. The values for each drug type are defined by TB_Drug_Params.
{	
    "TB_Drug_Types_For_This_Sim": [
        "CDCDrug", 
        "CDCDrugRetx", 
        "CDCDrugMDR"
    ]	
}	

Enable or disable features

The following parameters enable or disable features of the model, such as allowing births, deaths, or aging. Set to false (0) to disable; set to true (1) to enable.

Parameter Data type Minimum Maximum Default Description Example
Enable_Aging boolean 0 1 1 Controls whether or not individuals in a population age during the simulation. Enable_Vital_Dynamics must be set to true (1).
{
    "Enable_Vital_Dynamics": 1,
    "Enable_Aging": 1
}
Enable_Air_Migration boolean 0 1 0 Controls whether or not migration by air travel will occur. Migration_Model must be set to FIXED_RATE_MIGRATION.
{
     "Migration_Model": "FIXED_RATE_MIGRATION",
     "Enable_Air_Migration": 1,
     "Air_Migration_Filename": "../inputs/air_migration.bin"
}
Enable_Birth boolean 0 1 1 Controls whether or not individuals will be added to the simulation by birth. Enable_Vital_Dynamics must be set to true (1). If you want new individuals to have the same intervention coverage as existing individuals, you must add a BirthTriggeredIV to the campaign file.
{
    "Enable_Vital_Dynamics": 1,
    "Enable_Birth": 1
}
Enable_Climate_Stochasticity boolean 0 1 0 Controls whether or not the climate has stochasticity. Climate_Model must be set to CLIMATE_CONSTANT or CLIMATE_BY_DATA. Set the variance using the parameters Air_Temperature_Variance, Land_Temperature_Variance, Enable_Rainfall_Stochasticity, and Relative_Humidity_Variance.
{
    "Climate_Model": "CLIMATE_BY_DATA",
    "Enable_Climate_Stochasticity": 1, 
    "Air_Temperature_Variance": 2,
    "Enable_Rainfall_Stochasticity": 1,
    "Land_Temperature_Variance": 2,
    "Relative_Humidity_Variance": 0.05
}
Enable_Default_Reporting boolean 0 1 1 Controls whether or not the default InsetChart.json report is created.
{
    "Enable_Default_Reporting": 1
}
Enable_Demographics_Birth boolean 0 1 0 Controls whether or not newborns have identical or heterogeneous characteristics. Set to false (0) to give all newborns identical characteristics; set to true (1) to allow for heterogeneity in traits such as sickle-cell status. Enable_Birth must be set to true (1).
{
    "Enable_Birth": 1,
    "Enable_Demographics_Birth": 1
}
Enable_Demographics_Builtin boolean 0 1 0 Controls whether or not built-in demographics for default geography will be used. Note that the built-in demographics feature does not represent a real geographical location and is mostly used for testing. Set to true (1) to define the initial population and number of nodes using Default_Geography_Initial_Node_Population and Default_Geography_Torus_Size. Set to false (0) to use demographics input files defined in Demographics_Filenames.
{
    "Enable_Demographics_Builtin": 1,
    "Default_Geography_Initial_Node_Population": 1000,
    "Default_Geography_Torus_Size": 3
}
Enable_Demographics_Gender boolean 0 1 1 Controls whether or not gender ratios are drawn from a Gaussian or 50/50 draw. Set to true (1) to create gender ratios drawn from a male/female ratio that is randomly smeared by a Gaussian of width 1%; set to false (0) to assign a gender ratio based on a 50/50 draw.
{
    "Enable_Demographics_Gender": 1
}
Enable_Demographics_Other boolean 0 1 0 Controls whether or not other demographic factors are included in the simulation, such as the fraction of individuals above poverty, urban/rural characteristics, heterogeneous initial immunity, or risk. These factors are set in the demographics file.
{
    "Enable_Demographics_Other": 1
}
Enable_Demographics_Reporting boolean 0 1 1 Controls whether or not demographic summary data and age-binned reports are outputted to file.
{
    "Enable_Demographics_Reporting": 1
}
Enable_Disease_Mortality boolean 0 1 1 Controls whether or not individuals die due to disease.
{
    "Enable_Disease_Mortality": 1
}
Enable_Family_Migration boolean 0 1 0 Controls whether or not all members of a household can migrate together. All residents must be home before they can leave on the trip. Migration_Model must be set to FIXED_RATE_MIGRATION.
{
    "Enable_Migration": "FIXED_RATE_MIGRATION",
    "Enable_Family_Migration": 1,
    "Family_Migration_Filename": "../inputs/family_migration.bin"
}
Enable_Heterogeneous_Intranode_Transmission boolean 0 1 0

Controls whether or not individuals experience heterogeneous disease transmission within a node. When set to true (1), individual property definitions and the \beta matrix must be specified in the demographics file (see NodeProperties and IndividualProperties parameters). The \beta values are multiplied with the \beta 0 value configured by Base_Infectivity.

This is used only in generic simulations, but must be set to false (0) for all other simulation types. Heterogeneous transmission for other diseases uses other mechanistic parameters included with the simulation type.

{
    "Enable_Heterogeneous_Intranode_Transmission": 1
}
Enable_Immune_Decay boolean 0 1 1 Controls whether or not immunity decays after an infection clears. Set to true (1) if immunity decays; set to false (0) if recovery from the disease confers complete immunity for life. Enable_Immunity must be set to true (1).
{
    "Enable_Immunity": 1,
    "Enable_Immune_Decay": 0
}
Enable_Immunity boolean 0 1 1 Controls whether or not an individual has protective immunity after an infection clears.
{
    "Enable_Immunity": 1
}
Enable_Interventions boolean 0 1 0 Controls whether or not campaign interventions will be used in the simulation. Set Campaign_Filename to the path of the file that contains the campaign interventions.
{
    "Enable_Interventions": 1,
    "Campaign_Filename": "campaign.json"
}
Enable_Local_Migration boolean 0 1 0 Controls whether or not local migration (the diffusion of people in and out of nearby nodes by foot travel) occurs. Migration_Model must be set to FIXED_RATE_MIGRATION.
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Local_Migration": 1,
    "Local_Migration_Filename": "../inputs/local_migration.bin"
}
Enable_Maternal_Transmission boolean 0 1 0 Controls whether or not infectious mothers infect infants at birth. Enable_Birth must be set to true (1).
{
    "Enable_Birth": 1,
    "Enable_Maternal_Transmission": 1
}
Enable_Migration_Heterogeneity boolean 0 1 1 Controls whether or not migration rate is heterogeneous among individuals. Set to true (1) to use a migration rate distribution in the demographics file (see NodeAttributes parameters); set to false (0) to use the same migration rate applied to all individuals. Migration_Model must be set to FIXED_RATE_MIGRATION.
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Migration_Heterogeneity": 1
}
Enable_Property_Output boolean 0 1 0 Controls whether or not to create property output reports, which detail groups as defined in IndividualProperties in the demographics file (see NodeProperties and IndividualProperties parameters). When there is more than one property type, the report will display the channel information for all combinations of the property type groups.
{
    "Enable_Property_Output": 1
}
Enable_Rainfall_Stochasticity boolean 0 1 1 Controls whether or not there is stochastic variation in rainfall; set to true (1) for stochastic variation of rainfall that is drawn from an exponential distribution (with a mean value as the daily rainfall from the Climate_Model values CLIMATE_CONSTANT or CLIMATE_BY_DATA), or set to false (0) to disable rainfall stochasticity.
{
    "Enable_Climate_Stochasticity": 1, 
    "Air_Temperature_Variance": 2,
    "Enable_Rainfall_Stochasticity": 1,
    "Land_Temperature_Variance": 2,
    "Relative_Humidity_Variance": 0.05
}
Enable_Regional_Migration boolean 0 1 0 Controls whether or not there is migration by road vehicle into and out of nodes in the road network. Migration_Model must be set to FIXED_RATE_MIGRATION.
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Regional_Migration": 1,
    "Regional_Migration_Filename": "../inputs/regional_migration.bin"
}
Enable_Sea_Migration boolean 0 1 0 Controls whether or not there is migration on ships into and out of coastal cities with seaports. Migration_Model must be set to FIXED_RATE_MIGRATION.
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Sea_Migration": 1,
    "Sea_Migration_Filename": "../inputs/sea_migration.bin"
}
Enable_Spatial_Output boolean 0 1 0

Controls whether or not spatial output reports are created. If set to true (1), spatial output reports include all channels listed in the parameter Spatial_Output_Channels.

Note

Spatial output files require significant processing time and disk space.

{
    "Enable_Spatial_Output": 1,
    "Spatial_Output_Channels": [
        "Prevalence",
        "New_Infections"
    ]
}
Enable_Superinfection boolean 0 1 0 Controls whether or not an individual can have multiple infections simultaneously. Set to true (1) to allow for multiple simultaneous infections; set to false (0) if multiple infections are not possible. Set the Max_Individual_Infections parameter.
{
    "Enable_Superinfection": 1,
    "Max_Individual_Infections": 2
}
Enable_Vital_Dynamics boolean 0 1 1 Controls whether or not births and deaths occur in the simulation. Births and deaths must be individually enabled and set.
{
    "Enable_Vital_Dynamics":1,
    "Enable_Birth": 1,
    "Death_Rate_Dependence": "NONDISEASE_MORTALITY_OFF",
    "Base_Mortality": 0.002
}

General disease

The following parameters determine general disease characteristics.

Parameter Data type Minimum Maximum Default Description Example
Animal_Reservoir_Type enum NA NA NO_ZOONOSIS

The type of animal reservoir and configuration for zoonosis. Use of the animal reservoir sets a low constant baseline of infectivity beyond what is present in the human population. It allows a more random introduction of cases in continuous time, which is more applicable for various situations such as zoonosis. Possible values are:

NO_ZOONOSIS
There is no animal reservoir.
CONSTANT_ZOONOSIS
The daily rate of zoonotic infection is configured by the parameter Zoonosis_Rate.
ZOONOSIS_FROM_DEMOGRAPHICS
The zoonosis rate is scaled first by the node-specific Zoonosis value in the demographics file (see NodeAttributes parameters). If Zoonosis is not configured, the simulation will then use the value for Zoonosis_Rate.
{
    "Animal_Reservoir_Type": "CONSTANT_ZOONOSIS"
}
Number_Basestrains integer 1 10 1 The number of base strains in the simulation, such as antigenic variants.
{
    "Number_Basestrains": 1
}
Number_Substrains integer 1 16777200 256 The number of disease substrains for each base strain, such as genetic variants.
{
    "Number_Substrains": 16777216
}
Zoonosis_Rate float 0 1 0 The daily rate of zoonotic infection per individual. Animal_Reservoir_Type must be set to CONSTANT_ZOONOSIS or ZOONOSIS_FROM_DEMOGRAPHICS. If Animal_Reservoir_Type is set to ZOONOSIS_FROM_DEMOGRAPHICS, the value for the Zoonosis NodeAttribute in the demographics file will override the value set for Zoonosis_Rate.
{
    "Zoonosis_Rate": 0.005
}

Geography and environment

The following parameters determine characteristics of the geography and environment of the simulation. For example, how to use the temperature or rainfall data in the climate files and the size of the nodes in the simulation.

