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 malaria 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.
Contents
- Drugs and treatments
- Enable or disable features
- General disease
- Geography and environment
- Immunity
- Incubation
- Infectivity and transmission
- Input data files
- Larval habitat
- Migration
- Mortality and survival
- Output settings
- Parasite dynamics
- Population dynamics
- Sampling
- Scalars and multipliers
- Simulation setup
- Symptoms and diagnosis
- Vector control
- Vector life cycle
Drugs and treatments¶
The following parameters determine the efficacy of drugs and other treatments.
For more information on the drugs used to treat malaria, see Antimalarial drugs.
Parameter | Data type | Minimum | Maximum | Default | Description | Example |
---|---|---|---|---|---|---|
Bodyweight_Exponent | float | 0 | 100000 | 0 | The effect of bodyweight on maximum drug concentration in an individual patient. Drug_Cmax is divided by patient bodyweight raised to the power of Bodyweight_Exponent to account for the influence of body size on volume of distribution. | {
"Malaria_Drug_Params": {
"Artemether_Lumefantrine": {
"Bodyweight_Exponent": 2
}
}
}
|
Drug_Cmax | float | 0 | 100000 | 1000 | The maximum drug concentration used. Note This parameter and the Drug_PKPD_C50 parameter must use the same units. |
{
"Malaria_Drug_Params": {
"Artemether_Lumefantrine": {
"Drug_Cmax": 1000,
"Drug_PKPD_C50": 100
}
}
}
|
Drug_Decay_T1 | float | 0 | 100000 | 1 | The primary drug decay rate, in days. | {
"Malaria_Drug_Params": {
"Artemisinin": {
"Drug_Decay_T1": 1,
"Drug_Decay_T2": 1
}
}
}
|
Drug_Decay_T2 | float | 0 | 100000 | 1 | The secondary drug decay rate, in days. | {
"Malaria_Drug_Params": {
"Artemisinin": {
"Drug_Decay_T1": 1,
"Drug_Decay_T2": 1
}
}
}
|
Drug_Dose_Interval | float | 0 | 100000 | 1 | The interval between doses of drugs, in days. | {
"Malaria_Drug_Params": {
"Artemisinin": {
"Drug_Dose_Interval": 1
}
}
}
|
Drug_Fulltreatment_Doses | float | 1 | 100000 | 3 | The number of doses for a full treatment of a drug. | {
"Malaria_Drug_Params": {
"Chloroquine": {
"Drug_Fulltreatment_Doses": 3
}
}
}
|
Drug_Gametocyte02_Killrate | float | 0 | 100000 | 0 | The log reduction per day in early-stage gametocytes. | {
"Malaria_Drug_Params": {
"Chloroquine": {
"Drug_Gametocyte02_Killrate": 0,
"Drug_Gametocyte34_Killrate": 0,
"Drug_GametocyteM_Killrate": 0
}
}
}
|
Drug_Gametocyte34_Killrate | float | 0 | 100000 | 0 | The log reduction per day in late-stage gametocytes. | {
"Malaria_Drug_Params": {
"Chloroquine": {
"Drug_Gametocyte02_Killrate": 0,
"Drug_Gametocyte34_Killrate": 0,
"Drug_GametocyteM_Killrate": 0
}
}
}
|
Drug_GametocyteM_Killrate | float | 0 | 100000 | 0 | The log reduction per day in mature gametocyte numbers at saturated drug concentrations. | {
"Malaria_Drug_Params": {
"Chloroquine": {
"Drug_Gametocyte02_Killrate": 0,
"Drug_Gametocyte34_Killrate": 0,
"Drug_GametocyteM_Killrate": 0
}
}
}
|
Drug_Hepatocyte_Killrate | float | 0 | 100000 | 0 | The log reduction in hepatocyte numbers per day. | {
"Malaria_Drug_Params": {
"Chloroquine": {
"Drug_Hepatocyte_Killrate": 0
}
}
}
|
Drug_PKPD_C50 | float | 0 | 100000 | 100 | The concentration at which drug killing rates are half of the maximum. Note This parameter and the Drug_Cmax parameter must use the same units. |
{
"Malaria_Drug_Params": {
"Artemether_Lumefantrine": {
"Drug_Cmax": 1000,
"Drug_PKPD_C50": 100
}
}
}
|
Drug_Vd | float | 0 | 100000 | 10 | The volume of drug distribution in a pharmacokinetic two compartment model. The first compartment comprises central organs and tissues and the second compartment comprises peripheral tissues. This value is the ratio of the volume of the second compartment to that of the first. | {
"Malaria_Drug_Params": {
"Chloroquine": {
"Drug_Vd": 3
}
}
}
|
Fractional_Dose_By_Upper_Age | array of JSON objects | NA | NA | NA | An array to specify the fraction of the adult dose to use for children at various ages. Contains Upper_Age_In_Years and Fraction_Of_Adult_Dose values. | {
"Malaria_Drug_Params": {
"Artemether": {
"Fractional_Dose_By_Upper_Age": [{
"Fraction_Of_Adult_Dose": 0.25,
"Upper_Age_In_Years": 3
}, {
"Fraction_Of_Adult_Dose": 0.5,
"Upper_Age_In_Years": 6
}, {
"Fraction_Of_Adult_Dose": 0.75,
"Upper_Age_In_Years": 10
}]
}
}
}
|
Fraction_Of_Adult_Dose | float | 0 | 1 | NA | The fraction of the adult drug dose given to children below the age defined in Upper_Age_In_Years. Set in the Fractional_Dose_By_Upper_Age array. | {
"Malaria_Drug_Params": {
"Artemether": {
"Fractional_Dose_By_Upper_Age": [{
"Fraction_Of_Adult_Dose": 0.25,
"Upper_Age_In_Years": 3
}, {
"Fraction_Of_Adult_Dose": 0.5,
"Upper_Age_In_Years": 6
}, {
"Fraction_Of_Adult_Dose": 0.75,
"Upper_Age_In_Years": 10
}]
}
}
}
|
Malaria_Drug_Params | JSON object | NA | NA | NA | This JSON structure contains the names of anti-malarial drugs and the parameters that define them. | {
"Malaria_Drug_Params": {
"Artemether_Lumefantrine": {
"Bodyweight_Exponent": 0,
"Drug_Cmax": 1000,
"Drug_Decay_T1": 1,
"Drug_Decay_T2": 1,
"Drug_Dose_Interval": 1,
"Drug_Fulltreatment_Doses": 3,
"Drug_Gametocyte02_Killrate": 2.3,
"Drug_Gametocyte34_Killrate": 2.3,
"Drug_GametocyteM_Killrate": 0,
"Drug_Hepatocyte_Killrate": 0,
"Drug_PKPD_C50": 100,
"Drug_Vd": 10,
"Max_Drug_IRBC_Kill": 4.6
},
"Artemisinin": {
"Bodyweight_Exponent": 0,
"Drug_Cmax": 1000,
"Drug_Decay_T1": 1,
"Drug_Decay_T2": 1,
"Drug_Dose_Interval": 1,
"Drug_Fulltreatment_Doses": 3,
"Drug_Gametocyte02_Killrate": 2.3,
"Drug_Gametocyte34_Killrate": 2.3,
"Drug_GametocyteM_Killrate": 0,
"Drug_Hepatocyte_Killrate": 0,
"Drug_PKPD_C50": 100,
"Drug_Vd": 10,
"Max_Drug_IRBC_Kill": 4.61
}
}
}
|
Max_Drug_IRBC_Kill | float | 5 | 100000 | 5 | The maximum log reduction in IRBCs per day due to treatment. | {
"Malaria_Drug_Params": {
"Artemether_Lumefantrine": {
"Bodyweight_Exponent": 0,
"Drug_Cmax": 1000,
"Drug_Decay_T1": 1,
"Drug_Decay_T2": 1,
"Drug_Dose_Interval": 1,
"Drug_Fulltreatment_Doses": 3,
"Drug_Gametocyte02_Killrate": 2.3,
"Drug_Gametocyte34_Killrate": 2.3,
"Drug_GametocyteM_Killrate": 0,
"Drug_Hepatocyte_Killrate": 0,
"Drug_PKPD_C50": 100,
"Drug_Vd": 10,
"Max_Drug_IRBC_Kill": 4.61
}
}
}
|
PKPD_Model | enum | NA | NA | FIXED_DURATION_CONSTANT_EFFECT | Determines which pharmacokinetic pharmacodynamic module to use. Possible values are:
|
{
"PKPD_Model": "FIXED_DURATION_CONSTANT_EFFECT"
}
|
Upper_Age_In_Years | float | 0 | 125 | NA | The age, in years, below which children are given a fraction of the adult drug dose, as defined in Fraction_Of_Adult_Dose. Note that this parameter can be specified for each drug included in the configuration file, and different fractional doses may be used for different age groups. | {
"Malaria_Drug_Params": {
"Artemether": {
"Fractional_Dose_By_Upper_Age": [{
"Fraction_Of_Adult_Dose": 0.25,
"Upper_Age_In_Years": 3
}, {
"Fraction_Of_Adult_Dose": 0.5,
"Upper_Age_In_Years": 6
}, {
"Fraction_Of_Adult_Dose": 0.75,
"Upper_Age_In_Years": 10
}]
}
}
}
|
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_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. 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 matrix must be specified in the demographics file (see NodeProperties and IndividualProperties parameters). The values are multiplied with the 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). Set to false (0) for this simulation type. |
{
"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_Sexual_Combination | boolean | 0 | 1 | 0 | Controls whether or not male and female gametocytes undergo sexual combination. Set to true (1) to allow for sexual combination; set to false (0) for transmission of each strain only. Note This parameter is currently not in use. |
