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.
Note
Parameters are case-sensitive. For Boolean parameters, set to 1 for true or 0 for false. Minimum, maximum, or default values of “NA” indicate that those values are not applicable for that parameter.
EMOD does not use true defaults; that is, if the dependency relationships indicate that a parameter is required, you must supply a value for it. However, many of the tools used to work with EMOD will use the default values provided below.
JSON format does not permit comments, but you can add “dummy” parameters to add contextual information to your files. Any keys that are not EMOD parameter names will be ignored by the model.
Parameter |
Data type |
Minimum |
Maximum |
Default |
Description |
Example |
|---|---|---|---|---|---|---|
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 disease risk drawn from a distribution; uniform disease risk if false. Enable_Birth, Enable_Demographics_Risk, and Enable_Vital_Dynamics must be set to true (1). |
{
"Enable_Birth": 1,
"Enable_Demographics_Birth": 1,
"Enable_Vital_Dynamics": 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_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_Demographics_Risk |
boolean |
0 |
1 |
0 |
Controls whether or not the simulation includes the impact of disease risk in demographics. |
{
"Enable_Demographics_Risk": 1
}
|
Enable_Disease_Mortality |
boolean |
0 |
1 |
1 |
Controls whether or not individuals are removed from the simulation due to disease deaths. |
{
"Enable_Disease_Mortality": 1
}
|
Enable_Egg_Mortality |
boolean |
0 |
1 |
0 |
Controls whether or not to include a daily mortality rate on the egg population, which is independent of climatic factors. |
{
"Enable_Egg_Mortality": 1
}
|
Enable_Family_Migration |
boolean |
0 |
1 |
0 |
Controls whether or not all members of a household can migrate together when a MigrateFamily event occurs. 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, environmental, and typhoid 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_Immunity |
boolean |
0 |
1 |
1 |
Controls whether or not an individual has protective immunity after an infection clears. |
{
"Enable_Immunity": 1
}
|
Enable_Infectivity_Reservoir |
boolean |
0 |
1 |
0 |
Controls whether or not an exogeneous reservoir of infectivity will be included in the simulation and allows for the infectivity in a node to be increased additively. When set to 1 (true), the demographics parameter InfectivityReservoirSize is expected in NodeAtttributes for each node. Warning Do not set both Enable_Infectivity_Reservoir and Enable_Strain_Tracking to true (1) - as this combination will cause an exception error. |
{
"Enable_Infectivity_Reservoir": 1
}
|
Enable_Initial_Prevalence |
boolean |
0 |
1 |
0 |
Controls whether or not parameters in the demographics file are used to define a distribution for the number of infected people per node at the beginning of the simulation. Set the distribution under NodeAttributes using PrevalenceDistributionFlag, PrevalenceDistribution1, and PrevalenceDistribution2. |
{
"Enable_Initial_Prevalence": 1
}
|
Enable_Initial_Susceptibility_Distribution |
boolean |
0 |
1 |
0 |
Controls whether or not individuals in the population have immunity at the beginning of the simulation. If set to 0, individuals are not initialized with immunity but may acquire immunity. If set to 1, you must indicate the type of distribution to use for immunity in the configuration parameter Susceptibility_Initialization_Distribution_Type and the distribution values in the demographics file. Enable_Immunity must be set to 1. |
{
"Enable_Immunity": 1,
"Enable_Initial_Susceptibility_Distribution": 1,
"Susceptibility_Initialization_Distribution_Type": "DISTRIBUTION_SIMPLE"
}
|
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_Protection |
boolean |
0 |
1 |
0 |
Controls whether or not mothers pass immunity on to their infants. Setting to 1 (true) enables maternal protection as defined by Maternal_Protection_Type. Enable_Birth must be set to 1 (true). |
{
"Enable_Maternal_Protection": 1,
"Maternal_Protection_Type": "LINEAR_FRACTIONAL"
}
|
Enable_Migration_Heterogeneity |
boolean |
0 |
1 |
1 |