Parameter Data type Minimum Maximum Default Description Example
Air_Temperature_Filename string NA NA air_temp.json The path to the input data file that defines air temperature data measured two meters above ground. Climate_Model must be set to CLIMATE_BY_DATA. The file must be in .bin format.
{
    "Climate_Model": "CLIMATE_BY_DATA",
    "Air_Temperature_Filename": "Namawala_single_node_air_temperature_daily.bin"
}
Air_Temperature_Offset float -20 20 0 The linear shift of air temperature in degrees Celsius. Climate_Model must be set to CLIMATE_BY_DATA.
{
    "Air_Temperature_Offset": 1
}
Air_Temperature_Variance float 0 5 2 The standard deviation (in degrees Celsius) for normally distributed noise applied to the daily air temperature values when Climate_Model is configured as CLIMATE_CONSTANT or CLIMATE_BY_DATA. Enable_Climate_Stochasticity must be set to true (1).
{
    "Enable_Climate_Stochasticity": 1, 
    "Air_Temperature_Variance": 2,
}
Base_Air_Temperature float -55 45 22 The air temperature, in degrees Celsius, where Climate_Model is set to CLIMATE_CONSTANT.
{
    "Climate_Model": "CLIMATE_CONSTANT",
    "Base_Air_Temperature": 30
}
Base_Land_Temperature float -55 60 26 The land temperature, in degrees Celsius, where Climate_Model is set to CLIMATE_CONSTANT.
{
    "Climate_Model": "CLIMATE_CONSTANT",
    "Base_Land_Temperature": 20
}
Base_Rainfall float 0 150 10 The value of rainfall per day in millimeters when Climate_Model is set to CLIMATE_CONSTANT.
{ 
     "Climate_Model": "CLIMATE_CONSTANT", 
     "Base_Rainfall": 20
}
Base_Relative_Humidity float 0 1 0.75 The value of humidity where Climate_Model is set to CLIMATE_CONSTANT.
{ 
    "Base_Relative_Humidity": 0.1
}
Climate_Model enum NA NA CLIMATE_OFF

How and from what files the climate of a simulation is configured. The possible values are:

CLIMATE_OFF
No climate files used.
CLIMATE_CONSTANT
Uses the conditional parameters that give the fixed values of temperature or rain for land temperature, air temperature, rainfall, and humidity.
CLIMATE_KOPPEN
Uses an input data file that decodes Koppen codes by geographic location.
CLIMATE_BY_DATA
Reads everything out of several input data files with additional parameters that allow the addition of stochasticity or scale offsets.
{   
    "Climate_Model": "CLIMATE_CONSTANT"
}
Climate_Update_Resolution enum NA NA CLIMATE_UPDATE_YEAR

The resolution of data in climate files. Climate_Model must be set to CLIMATE_CONSTANT, CLIMATE_BY_DATA, or CLIMATE_KOPPEN. Possible values are:

CLIMATE_UPDATE_YEAR CLIMATE_UPDATE_MONTH CLIMATE_UPDATE_WEEK CLIMATE_UPDATE_DAY CLIMATE_UPDATE_HOUR

{
    "Climate_Update_Resolution": "CLIMATE_UPDATE_DAY"
}
Default_Geography_Initial_Node_Population integer 0 1000000 1000 When using the built-in demographics for default geography, the initial number of individuals in each node. Note that the built-in demographics feature does not represent a real geographical location and is mostly used for testing. Enable_Demographics_Builtin must be set to true (1).
{
    "Enable_Demographics_Builtin": 1,
    "Default_Geography_Initial_Node_Population": 1000,
    "Default_Geography_Torus_Size": 3
}
Default_Geography_Torus_Size integer 3 100 10

When using the built-in demographics for default geography, the square root of the number of nodes in the simulation. The simulation uses an N x N square grid of nodes with N specified by this parameter. If migration is enabled, the N x N nodes are assumed to be a torus and individuals can migrate from any node to all four adjacent nodes.

To enable migration, set Migration_Model to FIXED_RATE_MIGRATION. Built-in migration is a form of “local” migration where individuals only migrate to the adjacent nodes. You can use the x_Local_Migration parameter to control the rate of migration. The other migration parameters are ignored. Note that the built-in demographics feature does not represent a real geographical location and is mostly used for testing.

Enable_Demographics_Builtin must be set to true (1).

{
    "Enable_Demographics_Builtin": 1,
    "Default_Geography_Initial_Node_Population": 1000,
    "Default_Geography_Torus_Size": 3
}
Enable_Climate_Stochasticity boolean 0 1 0 Controls whether or not the climate has stochasticity. Climate_Model must be set to CLIMATE_CONSTANT or CLIMATE_BY_DATA. Set the variance using the parameters Air_Temperature_Variance, Land_Temperature_Variance, Enable_Rainfall_Stochasticity, and Relative_Humidity_Variance.
{
    "Climate_Model": "CLIMATE_BY_DATA",
    "Enable_Climate_Stochasticity": 1, 
    "Air_Temperature_Variance": 2,
    "Enable_Rainfall_Stochasticity": 1,
    "Land_Temperature_Variance": 2,
    "Relative_Humidity_Variance": 0.05
}
Enable_Rainfall_Stochasticity boolean 0 1 1 Controls whether or not there is stochastic variation in rainfall; set to true (1) for stochastic variation of rainfall that is drawn from an exponential distribution (with a mean value as the daily rainfall from the Climate_Model values CLIMATE_CONSTANT or CLIMATE_BY_DATA), or set to false (0) to disable rainfall stochasticity.
{
    "Enable_Climate_Stochasticity": 1, 
    "Air_Temperature_Variance": 2,
    "Enable_Rainfall_Stochasticity": 1,
    "Land_Temperature_Variance": 2,
    "Relative_Humidity_Variance": 0.05
}
Koppen_Filename string NA NA UNINITIALIZED STRING The path to the input file used to specify Koppen climate classifications; only used when Climate_Model is set to CLIMATE_KOPPEN. The file must be in .dat format.
{
    "Koppen_Filename": "Mad_2_5arcminute_koppen.dat"
}
Land_Temperature_Filename string NA NA land_temp.json The path of the input file defining temperature data measured at land surface; used only when Climate_Model is set to CLIMATE_BY_DATA. The file must be in .bin format.
{
    "Land_Temperature_Filename": "Namawala_single_node_land_temperature_daily.bin"
}

Land_Temperature_Offset float -20 20 0 The linear shift of land surface temperature in degrees Celsius; only used when Climate_Model is set to CLIMATE_BY_DATA.
{
    "Land_Temperature_Offset": 0
}
Land_Temperature_Variance float 0 7 2 The standard deviation (in degrees Celsius) for normally distributed noise applied to the daily land temperature values when Climate_Model is configured to CLIMATE_CONSTANT or CLIMATE_BY_DATA; only used if the Enable_Climate_Stochasticity is set to true (1).
{
    "Land_Temperature_Variance": 1.5
}

Node_Grid_Size float 0.00416 90 0.004167 The spatial resolution indicating the node grid size for a simulation in degrees.
{
    "Node_Grid_Size": 0.042
}
Rainfall_Filename string NA NA rainfall.json The path of the input file which defines rainfall data. Climate_Model must be set to CLIMATE_BY_DATA. The file must be in .bin format.
{
    "Rainfall_Filename": "Namawala_single_node_rainfall_daily.bin"
}
Rainfall_Scale_Factor float 0.1 10 1 The scale factor used in multiplying rainfall value(s). Climate_Model must be set to CLIMATE_BY_DATA.
{
    "Rainfall_Scale_Factor": 1
}
Relative_Humidity_Filename string NA NA rel_hum.json The path of the input file which defines relative humidity data measured 2 meters above ground. Climate_Model must be set to CLIMATE_BY_DATA. The file must be in .bin format.
{
    "Relative_Humidity_Filename": "Namawala_single_node_relative_humidity_daily.bin"
}
Relative_Humidity_Scale_Factor float 0.1 10 1 The scale factor used in multiplying relative humidity values. Climate_Model must be set to CLIMATE_BY_DATA.
{
    "Relative_Humidity_Scale_Factor": 1
}
Relative_Humidity_Variance float 0 0.12 0.05 The standard deviation (in percentage) for normally distributed noise applied to the daily relative humidity values when Climate_Model is configured as CLIMATE_CONSTANT or CLIMATE_BY_DATA. Enable_Climate_Stochasticity must be set to true (1).
{
    "Relative_Humidity_Variance": 0.05
}

Immunity

The following parameters determine the immune system response for the disease being modeled, including waning immunity after an infection clears.

Parameter Data type Minimum Maximum Default Description Example
Acquisition_Blocking_Immunity_Decay_Rate float 0 1000 0.001 The rate at which acquisition-blocking immunity decays after the initial period indicated by the base acquisition-blocking immunity offset. Only used when Enable_Immunity and Enable_Immune_Decay parameters are set to true (1).
{
    "Acquisition_Blocking_Immunity_Decay_Rate": 0.05
}
Acquisition_Blocking_Immunity_Duration_Before_Decay float 0 45000 0 The number of days after infection until acquisition-blocking immunity begins to decay. Enable_Immunity and Enable_Immune_Decay must be set to true (1).
{
    "Acquisition_Blocking_Immunity_Duration_Before_Decay": 10
}
Enable_Immune_Decay boolean 0 1 1 Controls whether or not immunity decays after an infection clears. Set to true (1) if immunity decays; set to false (0) if recovery from the disease confers complete immunity for life. Enable_Immunity must be set to true (1).
{
    "Enable_Immunity": 1,
    "Enable_Immune_Decay": 0
}
Enable_Immunity boolean 0 1 1 Controls whether or not an individual has protective immunity after an infection clears.
{
    "Enable_Immunity": 1
}
Immune_Threshold_For_Downsampling float 0 1 0 Threshold on acquisition immunity at which to apply immunity dependent downsampling. Individual_Sampling_Type must set to ADAPTED_SAMPLING_BY_IMMUNE_STATE.
{
    "Individual_Sampling_Type": "ADAPTED_SAMPLING_BY_IMMUNE_STATE", 
    "Immune_Threshold_For_Downsampling": 0.5
}
Immunity_Acquisition_Factor float 0 1000 0 The multiplicative reduction in the probability of reacquiring disease. Only used when Enable_Immunity and Enable_Immune_Decay are set to 1.
{
    "Enable_Immunity": 1,
    "Enable_Immune_Decay": 1,
    "Immunity_Acquisition_Factor": 0.9
}
Immunity_Initialization_Distribution_Type enum NA NA DISTRIBUTION_OFF

The method for initializing the immunity distribution in the simulated population. Enable_Immunity must be set to true (1). Possible values are:

DISTRIBUTION_OFF
All individuals default to no immunity.
DISTRIBUTION_SIMPLE
Individual immunities are drawn from a distribution whose functional form and parameters are specified in the demographics file in IndividualAttributes using ImmunityDistributionFlag, ImmunityDistribution1, and ImmunityDistribution2 (see Simple distributions parameters).
DISTRIBUTION_COMPLEX
Individual immunities are drawn from an age-dependent piecewise linear function for each specific antibody in the demographics file (see Complex distributions parameters).
{
    "Immunity_Initialization_Distribution_Type": "DISTRIBUTION_COMPLEX" 
}
Immunity_Mortality_Factor float 0 1000 0 The multiplicative reduction in the probability of dying from infection after getting re-infected. Enable_Immunity and Enable_Immune_Decay must be set to true (1).
{
    "Enable_Immunity": 1,
    "Enable_Immune_Decay": 1, 
    "Immunity_Mortality_Factor": 0.5
}
Immunity_Transmission_Factor float 0 1000 0 The multiplicative reduction in the probability of transmitting infection after getting re-infected. Only used when Enable_Immunity and Enable_Immune_Decay are set to 1.
{
    "Enable_Immunity": 1,
    "Enable_Immunity_Decay": 1, 
    "Immunity_Transmission_Factor": 0.9
}
Mortality_Blocking_Immunity_Decay_Rate float 0 1000 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_Blocking_Immunity_Duration_Before_Decay float 0 45000 0 The number of days after infection until mortality-blocking immunity begins to decay. Enable_Immunity and Enable_Immune_Decay must be set to 1.
{
    "Mortality_Blocking_Immunity_Duration_Before_Decay": 270
}
TB_Immune_Loss_Fraction float 0 1 0.5 The fraction of individuals that lose immunity with time.
{
    "TB_Immune_Loss_Fraction": 0
}

Transmission_Blocking_Immunity_Decay_Rate float 0 1000 0.001 The rate at which transmission-blocking immunity decays after the base transmission-blocking immunity offset period. Used only when Enable_Immunity and Enable_Immune_Decay parameters are set to true (1).
{
    "Transmission_Blocking_Immunity_Decay_Rate": 0.01
}
Transmission_Blocking_Immunity_Duration_Before_Decay float 0 45000 0 The number of days after infection until transmission-blocking immunity begins to decay. Only used when Enable_Immunity and Enable_Immune_Decay parameters are set to true (1).
{
    "Transmission_Blocking_Immunity_Duration_Before_Decay": 90
}

Incubation

The following parameters determine the characteristics of the incubation period.