{
"Enable_Sexual_Combination": 0
}
|
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_Vector_Aging | boolean | 0 | 1 | 0 | Controls whether or not vectors undergo senescence as they age. | {
"Enable_Vector_Aging": 1
}
|
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": "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:
|
{
"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_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_In_mm_To_Fill_Swamp | float | 1 | 10000 | 1000 | Millimeters of rain to fill larval habitat to capacity. This is only used for vector species with Larval_Habitat_Types set to BRACKISH_SWAMP. | {
"Rainfall_In_mm_To_Fill_Swamp": 1000.0
}
|
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
}
|
Antibody_Capacity_Growth_Rate | float | 0 | 1 | 0.1 | The maximum daily rate of specific antibody capacity increase. Antibody production begins at a capacity of 0.3., and hyperimmunity results at 0.4. The actual growth rate tends to be lower and is a function of antigen concentrations. | {
"Antibody_Capacity_Growth_Rate": 0.09
}
|
Antibody_CSP_Decay_Days | float | 1 | 3.40E+38 | 90 | Exponential decay time for the circumsporozoite protein (CSP) antibody concentration (in days) when boosted above natural maximum concentrations. | {
"Antibody_CSP_Decay_Days": 80
}
|
Antibody_CSP_Killing_Inverse_Width | float | 1.00E-0 | 1000000 | 1.5 | The inverse width of the sigmoidal sporozoite killing function of circumsporozoite protein (CSP) antibody concentration. | {
"Antibody_CSP_Killing_Inverse_Width": 1.7
}
|
Antibody_CSP_Killing_Threshold | float | 1.00E-0 | 1000000 | 10 | The threshold value on circumsporozoite protein (CSP) antibody concentration for sporozoite killing. | {
"Antibody_CSP_Killing_Threshold": 20
}
|
Antibody_IRBC_Kill_Rate | double | NA | NA | 2 | The scale factor multiplied by antibody level to produce the rate of clearance of the infected red blood cell (IRBC) population. | {
"Antibody_IRBC_Kill_Rate": 1.595
}
|
Antibody_Memory_Level | float | 0 | 0.35 | 0.2 | The limiting level of antibody capacity that remains after a prolonged absence of a specific antigen. The antibody capacity decays to this level gradually after infection is cleared. The decay rate in antibody capacity is set so that hyperimmunity is lost within 4 months, and capacity continues to decay to this level. The antibody memory level is relevant for year-scale dynamics, but not for long-term dynamics (10-20 years). | {
"Antibody_Memory_Level": 0.3
}
|
Antibody_Stimulation_C50 | float | 0.1 | 10000 | 10 | The concentration of an antigen, measured in IRBC/ul at which growth in antibody capacity against the antigen increases at half the maximum rate specified by Antibody_Capacity_Growth_Rate. | {
"Antibody_Stimulation_C50": 30,
"Antibody_Capacity_Growth_Rate": 0.09
}
|
Antigen_Switch_Rate | double | NA | NA | 2.00E-09 | The antigenic switching rate per infected red blood cell per asexual cycle. See Parasite_Switch_Type for different switching patterns. | {
"Antigen_Switch_Rate": 5e-09
}
|
Cytokine_Gametocyte_Inactivation | float | 0 | 1 | 0.02 | The strength of inflammatory response inactivation of gametocytes. | {
"Cytokine_Gametocyte_Inactivation": 0.0167
}
|
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
}
|
Erythropoiesis_Anemia_Effect | float | 0 | 1000 | 3.5 | The exponential rate of increased red-blood-cell production from reduced red-blood-cell availability. | {
"Erythropoiesis_Anemia_Effect": 3
}
|
Falciparum_MSP_Variants | integer | 0 | 1000 | 100 | The number of distinct merozoite surface protein (MSP) variants for P. falciparum malaria in the overall parasite population in the simulation, not necessarily in an individual. | {
"Falciparum_MSP_Variants": 4
}
|
Falciparum_Nonspecific_Types | integer | 0 | 1000 | 20 | The number of distinct non-specific types of P. falciparum malaria. | {
"Falciparum_Nonspecific_Types": 92
}
|
Falciparum_PfEMP1_Variants | integer | 0 | 100000 | 1000 | The number of distinct Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) variants for P. falciparum malaria in the overall parasite population in the simulation. | {
"Falciparum_PfEMP1_Variants": 300
}
|
Fever_IRBC_Kill_Rate | float | 0 | 1000 | 0.15 | The maximum kill rate for infected red blood cells due to the inflammatory innate immune response. As fever increases above 38.5 degrees Celsius, the kill rate becomes successively higher along a sigmoidal curve approaching this rate. | {
"Fever_IRBC_Kill_Rate": 1.4
}
|
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:
|
{
"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
}
|
Innate_Immune_Variation_Type | enum | NA | NA | NONE | The type of innate immunity on which to apply individual-level variation. Possible values are:
|
{
"Innate_Immune_Variation_Type": "PYROGENIC_THRESHOLD"
}
|
Maternal_Antibodies_Type | enum | NA | NA | OFF | The type of maternal antibody protection. Possible values are:
|
{
"Maternal_Antibodies_Type": "CONSTANT_INITIAL_IMMUNITY"
}
|
Maternal_Antibody_Decay_Rate | float | 0 | 3.40E+38 | 0.01 | The decay rate per day in protection from maternal antibodies. Maternal_Antibodies_Type must be set to SIMPLE_WANING or CONSTANT_INITIAL_IMMUNITY. | {
"Maternal_Antibodies_Type": "SIMPLE_WANING",
"Maternal_Antibody_Decay_Rate": 0.01,
"Maternal_Antibody_Protection": 0.1327
}
|
Maternal_Antibody_Protection | float | 0 | 1 | 0.1 | The strength of protection from maternal antibodies as a multiple of full antibody killing effect. Maternal_Antibodies_Type must be set to SIMPLE_WANING or CONSTANT_INITIAL_IMMUNITY. | {
"Maternal_Antibodies_Type": "SIMPLE_WANING",
"Maternal_Antibody_Decay_Rate": 0.01,
"Maternal_Antibody_Protection": 0.1327
}
|
Max_MSP1_Antibody_Growthrate | float | 0 | 1 | 0.02 | The maximum increase in MSP1 antibody capacity during each asexual cycle. The higher this value, the sooner early clearances are observed and the earlier the parasite density envelope decreases. | {
"Max_MSP1_Antibody_Growthrate": 0.045
}
|
Min_Adapted_Response | float | 0 | 1 | 0.02 | The minimum level of antibody stimulation to a novel antigen. The value sets the low-range asymptote for antibody capacity growth, which is calculated from Antibody_Capacity_Growth_Rate and antigen density, in the presence of any nonzero antigen level. | {
"Min_Adapted_Response": 0.01
}
|
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
}
|
MSP1_Merozoite_Kill_Fraction | double | NA | NA | 0.5 | The fraction of merozoites inhibited from invading new erythrocytes when MSP1-specific antibody level is 1. | {
"MSP1_Merozoite_Kill_Fraction": 0.4364623975644405
}
|
Nonspecific_Antibody_Growth_Rate_Factor | float | 0 | 1000 | 0.5 | The factor that adjusts Antibody_Capacity_Growth_Rate for less immunogenic surface proteins, called minor epitopes. | {
"Nonspecific_Antibody_Growth_Rate_Factor": 0.5
}
|
Nonspecific_Antigenicity_Factor | double | NA | NA | 0.2 | The nonspecific antigenicity factor that adjusts antibody IRBC kill rate to account for IRBCs caused by antibody responses to antigenically weak surface proteins. | {
"Nonspecific_Antigenicity_Factor": 0.39192559432597257
}
|
RBC_Destruction_Multiplier | double | NA | NA | 9.5 | The number of total red blood cells destroyed per infected rupturing schizont. | {
"RBC_Destruction_Multiplier": 3.291048711
}
|
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:
|
{
"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.