Controls whether or not migration rate is heterogeneous among individuals within each group that has a migration rate setting. Set to true (1) to apply a migration rate distribution (see NodeAttributes demographics parameters); set to false (0) to use the same migration rate applied to all individuals in the group. For example, if you are using a migration file that sets different migration rates for each age group in a node, you could apply an Gaussian distribution around a mean value in each age group or you could assign the same value to each individual in each age group. Migration_Model must be set to FIXED_RATE_MIGRATION. |
{
"Migration_Model": "FIXED_RATE_MIGRATION",
"Enable_Migration_Heterogeneity": 1
}
|
Enable_Natural_Mortality |
boolean |
0 |
1 |
0 |
Controls whether or not individuals are removed from the simulation due to natural (non-disease) deaths. Enable_Vital_Dynamics must be set to 1 (true). Use Death_Rate_Dependence to set the natural death rate. |
{
"Enable_Natural_Mortality": 1,
"Enable_Vital_Dynamics": 1
}
|
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 or rail network into and out of nodes in the simulation. 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_Strain_Tracking |
boolean |
0 |
1 |
0 |
Enable an association of an infection with a specified strain, defined by unique integers for a clade and a genome. For infections distributed through interventions, you specify clade and genome values using the Clade and Genome parameters with the Outbreak and OutbreakIndividual intervention classes in the campaign file. When using an initial prevalence distribution, you specify clade and genome values using the InitialPrevalenceStrains parameter as part of IndividualAttributes in the demographics file. When Enable_Strain_Tracking is set to false (0) or absent, all infections are associated with a single strain that has clade and genome identity (0, 0). When Enable_Strain_Tracking is set to true (1) then both Number_of_Clades and Log2_Number_of_Genomes_per_Clade parameters must be specified. Warning Do not set both Enable_Strain_Tracking and Enable_Infectivity_Reservoir to true (1) or Enable_Strain_Tracking and Enable_Maternal_Infection_Transmission to true (1) - as these combinations will cause an exception error. |
{
"Enable_Strain_Tracking": 1,
"Log2_Number_of_Genomes_per_Clade": 8,
"Number_of_Clades": 2
}
|
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_Vector_Aging |
boolean |
0 |
1 |
0 |
Controls whether or not vectors senesce as they get older. When enabled, the daily mortality rate (1/Adult_Life_Expectancy) is modified by environmental conditions such as dry heat, feeding on humans, etc. With vector aging enabled, Adult_Life_Expectancy equal to 20 days corresponds to a mean adult female mosquito lifespan of 9-9.5 days in calibrated settings. The senescence formula that EMOD uses was described by Styer, et al <https://www.ncbi.nlm.nih.gov/pubmed/17255238>. |
{
"Enable_Vector_Aging": 1,
"Adult_Life_Expectancy": 20
}
|
Enable_Vector_Migration |
boolean |
0 |
1 |
0 |
Controls whether or not vectors can migrate. Vector_Sampling_Type must be set to TRACK_ALL_VECTORS or SAMPLE_IND_VECTORS. Specific migration types must be enabled or disabled. |
{
"Vector_Sampling_Type": "TRACK_ALL_VECTORS",
"Enable_Vector_Migration": 1,
"Enable_Vector_Migration_Local": 1,
"Vector_Migration_Filename_Local": "../inputs/vector_local.bin"
}
|
Enable_Vector_Migration_Local |
boolean |
0 |
1 |
0 |
Controls whether or not vectors may migrate to adjacent nodes. Enable_Vector_Migration must be set to true (1). |
{
"Vector_Sampling_Type": "TRACK_ALL_VECTORS",
"Enable_Vector_Migration": 1,
"Enable_Vector_Migration_Local": 1,
"Vector_Migration_Filename_Local": "../inputs/vector_local.bin"
}
|
Enable_Vector_Migration_Regional |
boolean |
0 |
1 |
0 |
Controls whether or not vectors can migration to non-adjacent nodes. Enable_Vector_Migration must be set to true (1). |
{
"Vector_Sampling_Type": "TRACK_ALL_VECTORS",
"Enable_Vector_Migration": 1,
"Enable_Vector_Migration_Regional": 1,
"Vector_Migration_Filename_Regional": "../inputs/vector_regional.bin"
}
|
Enable_Vector_Mortality |
boolean |
0 |
1 |
1 |
Controls whether or not vectors can die. Vector_Sampling_Type must be set to TRACK_ALL_VECTORS. |
{
"Vector_Sampling_Type": "TRACK_ALL_VECTORS",
"Enable_Vector_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": "NOT_INITIALIZED",
"Base_Mortality": 0.002
}
|