Parameter Data type Minimum Maximum Default Description Example
Base_Incubation_Period float 0 3.40E+38 6 Average duration, in days, of the incubation period before infected individuals become infectious. Incubation_Period_Distribution must be set to either FIXED_DURATION or EXPONENTIAL_DURATION.
{
    "Incubation_Period_Distribution": "EXPONENTIAL_DURATION",
    "Base_Incubation_Period": 1
}
Incubation_Period_Distribution enum NA NA NOT_INITIALIZED

The distribution for the duration of the incubation period. Possible values are:

NOT_INITIALIZED
No distribution set.
FIXED_DURATION
Base_Incubation_Period is the constant duration incubation period.
UNIFORM_DURATION
Incubation_Period_Min and Incubation_Period_Max define the ranges of a uniform random draw for the duration of the incubation period.
GAUSSIAN_DURATION
Incubation_Period_Mean and Incubation_Period_Std_Dev define the mean and standard deviation of the Gaussian from which the incubation period is drawn. Negative values are truncated at zero.
EXPONENTIAL_DURATION
Base_Incubation_Period is the mean of the exponential random draw.
POISSON_DURATION
Incubation_Period_Mean is the mean of the random Poisson draw.
LOG_NORMAL_DURATION
Incubation_Period_Log_Mean is the mean of log normal and Incubation_Period_Log_Width is the log width of log normal.
BIMODAL_DURATION
The distribution is bimodal, the duration is a fraction of Base_Incubation_Period for a specified period of time and equal to Base_Incubation_Period otherwise.
PIECEWISE_CONSTANT
The distribution is specified with a list of years and a matching list of values. The duration at a given year is that specified for the nearest previous year.
PIECEWISE_LINEAR
The distribution is specified with a list of years and matching list of values. The duration at a given year is a linear interpolation of the specified values.
WEIBULL_DURATION
The duration is a Weibull distribution with a given scale and shape.
DUAL_TIMESCALE_DURATION
The duration is two exponential distributions with given means.
{
    "Base_Incubation_Period": 5,
    "Incubation_Period_Distribution": "EXPONENTIAL_DURATION"
}
Incubation_Period_Log_Mean float 0 3.40E+38 6 The mean of log normal for the incubation period distribution. Incubation_Period_Distribution must be set to LOG_NORMAL_DURATION.
{
    "Incubation_Period_Distribution": "LOG_NORMAL_DURATION",
    "Incubation_Period_Log_Mean": 5.758,
    "Incubation_Period_Log_Width": 0.27
}
Incubation_Period_Log_Width float 0 3.40E+38 1 The log width of log normal for the incubation period distribution. Incubation_Period_Distribution must be set to LOG_NORMAL_DURATION.
{
    "Incubation_Period_Distribution": "LOG_NORMAL_DURATION",
    "Incubation_Period_Log_Mean": 5.758,
    "Incubation_Period_Log_Width": 0.27
}
Incubation_Period_Max float 0.6 3.40E+38 0 The maximum length of the incubation period. Incubation_Period_Distribution must be set to UNIFORM_DURATION.
{
    "Incubation_Period_Distribution": "UNIFORM_DURATION",
    "Incubation_Period_Min": 2,
    "Incubation_Period_Max": 6
}
Incubation_Period_Mean float 0 3.40E+38 6 The mean of the incubation period. Incubation_Period_Distribution must be set to either GAUSSIAN_DURATION or POISSON_DURATION.
{
    "Incubation_Period_Distribution": "GAUSSIAN_DURATION",
    "Incubation_Period_Mean": 7,
    "Infectious_Period_Std_Dev": 2
}
Incubation_Period_Min float 0 3.40E+38 0 The minimum length of the incubation period. Incubation_Period_Distribution must be set to UNIFORM_DURATION.
{
    "Incubation_Period_Distribution": "UNIFORM_DURATION",
    "Incubation_Period_Min": 2,
    "Incubation_Period_Max": 6
}
Incubation_Period_Std_Dev float 0 3.40E+38 1 The standard deviation incubation period. Incubation_Period_Distribution must be set to GAUSSIAN_DURATION.
{
    "Incubation_Period_Distribution": "GAUSSIAN_DURATION",
    "Incubation_Period_Mean": 7,
    "Infectious_Period_Std_Dev": 2
}

Infectivity and transmission

The following parameters determine aspects of infectivity and disease transmission. For example, how infectious individuals are and the length of time for which they remain infectious, whether the disease can be maternally transmitted, and how population density affects infectivity.

Parameter Data type Minimum Maximum Default Description Example
Base_Infectious_Period float 0 3.40E+38 6 Average duration, in days, of the infectious period before the infection is cleared. Infectious_Period_Distribution must be set to either FIXED_DURATION or EXPONENTIAL_DURATION.
{
    "Base_Infectious_Period": 4
}
Base_Infectivity float 0 1000 0.3 The base infectiousness of individuals before accounting for transmission-blocking effects of acquired immunity and/or campaign interventions.
{
    "Base_Infectivity": 0.5
}
Enable_Heterogeneous_Intranode_Transmission boolean 0 1 0

Controls whether or not individuals experience heterogeneous disease transmission within a node. When set to true (1), individual property definitions and the \beta matrix must be specified in the demographics file (see NodeProperties and IndividualProperties parameters). The \beta values are multiplied with the \beta 0 value configured by Base_Infectivity.

This is used only in generic simulations, but must be set to false (0) for all other simulation types. Heterogeneous transmission for other diseases uses other mechanistic parameters included with the simulation type.

{
    "Enable_Heterogeneous_Intranode_Transmission": 1
}
Enable_Maternal_Transmission boolean 0 1 0 Controls whether or not infectious mothers infect infants at birth. Enable_Birth must be set to true (1).
{
    "Enable_Birth": 1,
    "Enable_Maternal_Transmission": 1
}
Enable_Superinfection boolean 0 1 0 Controls whether or not an individual can have multiple infections simultaneously. Set to true (1) to allow for multiple simultaneous infections; set to false (0) if multiple infections are not possible. Set the Max_Individual_Infections parameter.
{
    "Enable_Superinfection": 1,
    "Max_Individual_Infections": 2
}
Infection_Updates_Per_Timestep integer 0 144 1 The number of infection updates executed during each timestep; note that a timestep defaults to one day.
{
    "Infection_Updates_Per_Timestep": 1
}	
Infectious_Period_Distribution enum NA NA NOT_INITIALIZED

The distribution of the duration of the infectious period.

Possible values are:

NOT_INITIALIZED
No distribution set.
FIXED_DURATION
Base_Infectious_Period is the constant-duration infectious period.
UNIFORM_DURATION
Infectious_Period_Min and Infectious_Period_Max define the ranges of a uniform random draw for the duration of the infectious period.
GAUSSIAN_DURATION
Infectious_Period_Mean and Infectious_Period_Std_Dev define the mean and standard deviation of the Gaussian from which the infectious period is drawn. Negative values are truncated at zero.
EXPONENTIAL_DURATION
Base_Infectious_Period is the mean of the exponential random draw.
POISSON_DURATION
Infectious_Period_Mean is the mean of the random Poisson draw.
LOG_NORMAL_DURATION
The duration is a log normal distribution defined by a specified mean and log width.
BIMODAL_DURATION
The distribution is bimodal, the duration is a fraction of Base_Incubation_Period for a specified period of time and equal to Base_Incubation_Period otherwise.
PIECEWISE_CONSTANT
The distribution is specified with a list of years and a matching list of values. The duration at a given year is that specified for the nearest previous year.
PIECEWISE_LINEAR
The distribution is specified with a list of years and matching list of values. The duration at a given year is a linear interpolation of the specified values.
WEIBULL_DURATION
The duration is a Weibull distribution with a given scale and shape.
DUAL_TIMESCALE_DURATION
The duration is two exponential distributions with given means.
{
    "Infectious_Period_Distribution": "EXPONENTIAL_DURATION" 
    
}	
Infectious_Period_Max float 0.6 3.40E+38 0 The maximum length of the infectious period; used when Infectious_Period_Distribution is set to UNIFORM_DURATION.
{
    "Infectious_Period_Distribution": "UNIFORM_DURATION", 
    "Infectious_Period_Max": 15, 
    "Infectious_Period_Min": 5
}
Infectious_Period_Mean float 0 3.40E+38 6 The mean of the infectious period; used when Infectious_Period_Distribution is set to either GAUSSIAN_DURATION or POISSON_DURATION.
{
    "Infectious_Period_Distribution": "GAUSSIAN_DURATION", 
    "Infectious_Period_Mean": 12, 
    "Infectious_Period_Std_Dev": 10
}
Infectious_Period_Min float 0 3.40E+38 0 The minimum length of the infectious period; used when Infectious_Period_Distribution is set to UNIFORM_DURATION.
{
    "Infectious_Period_Distribution": "UNIFORM_DURATION", 
    "Infectious_Period_Max": 15, 
    "Infectious_Period_Min": 5
}			
Infectious_Period_Std_Dev float 0 3.40E+38 1 The standard deviation of the infectious period; used when Infectious_Period_Distribution is set to GAUSSIAN_DURATION.
{
    "Infectious_Period_Distribution": "GAUSSIAN_DURATION", 
    "Infectious_Period_Mean": 12, 
    "Infectious_Period_Std_Dev": 10
}
Infectivity_Boxcar_Forcing_Amplitude float 0 3.40E+38 0 The fractional increase in R0 during the high-infectivity season when Infectivity_Scale_Type is equal to ANNUAL_BOXCAR_FUNCTION.
{
    "Infectivity_Boxcar_Forcing_Amplitude": 0.25, 
    "Infectivity_Boxcar_Forcing_End_Time": 270, 
    "Infectivity_Boxcar_Forcing_Start_Time": 90, 
    "Infectivity_Scale_Type": "ANNUAL_BOXCAR_FUNCTION"
}		
Infectivity_Boxcar_Forcing_End_Time float 0 365 0 The end of the high-infectivity season when Infectivity_Scale_Type is equal to ANNUAL_BOXCAR_FUNCTION.
{
    "Infectivity_Boxcar_Forcing_Amplitude": 0.25, 
    "Infectivity_Boxcar_Forcing_End_Time": 270, 
    "Infectivity_Boxcar_Forcing_Start_Time": 90, 
    "Infectivity_Scale_Type": "ANNUAL_BOXCAR_FUNCTION"
}		
Infectivity_Boxcar_Forcing_Start_Time float 0 365 0 The beginning of the high-infectivity season, in days, when Infectivity_Scale_Type is equal to ANNUAL_BOXCAR_FUNCTION.
{
    "Infectivity_Boxcar_Forcing_Amplitude": 0.25, 
    "Infectivity_Boxcar_Forcing_End_Time": 270, 
    "Infectivity_Boxcar_Forcing_Start_Time": 90, 
    "Infectivity_Scale_Type": "ANNUAL_BOXCAR_FUNCTION"
}		
Infectivity_Exponential_Baseline float 0 1 0 The scale factor applied to Base_Infectivity at the beginning of a simulation, before the infectivity begins to grow exponentially. Infectivity_Scale_Type must be set to EXPONENTIAL_FUNCTION_OF_TIME.
{
    "Infectivity_Exponential_Baseline": 0.1, 
    "Infectivity_Exponential_Delay": 90, 
    "Infectivity_Exponential_Rate": 45, 
    "Infectivity_Scale_Type": "EXPONENTIAL_FUNCTION_OF_TIME"
}
Infectivity_Exponential_Delay float 0 3.40E+38 0 The number of days before infectivity begins to ramp up exponentially. Infectivity_Scale_Type must be set to EXPONENTIAL_FUNCTION_OF_TIME.
{
    "Infectivity_Exponential_Baseline": 0.1, 
    "Infectivity_Exponential_Delay": 90, 
    "Infectivity_Exponential_Rate": 45, 
    "Infectivity_Scale_Type": "EXPONENTIAL_FUNCTION_OF_TIME"
}
Infectivity_Exponential_Rate float 0 3.40E+38 0 The daily rate of exponential growth to approach to full infectivity after the delay set by Infectivity_Exponential_Delay has passed. Infectivity_Scale_Type must be set to EXPONENTIAL_FUNCTION_OF_TIME.
{
    "Infectivity_Exponential_Rate": 45
}
Infectivity_Scale_Type enum NA NA CONSTANT_INFECTIVITY