The vector transmission model does not use many of the parameters provided by the generic simulation type. Instead, gametocyte abundances and cytokine mediated infectiousness are modeled explicitly. See Vector transmission model for more information.
Parameter | Data type | Minimum | Maximum | Default | Description | Example |
---|---|---|---|---|---|---|
Acquire_Modifier | float | 0 | 1 | 1 | Modifier of the probability of successful infection of a mosquito by a malaria-infected individual, given the individual’s infectiousness. | {
"Vector_Species_Params": {
"aegypti": {
"Acquire_Modifier": 1
}
}
}
|
Age_Dependent_Biting_Risk_Type | enum | NA | NA | OFF | The type of functional form for age-dependent risk. Possible values are:
|
{
"Age_Dependent_Biting_Risk_Type": "SURFACE_AREA_DEPENDENT"
}
|
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. For vector simulations, this is the probability of infecting a mosquito during a successful blood meal (modulated by the vector parameter Acquire_Modifier). The sum infectiousness of an individual is not allowed to exceed 100%. For malaria simulations, you do not use scale factors to modify this value. Instead, gametocyte abundances and cytokine mediated infectiousness are modeled explicitly. |
{
"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 matrix must be specified in the demographics file (see NodeProperties and IndividualProperties parameters). The values are multiplied with the 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). Set to false (0) for this simulation type. |
{
"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
}
|
Infected_Arrhenius_1 | float | 0 | 1.00E+15 | 1.17E+11 | The Arrhenius equation, , with T in degrees Kelvin, parameterizes the daily rate of fractional progression of infected mosquitoes to an infectious state. The duration of sporogony is a decreasing function of temperature. The variable a1 is a temperature-independent scale factor on the progression rate to infectiousness. | {
"Vector_Species_Params": {
"arabiensis": {
"Acquire_Modifier": 0.2,
"Adult_Life_Expectancy": 10,
"Anthropophily": 0.95,
"Aquatic_Arrhenius_1": 84200000000,
"Aquatic_Arrhenius_2": 8328,
"Aquatic_Mortality_Rate": 0.1,
"Cycle_Arrhenius_1": 0,
"Cycle_Arrhenius_2": 0,
"Cycle_Arrhenius_Reduction_Factor": 0,
"Days_Between_Feeds": 3,
"Egg_Batch_Size": 100,
"Immature_Duration": 4,
"Indoor_Feeding_Fraction": 0.5,
"Infected_Arrhenius_1": 117000000000,
"Infected_Arrhenius_2": 8336,
"Infected_Egg_Batch_Factor": 0.8,
"Infectious_Human_Feed_Mortality_Factor": 1.5,
"Larval_Habitat_Types": {
"TEMPORARY_RAINFALL": 11250000000
},
"Nighttime_Feeding_Fraction": 1,
"Transmission_Rate": 0.5
}
}
}
|
Infected_Arrhenius_2 | float | 0 | 1.00E+15 | 8340 | The Arrhenius equation, , with T in degrees Kelvin, parameterizes the daily rate of fractional progression of infected mosquitoes to an infectious state. The duration of sporogony is a decreasing function of temperature. The variable a2 is a temperature-dependent scale factor on the progression rate to infectiousness. | {
"Vector_Species_Params": {
"arabiensis": {
"Acquire_Modifier": 0.2,
"Adult_Life_Expectancy": 10,
"Anthropophily": 0.95,
"Aquatic_Arrhenius_1": 84200000000,
"Aquatic_Arrhenius_2": 8328,
"Aquatic_Mortality_Rate": 0.1,
"Cycle_Arrhenius_1": 0,
"Cycle_Arrhenius_2": 0,
"Cycle_Arrhenius_Reduction_Factor": 0,
"Days_Between_Feeds": 3,
"Egg_Batch_Size": 100,
"Immature_Duration": 4,
"Indoor_Feeding_Fraction": 0.5,
"Infected_Arrhenius_1": 117000000000,
"Infected_Arrhenius_2": 8336,
"Infected_Egg_Batch_Factor": 0.8,
"Infectious_Human_Feed_Mortality_Factor": 1.5,
"Larval_Habitat_Types": {
"TEMPORARY_RAINFALL": 11250000000
},
"Nighttime_Feeding_Fraction": 1,
"Transmission_Rate": 0.5
}
}
}
|
Infected_Egg_Batch_Factor | float | 0 | 10 | 0.8 | The dimensionless factor used to modify mosquito egg batch size in order to account for reduced fertility effects arising due to infection (e.g. when females undergo sporogony). | {
"Vector_Species_Params": {
"arabiensis": {
"Acquire_Modifier": 0.2,
"Adult_Life_Expectancy": 10,
"Anthropophily": 0.95,
"Aquatic_Arrhenius_1": 84200000000,
"Aquatic_Arrhenius_2": 8328,
"Aquatic_Mortality_Rate": 0.1,
"Cycle_Arrhenius_1": 0,
"Cycle_Arrhenius_2": 0,
"Cycle_Arrhenius_Reduction_Factor": 0,
"Days_Between_Feeds": 3,
"Egg_Batch_Size": 100,
"Immature_Duration": 4,
"Indoor_Feeding_Fraction": 0.5,
"Infected_Arrhenius_1": 117000000000,
"Infected_Arrhenius_2": 8336,
"Infected_Egg_Batch_Factor": 0.8,
"Infectious_Human_Feed_Mortality_Factor": 1.5,
"Larval_Habitat_Types": {
"TEMPORARY_RAINFALL": 11250000000
},
"Nighttime_Feeding_Fraction": 1,
"Transmission_Rate": 0.5
}
}
}
|
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_Human_Feed_Mortality_Factor | float | 0 | 1000 | 1.5 | The (dimensionless) factor used to modify the death rate of mosquitoes when feeding on humans, to account for the higher mortality rate infected mosquitoes experience during human feeds versus uninfected mosquitoes. | {
"Vector_Species_Params": {
"arabiensis": {
"Acquire_Modifier": 0.2,
"Adult_Life_Expectancy": 10,
"Anthropophily": 0.95,
"Aquatic_Arrhenius_1": 84200000000,
"Aquatic_Arrhenius_2": 8328,
"Aquatic_Mortality_Rate": 0.1,
"Cycle_Arrhenius_1": 0,
"Cycle_Arrhenius_2": 0,
"Cycle_Arrhenius_Reduction_Factor": 0,
"Days_Between_Feeds": 3,
"Egg_Batch_Size": 100,
"Immature_Duration": 4,
"Indoor_Feeding_Fraction": 0.5,
"Infected_Arrhenius_1": 117000000000,
"Infected_Arrhenius_2": 8336,
"Infected_Egg_Batch_Factor": 0.8,
"Infectious_Human_Feed_Mortality_Factor": 1.5,
"Larval_Habitat_Types": {
"TEMPORARY_RAINFALL": 11250000000
},
"Nighttime_Feeding_Fraction": 1,
"Transmission_Rate": 0.5
}
}
}
|
Infectious_Period_Distribution | enum | NA | NA | NOT_INITIALIZED | The distribution of the duration of the infectious period. For malaria simulations, this parameter is not used. Instead, gametocyte abundances and cytokine mediated infectiousness are modeled explicitly. Possible values are:
|
{
"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. For malaria simulations, this parameter is not used. Instead, gametocyte abundances and cytokine-mediated infectiousness are modeled explicitly. |
{
"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. For malaria simulations, this parameter is not used. Instead, gametocyte abundances and cytokine-mediated infectiousness are modeled explicitly. |
{
"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. For malaria simulations, this parameter is not used. Instead, gametocyte abundances and cytokine-mediated infectiousness are modeled explicitly. |
{
"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. For malaria simulations, this parameter is not used. Instead, gametocyte abundances and cytokine-mediated infectiousness are modeled explicitly. |
{
"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:
|
{
"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
}
|
Malaria_Strain_Model | enum | NA | NA | FALCIPARUM_NONRANDOM_STRAIN | The generator that is used to construct the antigenic repertoire of a malaria infection. To create parasite diversity, various antigenic strains are created by conducting draws for merozoite surface protein (MSP) variants, Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) variants, and minor surface epitopes, out of available populations. Each possible value for this parameter utilizes different settings for the available population draws. Possible values are:
|
{
"Malaria_Strain_Model": "FALCIPARUM_STRAIN_GENERATOR"
}
|
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:
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"
}
|
Pyrogenic_Threshold | float | 0.1 | 20000 | 1000 | The level of bloodstream infection, measured in IRBC per microliter, at which stimulation of the innate inflammatory immune response is half its maximum value. | {
"Pyrogenic_Threshold": 15000
}
|
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"
}
|
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
}
|
Transmission_Rate | float | 0 | 1 | 0.5 | The probability that the bite of an infected mosquito establishes a new infection in an immunologically naive and uninfected individual, or the modifier of the probability of success for an individual with pre-erythrocytic immunity. Note that each mosquito species will have their own Transmission_Rate parameter. | {
"Vector_Species_Params": {
"arabiensis": {
"Cycle_Arrhenius_1" : 99.0,
"Cycle_Arrhenius_2" : 88.0,
"Cycle_Arrhenius_Reduction_Factor" : 0.77,
"Nighttime_Feeding_Fraction" : 1.0,
"Acquire_Modifier": 0.2,
"Adult_Life_Expectancy": 10,
"Anthropophily": 0.95,
"Aquatic_Arrhenius_1": 84200000000,
"Aquatic_Arrhenius_2": 8328,
"Aquatic_Mortality_Rate": 0.1,
"Days_Between_Feeds": 3,
"Egg_Batch_Size": 100,
"Immature_Duration": 4,
"Indoor_Feeding_Fraction": 0.5,
"Infected_Arrhenius_1": 117000000000,
"Infected_Arrhenius_2": 8336,
"Infected_Egg_Batch_Factor": 0.8,
"Infectious_Human_Feed_Mortality_Factor": 1.5,
"Larval_Habitat_Types": {
"TEMPORARY_RAINFALL": 11250000000,
"BRACKISH_SWAMP": 10000000000
},
"Transmission_Rate": 0.5
}
}
}
|
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"
}
|
Vector_Migration_Filename_Local | string | NA | NA | UNSPECIFIED_FILE | The path to the vector migration file which defines patterns of vector migration to adjacent nodes. Enable_Vector_Migration must be set to 1. The file must be in .bin format. | {
"Vector_Migration_Filename_Local": "5x5_Households_Local_Vector_Migration.bin"
}
|
Vector_Migration_Filename_Regional | string | NA | NA | UNSPECIFIED_FILE | The path to the vector migration file which defines patterns of vector migration to non-adjacent nodes. Enable_Vector_Migration must be set to 1. The file must be in .bin format. | {
"Vector_Migration_Filename_Regional": "5x5_Households_Regional_Vector_Migration.bin"
}
|
Larval habitat¶
The following parameters determine mosquito larval development related to habitat and climate. For more information, see Larval habitat. Parameters for the vector life cycle more broadly are described in Vector life cycle.
Parameter | Data type | Minimum | Maximum | Default | Description | Example |
---|---|---|---|---|---|---|
Aquatic_Arrhenius_1 | float | 0 | 1.00E+15 | 8.42E+10 | The Arrhenius equation, , with T in degrees Kelvin, parameterizes the daily rate of fractional progression of mosquito aquatic development (egg-hatching through emergence). This duration is a decreasing function of temperature. The variable a1 is a temperature-independent scale factor on development rate. | {
"Vector_Species_Params": {
"aegypti": {
"Aquatic_Arrhenius_1": 9752291.727
}
}
}
|
Aquatic_Arrhenius_2 | float | 0 | 1.00E+15 | 8328 | The Arrhenius equation, , with T in degrees Kelvin, parameterizes the daily rate of fractional progression of mosquito aquatic development (egg-hatching through emergence). This duration is a decreasing function of temperature. The variable a2 governs how quickly the rate changes with temperature. | {
"Vector_Species_Params": {
"arabiensis": {
"Aquatic_Arrhenius_2": 8328
}
}
}
|
Aquatic_Mortality_Rate | float | 0 | 1 | 0.1 | The base aquatic mortality per day for the species before adjusting for effects of overpopulation and drying out of aquatic habitat. | {
"Vector_Species_Params": {
"arabiensis": {
"Aquatic_Mortality_Rate": 0.1
}
}
}
|
Drought_Egg_Hatch_Delay | float | 0 | 1 | 0.33 | Proportion of regular egg hatching that still occurs when habitat dries up. Enable_Drought_Egg_Hatch_Delay must be set to 1. | {
"Enable_Drought_Egg_Hatch_Delay": 1,
"Drought_Egg_Hatch_Delay": 0.33
}
|
Egg_Arrhenius1 | float | 0 | 1.00E+10 | 6.16E+07 | The Arrhenius equation, math:a_1^{-a_2/T}, with T in degrees Kelvin, parameterizes the daily rate of mosquito egg hatching. This duration is a decreasing function of temperature. The variable a1 is a temperature-independent scale factor on hatching rate. Enable_Temperature_Dependent_Egg_Hatching must be set to 1. | {
"Enable_Temperature_Dependent_Egg_Hatching": 1,
"Egg_Arrhenius1": 61599956,
"Egg_Arrhenius2": 5754
}
|
Egg_Arrhenius2 | float | 0 | 1.00E+10 | 5754.03 | The Arrhenius equation, , with T in degrees Kelvin, parameterizes the daily rate of mosquito egg hatching. This duration is a decreasing function of temperature. The variable a2 is a temperature-dependent scale factor on hatching rate. Enable_Temperature_Dependent_Egg_Hatching must be set to 1. | {
"Enable_Temperature_Dependent_Egg_Hatching": 1,
"Egg_Arrhenius1": 61599956,
"Egg_Arrhenius2": 5754
}
|
Egg_Hatch_Density_Dependence | enum | NA | NA | NO_DENSITY_DEPENDENCE | The effect of larval density on egg hatching rate. Possible values are:
|
{
"Egg_Hatch_Density_Dependence": "NO_DENSITY_DEPENDENCE"
}
|
Egg_Saturation_At_Oviposition | enum | NA | NA | NO_SATURATION | If laying all eggs from ovipositing females would overflow the larval habitat capacity on a given day, the means by which the viable eggs become saturated. Possible values are:
|
{
"Egg_Saturation_At_Oviposition": "SATURATION_AT_OVIPOSITION"
}
|
Enable_Drought_Egg_Hatch_Delay | boolean | 0 | 1 | 0 | Controls whether or not eggs hatch at delayed rates, set by Drought_Egg_Hatch_Delay, when the habitat dries up completely. | {
"Enable_Drought_Egg_Hatch_Delay": 1,
"Drought_Egg_Hatch_Delay": 0.33
}
|
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_Temperature_Dependent_Egg_Hatching | boolean | 0 | 1 | 0 | Controls whether or not temperature has an effect on egg hatching, defined by Egg_Arrhenius_1 and Egg_Arrhenius_2. | {
"Enable_Temperature_Dependent_Egg_Hatching": 1,
"Egg_Arrhenius1": 61599956.864,
"Egg_Arrhenius2": 5754.033
}
|
Larval_Density_Dependence | enum | NA | NA | UNIFORM_WHEN_OVERPOPULATION | The functional form of mortality and growth delay for mosquito larvae based on population density. Possible values are:
|
{
"Larval_Density_Dependence": "GRADUAL_INSTAR_SPECIFIC"
}
|
Larval_Habitat_Types | JSON object | NA | NA | NA | A measure of the habitat type and scale factors used to estimate larval population. This parameter is a dictionary that specifies habitat type with a simple numeric scale factor or, for LINEAR_SPLINE, with a more detailed configuration for scaling. The numeric scaling value represents larval density with the number of larvae in a 1x1-degree area. The factor multiplicatively scales the resulting weather or population-dependent functional form. Possible habitat values are:
The values set here can be scaled per node using LarvalHabitatMultiplier in the demographics file (see NodeAttributes) or per intervention using Larval_Habitat_Multiplier in the campaign file (see ScaleLarvalHabitat). |
The following example shows how to specify larval habitat using LINEAR_SPLINE. {
"Vector_Species_Params": {
"arabiensis": {
"Larval_Habitat_Types": {
"LINEAR_SPLINE": {
"Capacity_Distribution_Per_Year": {
"Times": [0.0, 60.833, 121.667, 182.5, 243.333, 204.167],
"Values": [0.0, 0.0, 0.2, 1.0, 0.5, 0.0]
},
"Max_Larval_Capacity": 10000000000.0
}
}
}
}
}
The following example shows how to specify the larval habitat using climatological habitat types (you may use one or more for each vector species). {
"arabiensis": {
"Larval_Habitat_Types": {
"TEMPORARY_RAINFALL": 11250000000,
"WATER_VEGETATION": 6000000000,
"BRACKISH_SWAMP": 30000000
}
}
}
|
Larval_Rainfall_Mortality_Threshold | float | 0.01 | 1000 | 100 | The threshold value on daily rainfall in millimeters, above which larval mortality is applied when Vector_Larval_Rainfall_Mortality is set to either SIGMOID or SIGMOID_HABITAT_SHIFTING. | {