A scale factor that allows infectivity to be altered by time or season. Possible values are:

CONSTANT_INFECTIVITY
No infectivity correction is applied.
FUNCTION_OF_TIME_AND_LATITUDE
Infectivity is corrected for approximate seasonal forcing. The use of a seasonal infectivity correction is a proxy for the effects of varying climate. From October through March, infectivity increases in the Northern Hemisphere and decreases in the Southern Hemisphere. From April through September, the trend reverses: regions closer to the equator have reduced forcing compared to temperate regions.
FUNCTION_OF_CLIMATE
Allows infectivity to be modulated by weather directly, for example, relative humidity in airborne simulations or rainfall in waterborne simulations. There is no default climate dependence enabled for generic simulations.
EXPONENTIAL_FUNCTION_OF_TIME
To facilitate certain burn-in scenarios, infectivity ramps up from zero at the beginning of the simulation according to the functional form, 1-exp(-rate*time), where the rate is specified by the parameter Infectivity_Scaling_Rate.
SINUSOIDAL_FUNCTION_OF_TIME
Allows infectivity to be time-dependent, following a sinusoidal shape.
ANNUAL_BOXCAR_FUNCTION
Allows infectivity to follow a boxcar function, such that it will be equal to zero for an entire time period (e.g. year) except for a single interval in which it is equal to a constant.
{
    "Infectivity_Scale_Type": "FUNCTION_OF_CLIMATE"
}
Infectivity_Sinusoidal_Forcing_Amplitude float 0 1 0 Sets the amplitude of sinusoidal variations in Base_Infectivity. Only used when Infectivity_Scale_Type is set to SINUSOIDAL_FUNCTION_OF_TIME.
{
    "Infectivity_Scale_Type": "SINUSOIDAL_FUNCTION_OF_TIME", 
    "Infectivity_Sinusoidal_Forcing_Amplitude": 0.1, 
    "Infectivity_Sinusoidal_Forcing_Phase": 0
}	
Infectivity_Sinusoidal_Forcing_Phase float 0 365 0 Sets the phase of sinusoidal variations in Base_Infectivity. Only used when Infectivity_Scale_Type is set to SINUSOIDAL_FUNCTION_OF_TIME.
{
    "Infectivity_Scale_Type": "SINUSOIDAL_FUNCTION_OF_TIME", 
    "Infectivity_Sinusoidal_Forcing_Amplitude": 0.1, 
    "Infectivity_Sinusoidal_Forcing_Phase": 0
}	
Maternal_Transmission_Probability float 0 1 0 The probability of transmission of infection from mother to infant at birth. Enable_Maternal_Transmission must be set to 1. Note: For malaria and vector simulations, set this to 0. Instead, use the Maternal_Antibody_Protection, Maternal_Antibody_Decay_Rate, and Maternal_Antibodies_Type parameters.
{
    "Maternal_Transmission_Probability": 0.3
}
Max_Individual_Infections integer 0 1000 1 The limit on the number of infections that an individual can have simultaneously. Enable_Superinfection must be set to 1.
{
    "Max_Individual_Infections": 5
}
Population_Density_C50 float 0 3.40E+38 10 The population density at which R0 for a 2.5-arc minute square reaches half of its initial value. Population_Density_Infectivity_Correction must be set to SATURATING_FUNCTION_OF_DENSITY.
{
    "Population_Density_C50": 30
}

Population_Density_Infectivity_Correction enum NA NA CONSTANT_INFECTIVITY

Correction to alter infectivity by population density set in the Population_Density_C50 parameter. Measured in people per square kilometer. Possible values are:

  • CONSTANT_INFECTIVITY
  • SATURATING_FUNCTION_OF_DENSITY

Note

Sparsely populated areas have a lower infectivity, while densely populated areas have a higher infectivity, which rises to saturate at the Base_Infectivity value.

{
    "Population_Density_Infectivity_Correction": "SATURATING_FUNCTION_OF_DENSITY"
}

Relative_Sample_Rate_Immune float 0.001 1 0.1 The relative sampling rate for people who have acquired immunity through recovery or vaccination.
{
    "Relative_Sample_Rate_Immune": 0.1
}

Susceptibility_Scale_Type enum NA NA CONSTANT_SUSCEPTIBILITY

The effect of time or season on infectivity. Possible values are:

CONSTANT_SUSCEPTIBILITY LOG_LINEAR_FUNCTION_OF_TIME LINEAR_FUNCTION_OF_AGE LOG_LINEAR_FUNCTION_OF_AGE

{
    "Susceptibility_Scale_Type": "CONSTANT_SUSCEPTIBILITY"
}	

TB_MDR_Fitness_Multiplier float 0 1 1 The scale factor for Base_Infectivity to give the infectiousness of MDR-TB strains.
{
    "TB_MDR_Fitness_Multiplier": 0.65
}

TB_Smear_Negative_Infectivity_Multiplier float 0 1 0.25 The scale factor for Base_Infectivity to give the infectiousness of active smear-negative individuals.
{
    "TB_Smear_Negative_Infectivity_Multiplier": 1
}
Transmission_Blocking_Immunity_Decay_Rate float 0 1000 0.001 The rate at which transmission-blocking immunity decays after the base transmission-blocking immunity offset period. Used only when Enable_Immunity and Enable_Immune_Decay parameters are set to true (1).
{
    "Transmission_Blocking_Immunity_Decay_Rate": 0.01
}
Transmission_Blocking_Immunity_Duration_Before_Decay float 0 45000 0 The number of days after infection until transmission-blocking immunity begins to decay. Only used when Enable_Immunity and Enable_Immune_Decay parameters are set to true (1).
{
    "Transmission_Blocking_Immunity_Duration_Before_Decay": 90
}

Zoonosis_Rate float 0 1 0 The daily rate of zoonotic infection per individual. Animal_Reservoir_Type must be set to CONSTANT_ZOONOSIS or ZOONOSIS_FROM_DEMOGRAPHICS. If Animal_Reservoir_Type is set to ZOONOSIS_FROM_DEMOGRAPHICS, the value for the Zoonosis NodeAttribute in the demographics file will override the value set for Zoonosis_Rate.
{
    "Zoonosis_Rate": 0.005
}

Input data files

The following parameters set the paths to the the campaign file and the input data files for climate, migration, demographics, and load-balancing.

Parameter Data type Minimum Maximum Default Description Example
Air_Migration_Filename string NA NA   The path to the input data file that defines patterns of migration by airplane. Enable_Air_Migration must be set to true (1). The file must be in .bin format.
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Air_Migration" : 1,
    "Air_Migration_Filename": "../Global_1degree_air_migration.bin"
}
Air_Temperature_Filename string NA NA air_temp.json The path to the input data file that defines air temperature data measured two meters above ground. Climate_Model must be set to CLIMATE_BY_DATA. The file must be in .bin format.
{
    "Climate_Model": "CLIMATE_BY_DATA",
    "Air_Temperature_Filename": "Namawala_single_node_air_temperature_daily.bin"
}
Campaign_Filename string NA NA   The path to the campaign file. It is required when interventions are part of the simulation and Enable_Interventions is set to true (1). The file must be in .json format.
{
    "Enable_Interventions": 1,
    "Campaign_Filename": "campaign.json"
}
Demographics_Filenames array of strings NA NA   An array of the paths to demographics files containing information on the identity and demographics of the region to simulate. The files must be in .json format.
{
	"Demographics_Filenames": [    		
        "Namawala_single_node_demographics.json",
	    "Namawala_demographics_overlay.json"
	]
}
Family_Migration_Filename string NA NA   The name of the binary file to use to configure family migration. Enable_Family_Migration must be set to true (1). The file must be in .bin format.
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Family_Migration" 1,
    "Family_Migration_Filename": "../inputs/family_migration.bin"
}
Koppen_Filename string NA NA UNINITIALIZED STRING The path to the input file used to specify Koppen climate classifications; only used when Climate_Model is set to CLIMATE_KOPPEN. The file must be in .dat format.
{
    "Koppen_Filename": "Mad_2_5arcminute_koppen.dat"
}
Land_Temperature_Filename string NA NA land_temp.json The path of the input file defining temperature data measured at land surface; used only when Climate_Model is set to CLIMATE_BY_DATA. The file must be in .bin format.
{
    "Land_Temperature_Filename": "Namawala_single_node_land_temperature_daily.bin"
}

Load_Balance_Filename string NA NA UNINITIALIZED STRING The path to the input file used when a static load balancing scheme is selected. The file must be in .json format.
{
    "Load_Balance_Filename": "GitHub_426_LoadBalance.json"
}
Local_Migration_Filename string NA NA   The path of the input file which defines patterns of migration to adjacent nodes by foot travel. The file must be in .bin format.
{
    "Local_Migration_Filename": "Local_Migration.bin"
}
Rainfall_Filename string NA NA rainfall.json The path of the input file which defines rainfall data. Climate_Model must be set to CLIMATE_BY_DATA. The file must be in .bin format.
{
    "Rainfall_Filename": "Namawala_single_node_rainfall_daily.bin"
}
Regional_Migration_Filename string NA NA   The path of the input file which defines patterns of migration by vehicle via road or rail network. If the node is not on a road or rail network, regional migration focuses on the closest hub city in the network. The file must be in .bin format.
{
    "Regional_Migration_Filename": "Regional_Migration.bin"
}

Relative_Humidity_Filename string NA NA rel_hum.json The path of the input file which defines relative humidity data measured 2 meters above ground. Climate_Model must be set to CLIMATE_BY_DATA. The file must be in .bin format.
{
    "Relative_Humidity_Filename": "Namawala_single_node_relative_humidity_daily.bin"
}
Sea_Migration_Filename string NA NA   The path of the input file which defines patterns of migration by ship. Only used when Enable_Sea_Migration is set to true (1). The file must be in .bin format.
{
    "Sea_Migration_Filename": "5x5_Households_Work_Migration.bin"
}

Serialized_Population_Filenames array of strings NA NA NA Array of filenames with serialized population data. The number of filenames must match the number of cores used for the simulation. The file must be in .dtk format.
{
    "Serialized_Population_Filenames": [
        "state-00010.dtk"
    ]
}

Serialized_Population_Path string NA NA . The root path for the serialized population files.
{
    "Serialized_Population_Path": "../00_Generic_Version_1_save/output"
}

Migration

The following parameters determine aspects of population migration into and outside of a node, including daily commutes, seasonal migration, and one-way moves. Modes of transport includes travel by foot, automobile, sea, or air. Migration can also be configured to move all individuals in a family at the same time.