"Larval_Rainfall_Mortality_Threshold": 30.0
}
|
Rainfall_In_mm_To_Fill_Swamp | float | 1 | 10000 | 1000 | Millimeters of rain to fill larval habitat to capacity. This is only used for vector species with Larval_Habitat_Types set to BRACKISH_SWAMP. | {
"Rainfall_In_mm_To_Fill_Swamp": 1000.0
}
|
Semipermanent_Habitat_Decay_Rate | float | 0.0001 | 100 | 0.01 | Daily rate of larval habitat loss for semi-permanent habitats with Larval_Habitat_Types parameter value of WATER_VEGETATION or BRACKISH_SWAMP. | {
"Semipermanent_Habitat_Decay_Rate": 0.01
}
|
Temporary_Habitat_Decay_Factor | float | 0.001 | 100 | 0.05 | The factor to convert raw evaporation rate (ignoring boundary layer effects) to the daily rate of larval habitat loss for temporary habitats (Larval_Habitat_Types set to TEMPORARY_RAINFALL). Units are (larval carrying capacity per day) / (kg per square meter per second). | {
"Temporary_Habitat_Decay_Factor": 0.05
}
|
Vector_Larval_Rainfall_Mortality | enum | NA | NA | NONE | The type of vector larval mortality function due to rainfall. Possible values are:
|
{
"Vector_Larval_Rainfall_Mortality": "SIGMOID"
}
|
Vector_Migration_Habitat_Modifier | float | 0 | 3.40E+38 | 0 | The preference of a vector to migrate toward a node with more habitat. Only used when Vector_Sampling_Type is set to TRACK_ALL_VECTORS. Enable_Vector_Migration must be set to 1. | {
"Vector_Migration_Habitat_Modifier": 1.0
}
|
x_Temporary_Larval_Habitat | double | NA | NA | 1 | Scale factor for the habitat size for all mosquito populations. | {
"x_Temporary_Larval_Habitat": 1
}
|
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"
}
|
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"
}
|
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:
|
{
"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:
|
{
"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
}
|
Vector_Migration_Filename_Local | string | NA | NA | UNSPECIFIED_FILE | The path to the vector migration file which defines patterns of vector migration to adjacent nodes. Enable_Vector_Migration must be set to 1. The file must be in .bin format. | {
"Vector_Migration_Filename_Local": "5x5_Households_Local_Vector_Migration.bin"
}
|
Vector_Migration_Filename_Regional | string | NA | NA | UNSPECIFIED_FILE | The path to the vector migration file which defines patterns of vector migration to non-adjacent nodes. Enable_Vector_Migration must be set to 1. The file must be in .bin format. | {
"Vector_Migration_Filename_Regional": "5x5_Households_Regional_Vector_Migration.bin"
}
|
Vector_Migration_Food_Modifier | float | 0 | 3.40E+38 | 0 | The preference of a vector to migrate toward a node currently occupied by humans, independent of the number of humans in the node. Used only when Vector_Sampling_Type is set to TRACK_ALL_VECTORS. Enable_Vector_Migration must be set to 1. | {
"Vector_Migration_Food_Modifier": 1.0
}
|
Vector_Migration_Habitat_Modifier | float | 0 | 3.40E+38 | 0 | The preference of a vector to migrate toward a node with more habitat. Only used when Vector_Sampling_Type is set to TRACK_ALL_VECTORS. Enable_Vector_Migration must be set to 1. | {
"Vector_Migration_Habitat_Modifier": 1.0
}
|
Vector_Migration_Modifier_Equation | enum | NA | NA | LINEAR | The functional form of vector migration modifiers. Enable_Vector_Migration must be set to 1. Possible values are: LINEAR EXPONENTIAL | {
"Vector_Migration_Modifier_Equation": "EXPONENTIAL"
}
|
Vector_Migration_Stay_Put_Modifier | float | 0 | 3.40E+38 | 0 | The preference of a vector to remain in its current node rather than migrate to another node. Used only when Vector_Sampling_Type is set to TRACK_ALL_VECTORS. Enable_Vector_Migration must be set to 1. | {
"Vector_Migration_Stay_Put_Modifier": 1.0
}
|
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
}
|
x_Vector_Migration_Local | float | 0 | 3.40E+38 | 1 | Scale factor for the rate of vector migration to adjacent nodes, as provided by the vector migration file. Enable_Vector_Migration must be set to 1. | {
"x_Vector_Migration_Local": 1.0
}
|
x_Vector_Migration_Regional | float | 0 | 3.40E+38 | 1 | Scale factor for the rate of vector migration to non-adjacent nodes, as provided by the vector migration file. Enable_Vector_Migration must be set to 1. | {
"x_Vector_Migration_Regional": 1.0
}
|
Mortality and survival¶
The following parameter determine mortality and survival characteristics of the disease being modeled and the population in general (non-disease mortality).
See Severe disease and mortality for more information about how fever, anemia, and parasite counts lead to severe malaria and mortality.
Parameter | Data type | Minimum | Maximum | Default | Description | Example |
---|---|---|---|---|---|---|
Anemia_Mortality_Inverse_Width | float | 0.1 | 1000000 | 10 | The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function: probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) ) This parameter configures the inverse width relative to threshold value of severe disease turn-on around threshold for anemia. |
{
"Anemia_Mortality_Inverse_Width": 150
}
|
Anemia_Mortality_Threshold | double | NA | NA | 3 | The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function: probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) ) This parameter configures the inverse width relative to threshold value of mortality turn-on around threshold for hemoglobin count in grams per deciliter (g/dL) at which 50% of individuals die per day. |
{
"Anemia_Mortality_Threshold": 1.5
}
|
Anemia_Severe_Inverse_Width | float | 0.1 | 1000000 | 10 | The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function: probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) ) This parameter configures the inverse width relative to threshold value of severe disease turn-on around threshold for anemia. |
{
"Anemia_Severe_Inverse_Width": 20
}
|
Anemia_Severe_Threshold | float | 0 | 100 | 5 | The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function: probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) ) This parameter configures the severe disease threshold level for anemia. Threshold units are in grams per deciliter (g/dL). |
{
"Anemia_Severe_Threshold": 3.0
}
|
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:
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"
}
|
Fever_Mortality_Inverse_Width | float | 0.1 | 1000000 | 10 | The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function: probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) ) This parameter configures the inverse width relative to threshold value of mortality turn-on around threshold for fever. |
{
"Fever_Mortality_Inverse_Width": 1000
}
|
Fever_Mortality_Threshold | double | NA | NA | 3 | The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function: probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) ) This parameter configures the fever mortality threshold, in units of degrees Celsius above normal body temperature (defined as 37 C). |
{
"Fever_Mortality_Threshold": 10
}
|
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:
|
{
"Mortality_Time_Course": "MORTALITY_AFTER_INFECTIOUS"
}
|
x_Other_Mortality | float | 0 | 3.40E+38 | 1 | Scale factor for mortality from causes other than the disease being simulated, 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.
|
{
"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:
|
{
"Spatial_Output_Channels": [
"Prevalence",
"New_Infections"
]
}
|
Parasite dynamics¶
The following parameters determine the dynamics of the Plasmodium falciparum parasite life cycle, including dynamics within the host and human population. For more information, see Malaria infection and immune model.