Parameter Data type Minimum Maximum Default Description Example
Air_Migration_Filename string NA NA   The path to the input data file that defines patterns of migration by airplane. Enable_Air_Migration must be set to true (1). The file must be in .bin format.
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Air_Migration" : 1,
    "Air_Migration_Filename": "../Global_1degree_air_migration.bin"
}
Air_Migration_Roundtrip_Duration float 0 10000 1 The average time spent (in days) at the destination node during a round-trip migration by airplane. Enable_Air_Migration must be set to true (1).
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Air_Migration" : 1,
    "Air_Migration_Roundtrip_Duration": 2
}
Air_Migration_Roundtrip_Probability float 0 1 0.8 The likelihood that an individual who flies to another node will return to the node of origin during the next migration. Enable_Air_Migration must be set to true (1).
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Air_Migration" : 1,
    "Air_Migration_Roundtrip_Probability": 0.9
}
Enable_Air_Migration boolean 0 1 0 Controls whether or not migration by air travel will occur. Migration_Model must be set to FIXED_RATE_MIGRATION.
{
     "Migration_Model": "FIXED_RATE_MIGRATION",
     "Enable_Air_Migration": 1,
     "Air_Migration_Filename": "../inputs/air_migration.bin"
}
Enable_Family_Migration boolean 0 1 0 Controls whether or not all members of a household can migrate together. All residents must be home before they can leave on the trip. Migration_Model must be set to FIXED_RATE_MIGRATION.
{
    "Enable_Migration": "FIXED_RATE_MIGRATION",
    "Enable_Family_Migration": 1,
    "Family_Migration_Filename": "../inputs/family_migration.bin"
}
Enable_Local_Migration boolean 0 1 0 Controls whether or not local migration (the diffusion of people in and out of nearby nodes by foot travel) occurs. Migration_Model must be set to FIXED_RATE_MIGRATION.
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Local_Migration": 1,
    "Local_Migration_Filename": "../inputs/local_migration.bin"
}
Enable_Migration_Heterogeneity boolean 0 1 1 Controls whether or not migration rate is heterogeneous among individuals. Set to true (1) to use a migration rate distribution in the demographics file (see NodeAttributes parameters); set to false (0) to use the same migration rate applied to all individuals. Migration_Model must be set to FIXED_RATE_MIGRATION.
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Migration_Heterogeneity": 1
}
Enable_Regional_Migration boolean 0 1 0 Controls whether or not there is migration by road vehicle into and out of nodes in the road network. Migration_Model must be set to FIXED_RATE_MIGRATION.
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Regional_Migration": 1,
    "Regional_Migration_Filename": "../inputs/regional_migration.bin"
}
Enable_Sea_Migration boolean 0 1 0 Controls whether or not there is migration on ships into and out of coastal cities with seaports. Migration_Model must be set to FIXED_RATE_MIGRATION.
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Sea_Migration": 1,
    "Sea_Migration_Filename": "../inputs/sea_migration.bin"
}
Family_Migration_Filename string NA NA   The name of the binary file to use to configure family migration. Enable_Family_Migration must be set to true (1). The file must be in .bin format.
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Family_Migration" 1,
    "Family_Migration_Filename": "../inputs/family_migration.bin"
}
Family_Migration_Roundtrip_Duration float 0 10000 1 The number of days to complete the trip and return to the original node. Migration_Pattern must be set to SINGLE_ROUND_TRIPS.
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Migration_Pattern": "SINGLE_ROUND_TRIPS",
    "Family_Migration_Roundtrip_Duration": 100
}
Local_Migration_Filename string NA NA   The path of the input file which defines patterns of migration to adjacent nodes by foot travel. The file must be in .bin format.
{
    "Local_Migration_Filename": "Local_Migration.bin"
}
Local_Migration_Roundtrip_Duration float 0 10000 1 The average time spent (in days) at the destination node during a round-trip migration by foot travel. Only used if Enable_Local_Migration is set to true (1).
{
    "Local_Migration_Roundtrip_Duration": 1.0
}
Local_Migration_Roundtrip_Probability float 0 1 0.95 The likelihood that an individual who walks into a neighboring cell will return to the cell of origin during the next migration. Only used when Enable_Local_Migration is set to true (1).
{
    "Local_Migration_Roundtrip_Probability": 1.0
}
Migration_Model enum NA NA NO_MIGRATION

Model to use for migration. Possible values are:

NO_MIGRATION
Migration into and out of nodes will not occur.
FIXED_RATE_MIGRATION
Migration into and out of nodes will occur at a fixed rate as defined in the migration files. At the beginning of the simulation or whenever an individual has just moved, they pick their next destination and the time and type of the migration. If an individual is on an outbound leg of their journey, they will query the node’s MigrationInfo object and, through probability, pick a new destination; if the individual is inbound, they will travel back to their previous location.
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Local_Migration_Filename": "../inputs/local_migration.bin",
    "Enable_Local_Migration": 1
}
Migration_Pattern enum NA NA RANDOM_WALK_DIFFUSION

Describes the type of roundtrip used during migration. Migration_Model must be set to FIXED_RATE_MIGRATION. Possible values are:

RANDOM_WALK_DIFFUSION
Individuals retain no memory of where they came from; every move is to a new destination with no thought of returning home.
SINGLE_ROUND_TRIPS
There is a certain probability that an individual’s move will be a roundtrip (determined Local_Migration_Roundtrip_Probability, Air_Migration_Roundtrip_Probability, etc.). Otherwise, the departure point is forgotten and the individual does not return to their original location.
WAYPOINTS_HOME
Individuals go on a multi-step journey along several waypoints and then retrace their steps back along their path once they have reached a maximum number of waypoints from their home.
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Migration_Pattern": "SINGLE_ROUND_TRIPS"
}
Regional_Migration_Filename string NA NA   The path of the input file which defines patterns of migration by vehicle via road or rail network. If the node is not on a road or rail network, regional migration focuses on the closest hub city in the network. The file must be in .bin format.
{
    "Regional_Migration_Filename": "Regional_Migration.bin"
}

Regional_Migration_Roundtrip_Duration float 0 10000 1 The average time spent (in days) at the destination node during a round-trip migration by road network. Enable_Regional_Migration must be set to true (1).
{
    "Regional_Migration_Roundtrip_Duration": 1.0
}

Regional_Migration_Roundtrip_Probability float 0 1 0.1 The likelihood that an individual who travels by vehicle to another cell will return to the cell of origin during the next migration. Migration_Pattern must be set to SINGLE_ROUND_TRIPS.
{
    "Regional_Migration_Roundtrip_Probability": 1.0
}
Roundtrip_Waypoints integer 0 1000 10 The maximum number of points reached during a trip before steps are retraced on the return trip home. Migration_Pattern must be set to WAYPOINTS_HOME.
{
    "Roundtrip_Waypoints": 5
}
Sea_Migration_Filename string NA NA   The path of the input file which defines patterns of migration by ship. Only used when Enable_Sea_Migration is set to true (1). The file must be in .bin format.
{
    "Sea_Migration_Filename": "5x5_Households_Work_Migration.bin"
}

Sea_Migration_Roundtrip_Duration float 0 10000 1 The average time spent at the destination node during a round-trip migration by ship. Used only when Enable_Sea_Migration is set to true (1).
{
    "Sea_Migration_Roundtrip_Duration": 10000
}
Sea_Migration_Roundtrip_Probability float 0 1 0.25 The likelihood that an individual who travels by ship into a neighboring cell will return to the cell of origin during the next migration. Used only when Enable_Sea_Migration is set to true (1).
{
    "Sea_Migration_Roundtrip_Probability": 0
}
x_Air_Migration float 0 3.40E+38 1 Scale factor for the rate of migration by air, as provided by the migration file. Enable_Air_Migration must be set to 1.
{
    "x_Air_Migration": 1
}
x_Family_Migration float 0 3.40E+38 1 Scale factor for the rate of migration by families, as provided by the migration file. Enable_Family_Migration must be set to true (1).
{
    "x_Family_Migration": 1
}
x_Local_Migration float 0 3.40E+38 1 Scale factor for rate of migration by foot travel, as provided by the migration file. Enable_Local_Migration must be set to 1.
{
    "x_Local_Migration": 1
}
x_Regional_Migration float 0 3.40E+38 1 Scale factor for the rate of migration by road vehicle, as provided by the migration file. Enable_Regional_Migration must be set to 1.
{
    "x_Regional_Migration": 1
}
x_Sea_Migration float 0 3.40E+38 1 Scale factor for the rate of migration by sea, as provided by the migration file. Enable_Sea_Migration must be set to 1.
{
    "x_Sea_Migration": 1
}

Mortality and survival

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

Parameter Data type Minimum Maximum Default Description Example
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_Vital_Dynamics must be set to true (1).

This parameter is not used in this simulation type and any values set here will be overridden.

{
    "Enable_Vital_Dynamics": 1,
    "Mortality_Time_Course": "DAILY_MORTALITY",
    "Base_Mortality": 0.01
}
Death_Rate_Dependence enum NA NA NONDISEASE_MORTALITY_OFF

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

NONDISEASE_MORTALITY_OFF
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_OFF"
}
Mortality_Blocking_Immunity_Decay_Rate float 0 1000 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. 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. 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. This parameter, TB_Drug_Inactivation_Rate, TB_Drug_Relapse_Rate, and TB_Drug_Clearance_Rate specify the daily probability of a change in the TB disease state during the course of treatment. The sum of these rates and the total duration of treatment specify the probability that any event occurs. If no event occurs, the individual fails drug treatment.
{	
    "TB_Drug_Params": {
        "BurninDrug": {
            "TB_Drug_Clearance_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_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.
{
    "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, as provided by the demographics file (see Complex distributions parameters). Enable_Vital_Dynamics must be set to 1.
{
    "x_Other_Mortality": 1
}

Output settings

The following parameters configure whether or not output reports are created for the simulation, such as reports detailing spatial or demographic data at each time step. By default, the Inset chart output report is always created.

Parameter Data type Minimum Maximum Default Description Example
Custom_Reports_Filename string NA NA UNINITIALIZED STRING The name of the file containing custom report configuration parameters. Omitting this parameter or setting it to RunAllCustomReports will load all reporters found that are valid for the given simulation type. The file must be in JSON format.
{  
    "Custom_Reports_Filename": "custom_reports.json"
}
Enable_Default_Reporting boolean 0 1 1 Controls whether or not the default InsetChart.json report is created.
{
    "Enable_Default_Reporting": 1
}
Enable_Demographics_Reporting boolean 0 1 1 Controls whether or not demographic summary data and age-binned reports are outputted to file.
{
    "Enable_Demographics_Reporting": 1
}
Enable_Property_Output boolean 0 1 0 Controls whether or not to create property output reports, which detail groups as defined in IndividualProperties in the demographics file (see NodeProperties and IndividualProperties parameters). When there is more than one property type, the report will display the channel information for all combinations of the property type groups.
{
    "Enable_Property_Output": 1
}
Enable_Spatial_Output boolean 0 1 0

Controls whether or not spatial output reports are created. If set to true (1), spatial output reports include all channels listed in the parameter Spatial_Output_Channels.

Note

Spatial output files require significant processing time and disk space.

{
    "Enable_Spatial_Output": 1,
    "Spatial_Output_Channels": [
        "Prevalence",
        "New_Infections"
    ]
}
Report_Event_Recorder boolean 0 1 0 Set to true (1) to enable or to false (0) to disable the ReportEventRecorder.csv output report.
{
    "Report_Event_Recorder": 1, 
    "Report_Event_Recorder_Events": [
        "VaccinatedA", 
        "VaccineExpiredA", 
        "VaccinatedB", 
        "VaccineExpiredB"
    ], 
    "Report_Event_Recorder_Ignore_Events_In_List": 0 
}			
Report_Event_Recorder_Events array NA NA   The list of events to include or exclude in the ReportEventRecorder.csv output report, based on how Report_Event_Recorder_Ignore_Events_In_List is set.
{
    "Report_Event_Recorder": 1, 
    "Report_Event_Recorder_Events": [
        "VaccinatedA", 
        "VaccineExpiredA", 
        "VaccinatedB", 
        "VaccineExpiredB"
    ], 
    "Report_Event_Recorder_Ignore_Events_In_List": 0 
}				
Report_Event_Recorder_Ignore_Events_In_List boolean 0 1 0

If set to false (0), only the events listed in the Report_Event_Recorder_Events array will be included in the ReportEventRecorder.csv output report. If set to true (1), only the events listed in the array will be excluded, and all other events will be included. If you want to return all events from the simulation, leave the events array empty.

Value Events array Output file
0 No events No events
0 One or more events Only the listed events.
1 No events All events occurring in the simulation.
1 One or more events All simulation events occurring in the simulation, except for those listed.
{
    "Report_Event_Recorder": 1, 
    "Report_Event_Recorder_Events": [
        "VaccinatedA", 
        "VaccineExpiredA", 
        "VaccinatedB", 
        "VaccineExpiredB"
    ], 
    "Report_Event_Recorder_Ignore_Events_In_List": 0 
}			
Report_Event_Recorder_Individual_Properties array of strings NA NA [] Specifies an array of events that will be excluded from the property output report; all events NOT listed in the array will be included in the report. To report all events from the simulation, leave the events array empty.

This example demonstrates reporting all individual property events:

{
    "Report_Event_Recorder_Individual_Properties": []
}	

The following example demonstrates the syntax for excluding particular properties from the report:

{
    "Report_Event_Recorder_Individual_Properties": [
        "Accessibility", 
        "Risk"
    ]
}	
Spatial_Output_Channels array of strings NA NA []

An array of channel names for spatial output by node and time step. The data from each channel will be written to a separate binary file. Enable_Spatial_Output must be set to true (1). Possible values are:

Air_Temperature
Data related to air temperature.
Births
Data related to the number of births.
Campaign_Cost
Data related to the costs of a campaign.
Disease_Deaths
Data related to the number of deaths due to disease.
Human_Infectious_Reservoir
Data related to the total infectiousness of the population.
Infection_Rate
Data related to infection rates.
Land_Temperature
Data related to the average land temperature over all nodes.
New_Infections
Data related to the presence of new infections.
New_Reported_Infections
Data related to the presence of reported new infections.
Population
Data related to the total population in the simulation.
Prevalence
Data related to the fraction of the population that is infected.
Rainfall
Data related to the presence of rainfall.
Relative_Humidity
Data related to the presence of relative humidity.
{
    "Spatial_Output_Channels": [
        "Prevalence",
        "New_Infections"
    ]
}        

Population dynamics

The following parameters determine characteristics related to population dynamics, such as age distribution, births, deaths, and gender. The values set here generally interact closely with values in the demographics file.

Parameter Data type Minimum Maximum Default Description Example
Age_Initialization_Distribution_Type enum NA NA DISTRIBUTION_OFF

The method for initializing the age distribution in the simulated population. Possible values are:

DISTRIBUTION_OFF
All individuals default to age 20 years old.
DISTRIBUTION_SIMPLE
Individual ages are drawn from a distribution whose functional form is specified in the demographics file using the IndividualAttributes simple Age distribution parameters.
DISTRIBUTION_COMPLEX
Individual ages are drawn from a piecewise linear function specified in the demographics file complex distribution parameters.
{
    "Age_Initialization_Distribution_Type": "DISTRIBUTION_SIMPLE"
}
Base_Population_Scale_Factor float 0 3.40E+38 1 The scale factor for InitialPopulation in the demographics file (see NodeAttributes parameters). If Population_Scale_Type is set to FIXED_SCALING, the initial simulation population is uniformly scaled over the entire area to adjust for historical or future population density.
{
    "Base_Population_Scale_Factor": 0.0001
}
Birth_Rate_Boxcar_Forcing_Amplitude float 0 3.40E+38 0 Fractional increase in birth rate during high birth season when Birth_Rate_Time_Dependence is set to ANNUAL_BOXCAR_FUNCTION.
{
    "Enable_Vital_Dynamics": 1,
    "Enable_Birth": 1,
    "Birth_Rate_Time_Dependence": "ANNUAL_BOXCAR_FUNCTION",
    "Birth_Rate_Boxcar_Forcing_Amplitude": 0.1
}
Birth_Rate_Boxcar_Forcing_End_Time float 0 365 0 Day of the year when the high birth rate season ends when Birth_Rate_Time_Dependence is set to ANNUAL_BOXCAR_FUNCTION.
{
    "Enable_Vital_Dynamics": 1,
    "Enable_Birth": 1,
    "Birth_Rate_Time_Dependence": "ANNUAL_BOXCAR_FUNCTION", 
    "Birth_Rate_Boxcar_Forcing_End_Time": 220
}
Birth_Rate_Boxcar_Forcing_Start_Time float 0 365 0 Day of the year when the high birth rate season begins when Birth_Rate_Time_Dependence is set to ANNUAL_BOXCAR_FUNCTION.
{
    "Enable_Vital_Dynamics": 1,
    "Enable_Birth": 1,
    "Birth_Rate_Time_Dependence": "ANNUAL_BOXCAR_FUNCTION",
    "Birth_Rate_Boxcar_Forcing_Start_Time": 130
}
Birth_Rate_Dependence enum NA NA FIXED_BIRTH_RATE

The method used to modify the value set in BirthRate in the demographics file (see NodeAttributes parameters). Possible values are:

NONE
Births are not allowed during the simulation, even if Enable_Birth is set to true (1).
FIXED_BIRTH_RATE
The absolute rate at which new individuals are born, as set by BirthRate.
POPULATION_DEP_RATE
Scales the node population to determine the birth rate. If BirthRate is greater than 0.005, a value of 2% per year (0.02/365) is used instead.
DEMOGRAPHIC_DEP_RATE
Scales the female population within fertility age ranges to determine the birth rate. If BirthRate is greater than 0.005, a value of 1 child every 8 years of fertility [1/8/365(~0.000342)] is used instead.
INDIVIDUAL_PREGNANCIES
Scales the female population within fertility age ranges to determine the birth rate, but pregnancies are assigned on an individual basis and result in a 40-week pregnancy for a specific individual with a birth at the end.
INDIVIDUAL_PREGNANCIES_BY_URBAN_AND_AGE
Similar to INDIVIDUAL_PREGNANCIES, but determines the rate based on the FertilityDistribution (in IndividualAttributes) and Urban (in NodeAttributes), as well as the individual’s age.
INDIVIDUAL_PREGNANCIES_BY_AGE_AND_YEAR
Similar to INDIVIDUAL_PREGNANCIES, but determines the rate based on the FertilityDistribution (in IndividualAttributes), using the individual’s age and the year of the simulation.
{
    "Enable_Vital_Dynamics": 1,
    "Enable_Birth": 1,
    "Birth_Rate_Dependence": "POPULATION_DEP_RATE"
}
Birth_Rate_Sinusoidal_Forcing_Amplitude float 0 1 0 The amplitude of sinusoidal variations in birth rate when Birth_Rate_Time_Dependence is set to SINUSOIDAL_FUNCTION_OF_TIME.
{
    "Enable_Vital_Dynamics": 1,
    "Enable_Birth": 1,
    "Birth_Rate_Time_Dependence": "SINUSOIDAL_FUNCTION_OF_TIME",
    "Birth_Rate_Sinusoidal_Forcing_Amplitude": 0.1
}
Birth_Rate_Sinusoidal_Forcing_Phase float 0 365 0 The phase of sinusoidal variations in birth rate. Birth_Rate_Time_Dependence must be set to SINUSOIDAL_FUNCTION_OF_TIME.
{
    "Birth_Rate_Sinusoidal_Forcing_Phase": 20
}
Birth_Rate_Time_Dependence enum NA NA NONE

A scale factor that allows the birth rate to be altered by time or season. Enable_Birth must be set to true (1). Possible values are:

NONE
Birth rate does not vary by time.
SINUSOIDAL_FUNCTION_OF_TIME
Allows birth rate to be time-dependent, following a sinusoidal shape. Set Birth_Rate_Sinusoidal_Forcing_Amplitude and Birth_Rate_Sinusoidal_Forcing_Phase.
ANNUAL_BOXCAR_FUNCTION
Allows birth rate to follow a boxcar function, such that it will be equal to zero for an entire time period (e.g. year) except for a single interval in which it is equal to a constant. Set Birth_Rate_Boxcar_Forcing_Amplitude, Birth_Rate_Boxcar_Forcing_End_Time, and Birth_Rate_Boxcar_Forcing_Start_Time.
{
    "Enable_Vital_Dynamics": 1,
    "Enable_Birth": 1,
    "Birth_Rate_Time_Dependence": "ANNUAL_BOXCAR_FUNCTION"
}
Death_Rate_Dependence enum NA NA NONDISEASE_MORTALITY_OFF