Parameter | Data type | Minimum | Maximum | Default | Description | Example |
---|---|---|---|---|---|---|
Base_Gametocyte_Fraction_Male | double | NA | NA | 0.2 | Fraction of gametocytes that are male. | {
"Base_Gametocyte_Fraction_Male": 0.25
}
|
Base_Gametocyte_Mosquito_Survival_Rate | float | 0 | 1 | 0.01 | Average fraction of gametocytes in a blood meal that are successful in infecting the mosquito in the absence of other modulating effects, such as fever. | {
"Base_Gametocyte_Mosquito_Survival_Rate": 0.015
}
|
Base_Gametocyte_Production_Rate | double | NA | NA | 0.02 | The fraction of infected red blood cells (IRBCs) producing gametocytes. | {
"Base_Gametocyte_Mosquito_Survival_Rate": 0.01
}
|
Base_Sporozoite_Survival_Fraction | float | 0 | 1 | 0.25 | The fraction of sporozoites that survive to infect a hepatocyte in the absence of anti-CSP protection. | {
"Base_Sporozoite_Survival_Fraction": 0.25
}
|
Cytokine_Gametocyte_Inactivation | float | 0 | 1 | 0.02 | The strength of inflammatory response inactivation of gametocytes. | {
"Cytokine_Gametocyte_Inactivation": 0.0167
}
|
Enable_Sexual_Combination | boolean | 0 | 1 | 0 | Controls whether or not male and female gametocytes undergo sexual combination. Set to true (1) to allow for sexual combination; set to false (0) for transmission of each strain only. Note This parameter is currently not in use. |
{
"Enable_Sexual_Combination": 0
}
|
Gametocyte_Stage_Survival_Rate | double | 0 | 1 | 1 | The rate of gametocyte survival from one development stage to the next in the absence of drugs or inflammatory immune response. | {
"Gametocyte_Stage_Survival_Rate": 0.8
}
|
Mean_Sporozoites_Per_Bite | float | 0 | 1000 | 11 | The mean number of sporozoites per infectious mosquito bite. | {
"Mean_Sporozoites_Per_Bite": 11
}
|
Merozoites_Per_Hepatocyte | double | NA | NA | 15000 | The number of IRBCs caused by a single infected hepatocyte at the start of infection. | {
"Merozoites_Per_Hepatocyte": 15000
}
|
Merozoites_Per_Schizont | double | NA | NA | 16 | The number of merozoites released by a single infected schizont after each asexual cycle. The number of resulting IRBC’s depends on the RBC availability and merozoite-specific immunity. | {
"Merozoites_Per_Schizont": 16
}
|
Number_Of_Asexual_Cycles_Without_Gametocytes | integer | 0 | 500 | 1 | The number of asexual reproduction cycles that do not produce gametocytes. All later cycles will produce gametocytes according to Base_Gametocyte_Production_Rate. | {
"Number_Of_Asexual_Cycles_Without_Gametocytes": 1
}
|
Parasite_Mortality_Inverse_Width | float | 0.1 | 1000000 | 10 | The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function: probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) ). This parameter configures the inverse width relative to threshold value of mortality turn-on around threshold for parasite density. |
{
"Parasite_Mortality_Inverse_Width": 100
}
|
Parasite_Mortality_Threshold | double | NA | NA | 2000000 | The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function: probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) ) This parameter configures the parasite-density mortality threshold for a simulation. |
{
"Parasite_Mortality_Threshold": 3000000
}
|
Parasite_Severe_Inverse_Width | float | 0.1 | 1000000 | 10 | The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function: probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) ) This parameter configures the inverse width relative to threshold value of severe disease turn-on around threshold for parasite density. |
{
"Parasite_Severe_Inverse_Width": 48.66825295
}
|
Parasite_Severe_Threshold | float | 0 | 3.40E+38 | 1000000 | The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function: probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) ) This parameter configures parasite density threshold level that results in severe disease. |
{
"Parasite_Severe_Threshold": 253871
}
|
Parasite_Smear_Sensitivity | float | 0.0001 | 100 | 0.1 | The number of microliters of blood tested to find single parasites in a traditional smear (corresponds to inverse parasites/microliters sensitivity). | {
"Parasite_Smear_Sensitivity": 0.1
}
|
Parasite_Switch_Type | enum | NA | NA | CONSTANT_SWITCH_RATE_2VARS | The parasite switch type for erythrocyte surface antigens. Possible values are:
|
{
"Parasite_Switch_Type": "RATE_PER_PARASITE_7VARS"
}
|
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:
|
{
"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:
|
{
"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:
|
{
"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:
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:
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:
|
{
"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.
For vector and malaria simulations, the same concepts apply to sampling the vector population.
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:
|
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
}
|
Mosquito_Weight | integer | 1 | 10000 | 1 | The value indicating how many mosquitoes are represented by a sample mosquito in the simulation. Vector_Sampling_Type must be set to SAMPLE_IND_VECTORS. | {
"Mosquito_Weight": 10
}
|
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
}
|
Vector_Sampling_Type | enum | NA | NA | TRACK_ALL_VECTORS | The type of vector sampling used. Possible values are:
|
{
"Vector_Sampling_Type": "TRACK_ALL_VECTORS"
}
|
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 |
---|---|---|---|---|---|---|
Acquire_Modifier | float | 0 | 1 | 1 | Modifier of the probability of successful infection of a mosquito by a malaria-infected individual, given the individual’s infectiousness. | {
"Vector_Species_Params": {
"aegypti": {
"Acquire_Modifier": 1
}
}
}
|
Antibody_IRBC_Kill_Rate | double | NA | NA | 2 | The scale factor multiplied by antibody level to produce the rate of clearance of the infected red blood cell (IRBC) population. | {
"Antibody_IRBC_Kill_Rate": 1.595
}
|
Aquatic_Arrhenius_1 | float | 0 | 1.00E+15 | 8.42E+10 | The Arrhenius equation, , with T in degrees Kelvin, parameterizes the daily rate of fractional progression of mosquito aquatic development (egg-hatching through emergence). This duration is a decreasing function of temperature. The variable a1 is a temperature-independent scale factor on development rate. | {
"Vector_Species_Params": {
"aegypti": {
"Aquatic_Arrhenius_1": 9752291.727
}
}
}
|
Aquatic_Arrhenius_2 | float | 0 | 1.00E+15 | 8328 | The Arrhenius equation, , with T in degrees Kelvin, parameterizes the daily rate of fractional progression of mosquito aquatic development (egg-hatching through emergence). This duration is a decreasing function of temperature. The variable a2 governs how quickly the rate changes with temperature. | {
"Vector_Species_Params": {
"arabiensis": {
"Aquatic_Arrhenius_2": 8328
}
}
}
|
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:
|
{
"Enable_Vital_Dynamics": 1,
"Enable_Birth": 1,
"Birth_Rate_Time_Dependence": "ANNUAL_BOXCAR_FUNCTION"
}
|
Cycle_Arrhenius_1 | float | 0 | 1.00E+15 | 4.09E+10 | The Arrhenius equation, , with T in degrees Kelvin, parameterizes the mosquito feeding cycle rate. This duration is a decreasing function of temperature. The variable a1 is a temperature-independent scale factor on feeding rate. Temperature_Dependent_Feeding_Cycle must be set to ARRHENIUS_DEPENDENCE. | {
"Temperature_Dependent_Feeding_Cycle": "ARRHENIUS_DEPENDENCE",