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

NONDISEASE_MORTALITY_OFF
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_OFF"
}
Default_Geography_Initial_Node_Population integer 0 1000000 1000 When using the built-in demographics for default geography, the initial number of individuals in each node. Note that the built-in demographics feature does not represent a real geographical location and is mostly used for testing. Enable_Demographics_Builtin must be set to true (1).
{
    "Enable_Demographics_Builtin": 1,
    "Default_Geography_Initial_Node_Population": 1000,
    "Default_Geography_Torus_Size": 3
}
Demographics_Filenames array of strings NA NA   An array of the paths to demographics files containing information on the identity and demographics of the region to simulate. The files must be in .json format.
{
	"Demographics_Filenames": [    		
        "Namawala_single_node_demographics.json",
	    "Namawala_demographics_overlay.json"
	]
}
Enable_Aging boolean 0 1 1 Controls whether or not individuals in a population age during the simulation. Enable_Vital_Dynamics must be set to true (1).
{
    "Enable_Vital_Dynamics": 1,
    "Enable_Aging": 1
}
Enable_Birth boolean 0 1 1 Controls whether or not individuals will be added to the simulation by birth. Enable_Vital_Dynamics must be set to true (1). If you want new individuals to have the same intervention coverage as existing individuals, you must add a BirthTriggeredIV to the campaign file.
{
    "Enable_Vital_Dynamics": 1,
    "Enable_Birth": 1
}
Enable_Demographics_Birth boolean 0 1 0 Controls whether or not newborns have identical or heterogeneous characteristics. Set to false (0) to give all newborns identical characteristics; set to true (1) to allow for heterogeneity in traits such as sickle-cell status. Enable_Birth must be set to true (1).
{
    "Enable_Birth": 1,
    "Enable_Demographics_Birth": 1
}
Enable_Demographics_Builtin boolean 0 1 0 Controls whether or not built-in demographics for default geography will be used. Note that the built-in demographics feature does not represent a real geographical location and is mostly used for testing. Set to true (1) to define the initial population and number of nodes using Default_Geography_Initial_Node_Population and Default_Geography_Torus_Size. Set to false (0) to use demographics input files defined in Demographics_Filenames.
{
    "Enable_Demographics_Builtin": 1,
    "Default_Geography_Initial_Node_Population": 1000,
    "Default_Geography_Torus_Size": 3
}
Enable_Demographics_Gender boolean 0 1 1 Controls whether or not gender ratios are drawn from a Gaussian or 50/50 draw. Set to true (1) to create gender ratios drawn from a male/female ratio that is randomly smeared by a Gaussian of width 1%; set to false (0) to assign a gender ratio based on a 50/50 draw.
{
    "Enable_Demographics_Gender": 1
}
Enable_Demographics_Other boolean 0 1 0 Controls whether or not other demographic factors are included in the simulation, such as the fraction of individuals above poverty, urban/rural characteristics, heterogeneous initial immunity, or risk. These factors are set in the demographics file.
{
    "Enable_Demographics_Other": 1
}
Enable_Disease_Mortality boolean 0 1 1 Controls whether or not individuals die due to disease.
{
    "Enable_Disease_Mortality": 1
}
Enable_Vital_Dynamics boolean 0 1 1 Controls whether or not births and deaths occur in the simulation. Births and deaths must be individually enabled and set.
{
    "Enable_Vital_Dynamics":1,
    "Enable_Birth": 1,
    "Death_Rate_Dependence": "NONDISEASE_MORTALITY_OFF",
    "Base_Mortality": 0.002
}
Minimum_Adult_Age_Years float 0 3.40E+38 15 The age, in years, after which an individual is considered an adult. Individual_Sampling_Type must be set to ADAPTED_SAMPLING_BY_AGE_GROUP.
{
    "Minimum_Adult_Age_Years": 17
}
Population_Density_Infectivity_Correction enum NA NA CONSTANT_INFECTIVITY

Correction to alter infectivity by population density set in the Population_Density_C50 parameter. Measured in people per square kilometer. Possible values are:

  • CONSTANT_INFECTIVITY
  • SATURATING_FUNCTION_OF_DENSITY

Note

Sparsely populated areas have a lower infectivity, while densely populated areas have a higher infectivity, which rises to saturate at the Base_Infectivity value.

{
    "Population_Density_Infectivity_Correction": "SATURATING_FUNCTION_OF_DENSITY"
}

Population_Scale_Type enum NA NA USE_INPUT_FILE

The method to use for scaling the initial population specified in the demographics input file. Possible values are:

USE_INPUT_FILE
Turns off population scaling and uses InitialPopulation in the demographics file (see NodeAttributes parameters).
FIXED_SCALING
Enables Base_Population_Scale_Factor.
{
    "Population_Scale_Type": "FIXED_SCALING"
}

x_Birth float 0 3.40E+38 1 Scale factor for birth rate, as provided by the demographics file (see NodeAttributes parameters). Enable_Birth must be set to 1.
{
    "x_Birth": 1
}

Sampling

The following parameters determine how a population is sampled in the simulation. While you may want every agent (individual object) to represent a single person, you can often optimize CPU time with without degrading the accuracy of the simulation but having an agent represent multiple people. The sampling rate may be adapted to have a higher or lower sampling rate for particular regions or age groups.

Parameter Data type Minimum Maximum Default Description Example
Base_Individual_Sample_Rate float 0 1 1 The base rate of sampling for individuals, equal to the fraction of individuals in each node being sampled. Reducing the sampling rate will reduce the time needed to run simulations. Individual_Sampling_Type must be set to FIXED_SAMPLING or ADAPTED_SAMPLING_BY_IMMUNE_STATE.
{
    "Base_Individual_Sample_Rate": 0.01
}
Immune_Threshold_For_Downsampling float 0 1 0 Threshold on acquisition immunity at which to apply immunity dependent downsampling. Individual_Sampling_Type must set to ADAPTED_SAMPLING_BY_IMMUNE_STATE.
{
    "Individual_Sampling_Type": "ADAPTED_SAMPLING_BY_IMMUNE_STATE", 
    "Immune_Threshold_For_Downsampling": 0.5
}
Individual_Sampling_Type enum NA NA TRACK_ALL

The type of individual human sampling. Possible values are:

TRACK_ALL
Each person in the population is tracked as a single Individual object with a sampling weight of 1.
FIXED_SAMPLING
Members of the population are added to the simulation with a probability of Base_Individual_Sample_Rate and sampling weight of 1 / Base_Individual_Sample_Rate. This allows a smaller set of Individual objects to represent the overall population.
ADAPTED_SAMPLING_BY_POPULATION_SIZE
For each node, a maximum number of Individual objects is tracked (set in Max_Node_Population_Samples). If the population is smaller than this number, each person is tracked with a sampling rate of 1; if the population is larger, members of the population are added to the simulation with a probability of Max_Node_Population_Samples / population and sampling weight of population / Max_Node_Population_Samples. This setting is useful for simulations over large geographic areas with large heterogeneities in population density.
ADAPTED_SAMPLING_BY_AGE_GROUP
The population is binned by age and each age bin is sampled at a different rate as defined by Sample_Rate parameters. The setting is useful for diseases in which only infants or children are relevant by allowing full sampling of these age groups while using fewer objects to represent the rest of the population.
ADAPTED_SAMPLING_BY_AGE_GROUP_AND_POP_SIZE
Each node has a maximum number of Individual objects as described in ADAPTED_SAMPLING_BY_POPULATION_SIZE, but when the population grows beyond that threshold, sampling is not done at a fixed rate, but varies by age as described in ADAPTED_SAMPLING_BY_AGE_GROUP.
ADAPTED_SAMPLING_BY_IMMUNE_STATE
Individuals who have acquired immunity are sampled at a lower rate as defined by Relative_Sample_Rate_Immune and Immune_Threshold_For_Downsampling parameters.

The following example shows how to sampling immune individuals at a lower rate.

{
    "Individual_Sampling_Type": "ADAPTED_SAMPLING_BY_IMMUNE_STATE",
    "Immune_Threshold_For_Downsampling": 0.5,  
    "Relative_Sample_Rate_Immune": 0.1 
}

The following example shows how to sampling older individuals at a lower rate.

{
    "Individual_Sampling_Type": "ADAPTED_SAMPLING_BY_AGE_GROUP",
    "Sample_Rate_0_18mo": 1, 
    "Sample_Rate_10_14": 0.5, 
    "Sample_Rate_15_19": 0.3, 
    "Sample_Rate_18mo_4yr": 1, 
    "Sample_Rate_20_Plus": 0.2, 
    "Sample_Rate_5_9": 1, 
    "Sample_Rate_Birth": 1
}
Max_Node_Population_Samples float 1 3.40E+38 30 The maximum number of individuals to track in a node. When the population exceeds this number, the sampling rate will drop according to the value set in Individual_Sampling_Type.
{
    "Individual_Sampling_Type": "ADAPTED_SAMPLING_BY_POPULATION_SIZE",
    "Max_Node_Population_Samples": 100000
}
Relative_Sample_Rate_Immune float 0.001 1 0.1 The relative sampling rate for people who have acquired immunity through recovery or vaccination.
{
    "Relative_Sample_Rate_Immune": 0.1
}

Sample_Rate_0_18mo float 0 1000 1 For age-adapted sampling, the relative sampling rate for infants age 0 to 18 months. Individual_Sampling_Type must be set to ADAPTED_SAMPLING_BY_AGE_GROUP or ADAPTED_SAMPLING_BY_AGE_GROUP_AND_POP_SIZE.
{
    "Sample_Rate_0_18mo": 1
}
Sample_Rate_10_14 float 0 1000 1 For age-adapted sampling, the relative sampling rate for children age 10 to 14 years. Individual_Sampling_Type must be set to ADAPTED_SAMPLING_BY_AGE_GROUP or ADAPTED_SAMPLING_BY_AGE_GROUP_AND_POP_SIZE.
{
    "Sample_Rate_10_14": 1
}
Sample_Rate_15_19 float 0 1000 1 For age-adapted sampling, the relative sampling rate for adolescents age 15 to 19 years. Individual_Sampling_Type must be set to ADAPTED_SAMPLING_BY_AGE_GROUP or ADAPTED_SAMPLING_BY_AGE_GROUP_AND_POP_SIZE.
{
    "Sample_Rate_15_19": 1
}
Sample_Rate_18mo_4yr float 0 1000 1 For age-adapted sampling, the relative sampling rate for children age 18 months to 4 years. Individual_Sampling_Type must be set to ADAPTED_SAMPLING_BY_AGE_GROUP or ADAPTED_SAMPLING_BY_AGE_GROUP_AND_POP_SIZE.
{
    "Sample_Rate_18mo_4yr": 1
}

Sample_Rate_20_plus float 0 1000 1 For age-adapted sampling, the relative sampling rate for adults age 20 and older. Individual_Sampling_Type must be set to ADAPTED_SAMPLING_BY_AGE_GROUP or ADAPTED_SAMPLING_BY_AGE_GROUP_AND_POP_SIZE.
{
    "Sample_Rate_20_plus": 1
}
Sample_Rate_5_9 float 0 1000 1 For age-adapted sampling, the relative sampling rate for children age 5 to 9 years. Individual_Sampling_Type must be set to ADAPTED_SAMPLING_BY_AGE_GROUP or ADAPTED_SAMPLING_BY_AGE_GROUP_AND_POP_SIZE.
{
    "Sample_Rate_5_9": 1
}
Sample_Rate_Birth float 0 1000 1 For age-adapted sampling, the relative sampling rate for births. Individual_Sampling_Type must be set to ADAPTED_SAMPLING_BY_AGE_GROUP or ADAPTED_SAMPLING_BY_AGE_GROUP_AND_POP_SIZE.
{
    "Sample_Rate_Birth": 1
}

Scalars and multipliers

The following parameters scale or multiply values set in other areas of the configuration file or input data files. This can be especially useful for understanding the sensitivities of disease dynamics to input data without requiring modifications to those base values. For example, one might set x_Birth to a value less than 1 to simulate a lower future birth rate due to increased economic prosperity and available medical technology.

Parameter Data type Minimum Maximum Default Description Example
Base_Population_Scale_Factor float 0 3.40E+38 1 The scale factor for InitialPopulation in the demographics file (see NodeAttributes parameters). If Population_Scale_Type is set to FIXED_SCALING, the initial simulation population is uniformly scaled over the entire area to adjust for historical or future population density.
{
    "Base_Population_Scale_Factor": 0.0001
}
Birth_Rate_Time_Dependence enum NA NA NONE

A scale factor that allows the birth rate to be altered by time or season. Enable_Birth must be set to true (1). Possible values are:

NONE
Birth rate does not vary by time.
SINUSOIDAL_FUNCTION_OF_TIME
Allows birth rate to be time-dependent, following a sinusoidal shape. Set Birth_Rate_Sinusoidal_Forcing_Amplitude and Birth_Rate_Sinusoidal_Forcing_Phase.
ANNUAL_BOXCAR_FUNCTION
Allows birth rate to follow a boxcar function, such that it will be equal to zero for an entire time period (e.g. year) except for a single interval in which it is equal to a constant. Set Birth_Rate_Boxcar_Forcing_Amplitude, Birth_Rate_Boxcar_Forcing_End_Time, and Birth_Rate_Boxcar_Forcing_Start_Time.
{
    "Enable_Vital_Dynamics": 1,
    "Enable_Birth": 1,
    "Birth_Rate_Time_Dependence": "ANNUAL_BOXCAR_FUNCTION"
}
Immunity_Acquisition_Factor float 0 1000 0 The multiplicative reduction in the probability of reacquiring disease. Only used when Enable_Immunity and Enable_Immune_Decay are set to 1.
{
    "Enable_Immunity": 1,
    "Enable_Immune_Decay": 1,
    "Immunity_Acquisition_Factor": 0.9
}
Infectivity_Exponential_Baseline float 0 1 0 The scale factor applied to Base_Infectivity at the beginning of a simulation, before the infectivity begins to grow exponentially. Infectivity_Scale_Type must be set to EXPONENTIAL_FUNCTION_OF_TIME.
{
    "Infectivity_Exponential_Baseline": 0.1, 
    "Infectivity_Exponential_Delay": 90, 
    "Infectivity_Exponential_Rate": 45, 
    "Infectivity_Scale_Type": "EXPONENTIAL_FUNCTION_OF_TIME"
}
Population_Scale_Type enum NA NA USE_INPUT_FILE

The method to use for scaling the initial population specified in the demographics input file. Possible values are:

USE_INPUT_FILE
Turns off population scaling and uses InitialPopulation in the demographics file (see NodeAttributes parameters).
FIXED_SCALING
Enables Base_Population_Scale_Factor.
{
    "Population_Scale_Type": "FIXED_SCALING"
}

Susceptibility_Scale_Type enum NA NA CONSTANT_SUSCEPTIBILITY

The effect of time or season on infectivity. Possible values are:

CONSTANT_SUSCEPTIBILITY LOG_LINEAR_FUNCTION_OF_TIME LINEAR_FUNCTION_OF_AGE LOG_LINEAR_FUNCTION_OF_AGE

{
    "Susceptibility_Scale_Type": "CONSTANT_SUSCEPTIBILITY"
}	

TB_Active_Presymptomatic_Infectivity_Multiplier float 0 1 0.0274 The scale factor for Base_Infectivity to give the infectiousness of active presymptomatic individuals.
{
    "TB_Active_Presymptomatic_Infectivity_Multiplier": 0.19999999999999998
}
TB_Drug_Efficacy_Multiplier_Failed float 0 1 1 The scale factor for drug efficacy parameters (TB_Drug_Inactivation_Rate and TB_Drug_Clearance_Rate) to give the efficacy of first-line drugs when given to individuals who have failed treatment.
{
    "TB_Drug_Efficacy_Multiplier_Failed": 1.0
}

TB_Drug_Efficacy_Multiplier_MDR float 0 1 1 The scale factor for drug efficacy parameters (TB_Drug_Inactivation_Rate and TB_Drug_Clearance_Rate) to give the efficacy of first-line drugs when given to individuals with MDR-TB.
{
    "TB_Drug_Efficacy_Multiplier_MDR": 1.0
}

TB_Drug_Efficacy_Multiplier_Relapsed float 0 1 1 The scale factor for drug efficacy parameters (TB_Drug_Inactivation_Rate and TB_Drug_Clearance_Rate) to give the efficacy of first-line drugs when given to individuals who have relapsed after treatment.
{
    "TB_Drug_Efficacy_Multiplier_Relapsed": 1.0
}

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.
{
    "TB_Extrapulmonary_Mortality_Multiplier": 1
}
TB_MDR_Fitness_Multiplier float 0 1 1 The scale factor for Base_Infectivity to give the infectiousness of MDR-TB strains.
{
    "TB_MDR_Fitness_Multiplier": 0.65
}

TB_Smear_Negative_Infectivity_Multiplier float 0 1 0.25 The scale factor for Base_Infectivity to give the infectiousness of active smear-negative individuals.
{
    "TB_Smear_Negative_Infectivity_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_Air_Migration float 0 3.40E+38 1 Scale factor for the rate of migration by air, as provided by the migration file. Enable_Air_Migration must be set to 1.
{
    "x_Air_Migration": 1
}
x_Birth float 0 3.40E+38 1 Scale factor for birth rate, as provided by the demographics file (see NodeAttributes parameters). Enable_Birth must be set to 1.
{
    "x_Birth": 1
}
x_Family_Migration float 0 3.40E+38 1 Scale factor for the rate of migration by families, as provided by the migration file. Enable_Family_Migration must be set to true (1).
{
    "x_Family_Migration": 1
}
x_Local_Migration float 0 3.40E+38 1 Scale factor for rate of migration by foot travel, as provided by the migration file. Enable_Local_Migration must be set to 1.
{
    "x_Local_Migration": 1
}
x_Other_Mortality float 0 3.40E+38 1 Scale factor for mortality from causes other than the disease being simulated, as provided by the demographics file (see Complex distributions parameters). Enable_Vital_Dynamics must be set to 1.
{
    "x_Other_Mortality": 1
}

x_Regional_Migration float 0 3.40E+38 1 Scale factor for the rate of migration by road vehicle, as provided by the migration file. Enable_Regional_Migration must be set to 1.
{
    "x_Regional_Migration": 1
}
x_Sea_Migration float 0 3.40E+38 1 Scale factor for the rate of migration by sea, as provided by the migration file. Enable_Sea_Migration must be set to 1.
{
    "x_Sea_Migration": 1
}

Simulation setup

These parameters determine the basic setup of a simulation including the type of simulation you are running, such as “GENERIC_SIM” or “MALARIA_SIM”, the simulation duration, and the time step duration.

Parameter Data type Minimum Maximum Default Description Example
Base_Year float 1900 2200 2015

The absolute time in years when the simulation begins. This can be combined with CampaignEventByYear to trigger campaign events.

This parameter is not used in this simulation type.

{
    "Base_Year": 1960
}
Config_Name string NA NA UNINITIALIZED STRING The optional, user-supplied title naming a configuration file.
{
     "Config_Name": "My_First_Config"
}
Enable_Interventions boolean 0 1 0 Controls whether or not campaign interventions will be used in the simulation. Set Campaign_Filename to the path of the file that contains the campaign interventions.
{
    "Enable_Interventions": 1,
    "Campaign_Filename": "campaign.json"
}
Listed_Events array of strings NA NA [] The list of valid, user-defined events that will be included in the campaign. Any event used in the campaign must either be one of the built-in events or in this list.
{
    "Listed_Events": [
        "Vaccinated",
        "VaccineExpired"
    ]
}
Memory_Usage_Halting_Threshold_Working_Set_MB integer 0 1.00E+06 8000 The maximum size (in MB) of working set memory before the system throws an exception and halts.
{
    "Memory_Usage_Halting_Threshold_Working_Set_MB": 4000
}
Memory_Usage_Warning_Threshold_Working_Set_MB integer 0 1.00E+06 7000 The maximum size (in MB) of working set memory before memory usage statistics are written to the log regardless of log level.
{
    "Memory_Usage_Warning_Threshold_Working_Set_MB": 3500
}
Node_Grid_Size float 0.00416 90 0.004167 The spatial resolution indicating the node grid size for a simulation in degrees.
{
    "Node_Grid_Size": 0.042
}
Number_Basestrains integer 1 10 1 The number of base strains in the simulation, such as antigenic variants.
{
    "Number_Basestrains": 1
}
Num_Cores integer NA NA NA The number of cores used to run a simulation.
{
    "Num_Cores": 4
}
Run_Number integer 0 2147480000 1 Sets the random number seed through a bit manipulation process. When running a multi-core simulation, combines with processor rank to produce independent random number streams for each process.
{
    "Run_Number": 1
}
Serialization_Time_Steps array of integers 0 2.15E+09   The list of time steps after which to save the serialized state. 0 (zero) indicates the initial state before simulation, n indicates after the nth time step. By default, no serialized state is saved.
{
    "Serialization_Time_Steps": [
        0, 
        10
    ]
}
Serialized_Population_Filenames array of strings NA NA NA Array of filenames with serialized population data. The number of filenames must match the number of cores used for the simulation. The file must be in .dtk format.
{
    "Serialized_Population_Filenames": [
        "state-00010.dtk"
    ]
}

Serialized_Population_Path string NA NA . The root path for the serialized population files.
{
    "Serialized_Population_Path": "../00_Generic_Version_1_save/output"
}

Simulation_Duration float 0 1000000 1 The elapsed time (in days) from the start to the end of a simulation.
{
    "Simulation_Duration": 7300
}
Simulation_Timestep float 0 1000000 1 The duration of a simulation time step, in days.
{
    "Simulation_Timestep": 1
}	

Simulation_Type enum NA NA GENERIC_SIM

The type of disease being simulated. Possible IDM-supported values are:

  • GENERIC_SIM
  • VECTOR_SIM
  • MALARIA_SIM
  • TB_SIM
  • STI_SIM
  • HIV_SIM
{
    "Simulation_Type": "STI_SIM"
}	

Start_Time float 0 1000000 1

The time, in days, when the simulation begins. This time is used to identify the starting values of the temporal input data, such as specifying which day’s climate values should be used for the first day of the simulation.

Note

The Start_Day of campaign events is in absolute time, so time relative to the beginning of the simulation depends on this parameter.

{
    "Start_Time": 365
}	

Symptoms and diagnosis

The following parameters determine the characteristics of tuberculosis diagnosis and symptoms.

Parameter Data type Minimum Maximum Default Description Example
TB_Extrapulmonary_Fraction_Adult float 0 1 0 The fraction of active cases in adults (age 15 or over) that are extrapulmonary. The sum of this and TB_Smear_Positive_Fraction_Adult must be less than or equal to 1.
{
    "TB_Extrapulmonary_Fraction_Adult": 0.33
}	

TB_Extrapulmonary_Fraction_Child float 0 1 0 The fraction of active cases in children (under age 15) that are extrapulmonary. The sum of this and TB_Smear_Positive_Fraction_Child must be less than or equal to 1.
{
    "TB_Extrapulmonary_Fraction_Child": 0.33
}

TB_Smear_Negative_Infectivity_Multiplier float 0 1 0.25 The scale factor for Base_Infectivity to give the infectiousness of active smear-negative individuals.
{
    "TB_Smear_Negative_Infectivity_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
}
TB_Smear_Positive_Fraction_Adult float 0 1 1 The fraction of active cases in adults (age 15 and over) that are smear-positive. The sum of TB_Smear_Positive_Fraction_Adult and TB_Extrapulmonary_Fraction_Adult must be less than or equal to 1. This sum plus the fraction of smear-negative adults is equal to 1.
{
    "TB_Smear_Positive_Fraction_Adult": 1
}
TB_Smear_Positive_Fraction_Child float 0 1 1 The fraction of active cases in children (under age 15) that are smear-positive. The sum of TB_Smear_Positive_Fraction_Child and TB_Extrapulmonary_Fraction_Child must be less than or equal to 1. This sum plus the fraction of smear-negative children is equal to 1.
{
    "TB_Smear_Positive_Fraction_Child": 1
}