"Vector_Species_Params": {
"arabiensis": {
"Cycle_Arrhenius_1": 99,
"Cycle_Arrhenius_2": 88
}
}
}
|
Cycle_Arrhenius_2 | float | 0 | 1.00E+15 | 7740 | The Arrhenius equation, , with T in degrees Kelvin, parameterizes the mosquito feeding cycle rate. This duration is a decreasing function of temperature. The variable a2 is a temperature-independent scale factor on feeding rate. Temperature_Dependent_Feeding_Cycle must be set to ARRHENIUS_DEPENDENCE. | {
"Temperature_Dependent_Feeding_Cycle": "ARRHENIUS_DEPENDENCE",
"Vector_Species_Params": {
"arabiensis": {
"Cycle_Arrhenius_1": 99,
"Cycle_Arrhenius_2": 88
}
}
}
|
Cycle_Arrhenius_Reduction_Factor | float | 0 | 1 | 1 | The scale factor applied to cycle duration (from oviposition to oviposition) to reduce the duration when primary follicles are at stage II rather than I in the case of newly emerged females. Temperature_Dependent_Feeding_Cycle must be set to ARRHENIUS_DEPENDENCE. | {
"Temperature_Dependent_Feeding_Cycle": "ARRHENIUS_DEPENDENCE",
"Vector_Species_Params": {
"funestus": {
"Cycle_Arrhenius_Reduction_Factor": 0.44
}
}
}
|
Egg_Arrhenius1 | float | 0 | 1.00E+10 | 6.16E+07 | The Arrhenius equation, math:a_1^{-a_2/T}, with T in degrees Kelvin, parameterizes the daily rate of mosquito egg hatching. This duration is a decreasing function of temperature. The variable a1 is a temperature-independent scale factor on hatching rate. Enable_Temperature_Dependent_Egg_Hatching must be set to 1. | {
"Enable_Temperature_Dependent_Egg_Hatching": 1,
"Egg_Arrhenius1": 61599956,
"Egg_Arrhenius2": 5754
}
|
Egg_Arrhenius2 | float | 0 | 1.00E+10 | 5754.03 | The Arrhenius equation, , with T in degrees Kelvin, parameterizes the daily rate of mosquito egg hatching. This duration is a decreasing function of temperature. The variable a2 is a temperature-dependent scale factor on hatching rate. Enable_Temperature_Dependent_Egg_Hatching must be set to 1. | {
"Enable_Temperature_Dependent_Egg_Hatching": 1,
"Egg_Arrhenius1": 61599956,
"Egg_Arrhenius2": 5754
}
|
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
}
|
Infected_Arrhenius_1 | float | 0 | 1.00E+15 | 1.17E+11 | The Arrhenius equation, , with T in degrees Kelvin, parameterizes the daily rate of fractional progression of infected mosquitoes to an infectious state. The duration of sporogony is a decreasing function of temperature. The variable a1 is a temperature-independent scale factor on the progression rate to infectiousness. | {
"Vector_Species_Params": {
"arabiensis": {
"Acquire_Modifier": 0.2,
"Adult_Life_Expectancy": 10,
"Anthropophily": 0.95,
"Aquatic_Arrhenius_1": 84200000000,
"Aquatic_Arrhenius_2": 8328,
"Aquatic_Mortality_Rate": 0.1,
"Cycle_Arrhenius_1": 0,
"Cycle_Arrhenius_2": 0,
"Cycle_Arrhenius_Reduction_Factor": 0,
"Days_Between_Feeds": 3,
"Egg_Batch_Size": 100,
"Immature_Duration": 4,
"Indoor_Feeding_Fraction": 0.5,
"Infected_Arrhenius_1": 117000000000,
"Infected_Arrhenius_2": 8336,
"Infected_Egg_Batch_Factor": 0.8,
"Infectious_Human_Feed_Mortality_Factor": 1.5,
"Larval_Habitat_Types": {
"TEMPORARY_RAINFALL": 11250000000
},
"Nighttime_Feeding_Fraction": 1,
"Transmission_Rate": 0.5
}
}
}
|
Infected_Arrhenius_2 | float | 0 | 1.00E+15 | 8340 | The Arrhenius equation, , with T in degrees Kelvin, parameterizes the daily rate of fractional progression of infected mosquitoes to an infectious state. The duration of sporogony is a decreasing function of temperature. The variable a2 is a temperature-dependent scale factor on the progression rate to infectiousness. | {
"Vector_Species_Params": {
"arabiensis": {
"Acquire_Modifier": 0.2,
"Adult_Life_Expectancy": 10,
"Anthropophily": 0.95,
"Aquatic_Arrhenius_1": 84200000000,
"Aquatic_Arrhenius_2": 8328,
"Aquatic_Mortality_Rate": 0.1,
"Cycle_Arrhenius_1": 0,
"Cycle_Arrhenius_2": 0,
"Cycle_Arrhenius_Reduction_Factor": 0,
"Days_Between_Feeds": 3,
"Egg_Batch_Size": 100,
"Immature_Duration": 4,
"Indoor_Feeding_Fraction": 0.5,
"Infected_Arrhenius_1": 117000000000,
"Infected_Arrhenius_2": 8336,
"Infected_Egg_Batch_Factor": 0.8,
"Infectious_Human_Feed_Mortality_Factor": 1.5,
"Larval_Habitat_Types": {
"TEMPORARY_RAINFALL": 11250000000
},
"Nighttime_Feeding_Fraction": 1,
"Transmission_Rate": 0.5
}
}
}
|
Infected_Egg_Batch_Factor | float | 0 | 10 | 0.8 | The dimensionless factor used to modify mosquito egg batch size in order to account for reduced fertility effects arising due to infection (e.g. when females undergo sporogony). | {
"Vector_Species_Params": {
"arabiensis": {
"Acquire_Modifier": 0.2,
"Adult_Life_Expectancy": 10,
"Anthropophily": 0.95,
"Aquatic_Arrhenius_1": 84200000000,
"Aquatic_Arrhenius_2": 8328,
"Aquatic_Mortality_Rate": 0.1,
"Cycle_Arrhenius_1": 0,
"Cycle_Arrhenius_2": 0,
"Cycle_Arrhenius_Reduction_Factor": 0,
"Days_Between_Feeds": 3,
"Egg_Batch_Size": 100,
"Immature_Duration": 4,
"Indoor_Feeding_Fraction": 0.5,
"Infected_Arrhenius_1": 117000000000,
"Infected_Arrhenius_2": 8336,
"Infected_Egg_Batch_Factor": 0.8,
"Infectious_Human_Feed_Mortality_Factor": 1.5,
"Larval_Habitat_Types": {
"TEMPORARY_RAINFALL": 11250000000
},
"Nighttime_Feeding_Fraction": 1,
"Transmission_Rate": 0.5
}
}
}
|
Infectious_Human_Feed_Mortality_Factor | float | 0 | 1000 | 1.5 | The (dimensionless) factor used to modify the death rate of mosquitoes when feeding on humans, to account for the higher mortality rate infected mosquitoes experience during human feeds versus uninfected mosquitoes. | {
"Vector_Species_Params": {
"arabiensis": {
"Acquire_Modifier": 0.2,
"Adult_Life_Expectancy": 10,
"Anthropophily": 0.95,
"Aquatic_Arrhenius_1": 84200000000,
"Aquatic_Arrhenius_2": 8328,
"Aquatic_Mortality_Rate": 0.1,
"Cycle_Arrhenius_1": 0,
"Cycle_Arrhenius_2": 0,
"Cycle_Arrhenius_Reduction_Factor": 0,
"Days_Between_Feeds": 3,
"Egg_Batch_Size": 100,
"Immature_Duration": 4,
"Indoor_Feeding_Fraction": 0.5,
"Infected_Arrhenius_1": 117000000000,
"Infected_Arrhenius_2": 8336,
"Infected_Egg_Batch_Factor": 0.8,
"Infectious_Human_Feed_Mortality_Factor": 1.5,
"Larval_Habitat_Types": {
"TEMPORARY_RAINFALL": 11250000000
},
"Nighttime_Feeding_Fraction": 1,
"Transmission_Rate": 0.5
}
}
}
|
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"
}
|
Larval_Density_Mortality_Scalar | float | 0.01 | 1000 | 10 | A scale factor in the formula determining the larval-age-dependent mortality for the GRADUAL_INSTAR_SPECIFIC and LARVAL_AGE_DENSITY_DEPENDENT_MORTALITY_ONLY models. | {
"Larval_Density_Mortality_Scalar": 1.0
}
|
Newborn_Biting_Risk_Multiplier | float | 0 | 1 | 0.2 | The scale factor that defines the y-intercept of the linear portion of the biting risk curve when Age_Dependent_Biting_Risk_Type is set to LINEAR. | {
"Newborn_Biting_Risk_Multiplier": 0.2
}
|
Nonspecific_Antibody_Growth_Rate_Factor | float | 0 | 1000 | 0.5 | The factor that adjusts Antibody_Capacity_Growth_Rate for less immunogenic surface proteins, called minor epitopes. | {
"Nonspecific_Antibody_Growth_Rate_Factor": 0.5
}
|
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:
|
{
"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"
}
|
Vector_Migration_Food_Modifier | float | 0 | 3.40E+38 | 0 | The preference of a vector to migrate toward a node currently occupied by humans, independent of the number of humans in the node. Used only when Vector_Sampling_Type is set to TRACK_ALL_VECTORS. Enable_Vector_Migration must be set to 1. | {
"Vector_Migration_Food_Modifier": 1.0
}
|
Vector_Migration_Habitat_Modifier | float | 0 | 3.40E+38 | 0 | The preference of a vector to migrate toward a node with more habitat. Only used when Vector_Sampling_Type is set to TRACK_ALL_VECTORS. Enable_Vector_Migration must be set to 1. | {
"Vector_Migration_Habitat_Modifier": 1.0
}
|
Vector_Migration_Modifier_Equation | enum | NA | NA | LINEAR | The functional form of vector migration modifiers. Enable_Vector_Migration must be set to 1. Possible values are: LINEAR EXPONENTIAL | {
"Vector_Migration_Modifier_Equation": "EXPONENTIAL"
}
|
Vector_Migration_Stay_Put_Modifier | float | 0 | 3.40E+38 | 0 | The preference of a vector to remain in its current node rather than migrate to another node. Used only when Vector_Sampling_Type is set to TRACK_ALL_VECTORS. Enable_Vector_Migration must be set to 1. | {
"Vector_Migration_Stay_Put_Modifier": 1.0
}
|
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_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
}
|
x_Temporary_Larval_Habitat | double | NA | NA | 1 | Scale factor for the habitat size for all mosquito populations. | {
"x_Temporary_Larval_Habitat": 1
}
|
x_Vector_Migration_Local | float | 0 | 3.40E+38 | 1 | Scale factor for the rate of vector migration to adjacent nodes, as provided by the vector migration file. Enable_Vector_Migration must be set to 1. | {
"x_Vector_Migration_Local": 1.0
}
|
x_Vector_Migration_Regional | float | 0 | 3.40E+38 | 1 | Scale factor for the rate of vector migration to non-adjacent nodes, as provided by the vector migration file. Enable_Vector_Migration must be set to 1. | {
"x_Vector_Migration_Regional": 1.0
}
|
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"
]
}
|
Malaria_Model | enum | NA | NA | MALARIA_MECHANISTIC_MODEL | The type of malaria model used in a simulation. Possible values are:
Note All malaria simulations should use MALARIA_MECHANISTIC_MODEL. The others are placeholder values. |
{
"Malaria_Model": "MALARIA_MECHANISTIC_MODEL"
}
|
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:
|
{
"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 malaria diagnosis and symptoms as the disease progresses, such as anemia and fever. See Malaria symptoms and diagnostics for more information on malaria diagnostics and symptoms.
Parameter | Data type | Minimum | Maximum | Default | Description | Example |
---|---|---|---|---|---|---|
Anemia_Mortality_Inverse_Width | float | 0.1 | 1000000 | 10 | The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function: probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) ) This parameter configures the inverse width relative to threshold value of severe disease turn-on around threshold for anemia. |
{
"Anemia_Mortality_Inverse_Width": 150
}
|
Anemia_Mortality_Threshold | double | NA | NA | 3 | The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function: probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) ) This parameter configures the inverse width relative to threshold value of mortality turn-on around threshold for hemoglobin count in grams per deciliter (g/dL) at which 50% of individuals die per day. |
{
"Anemia_Mortality_Threshold": 1.5
}
|
Anemia_Severe_Inverse_Width | float | 0.1 | 1000000 | 10 | The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function: probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) ) This parameter configures the inverse width relative to threshold value of severe disease turn-on around threshold for anemia. |
{
"Anemia_Severe_Inverse_Width": 20
}
|
Anemia_Severe_Threshold | float | 0 | 100 | 5 | The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function: probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) ) This parameter configures the severe disease threshold level for anemia. Threshold units are in grams per deciliter (g/dL). |
{
"Anemia_Severe_Threshold": 3.0
}
|
Clinical_Fever_Threshold_High | float | 0 | 15 | 1 | The fever threshold (in degrees Celsius above normal) to start a clinical incident. | {
"Clinical_Fever_Threshold_High": 1.5
}
|
Clinical_Fever_Threshold_Low | float | 0 | 5 | 1 | The fever threshold (in degrees Celsius above normal) to end a clinical incident. | {
"Clinical_Fever_Threshold_Low": 0.5
}
|
Erythropoiesis_Anemia_Effect | float | 0 | 1000 | 3.5 | The exponential rate of increased red-blood-cell production from reduced red-blood-cell availability. | {
"Erythropoiesis_Anemia_Effect": 3
}
|
Fever_Detection_Threshold | float | 0.5 | 5 | 1 | The level of body temperature above normal (defined as 37 C), in degrees Celsius, corresponding to detectable fever. | {
"Fever_Detection_Threshold": 1
}
|
Fever_IRBC_Kill_Rate | float | 0 | 1000 | 0.15 | The maximum kill rate for infected red blood cells due to the inflammatory innate immune response. As fever increases above 38.5 degrees Celsius, the kill rate becomes successively higher along a sigmoidal curve approaching this rate. | {
"Fever_IRBC_Kill_Rate": 1.4
}
|
Fever_Mortality_Inverse_Width | float | 0.1 | 1000000 | 10 | The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function: probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) ) This parameter configures the inverse width relative to threshold value of mortality turn-on around threshold for fever. |
{
"Fever_Mortality_Inverse_Width": 1000
}
|
Fever_Mortality_Threshold | double | NA | NA | 3 | The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function: probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) ) This parameter configures the fever mortality threshold, in units of degrees Celsius above normal body temperature (defined as 37 C). |
{
"Fever_Mortality_Threshold": 10
}
|
Fever_Severe_Inverse_Width | float | 0.1 | 1000000 | 10 | The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function: probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) ) This parameter configures the inverse width relative to threshold value of mortality turn-on around threshold for fever. |
{
"Fever_Severe_Inverse_Width": 18.7
}
|
Fever_Severe_Threshold | float | 0 | 10 | 1.5 | The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function: probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) ) This parameter configures the threshold (in degrees Celsius above normal) for fever indicating severe disease. |
{
"Fever_Severe_Threshold": 2.5
}
|
Min_Days_Between_Clinical_Incidents | float | 0 | 1000000 | 3 | The number of days with fever below the low-threshold before a new incident can start, when fever again exceeds the high-threshold. | {
"Min_Days_Between_Clinical_Incidents": 14
}
|
New_Diagnostic_Sensitivity | float | 0.0001 | 100000 | 0.01 | The number of microliters of blood tested to find single parasites in a new diagnostic (corresponds to inverse parasites/microliters sensitivity). | {
"New_Diagnostic_Sensitivity": 0.025
}
|
Vector control¶
The following parameters determine the characteristics of campaign interventions aimed at vector control, such as the homing endonuclease gene (HEG), sugar feeding, and Wolbachia infection. When, to whom, and how those interventions are distributed is determined by the campaign file.
Parameter | Data type | Minimum | Maximum | Default | Description | Example |
---|---|---|---|---|---|---|
HEG_Fecundity_Limiting | float | 0 | 1 | 0 | The fractional reduction in the number of eggs laid by a female mosquito who is homozygous in the homing endonuclease gene (HEG). HEG_Model must be set to GERMLINE_HOMING, EGG_HOMING, DUAL_GERMLINE_HOMING, or DRIVING_Y. | {
"HEG_Model": "EGG_HOMING",
"HEG_Fecundity_Limiting": 0.7
}
|
HEG_Homing_Rate | float | 0 | 1 | 0 | The fractional redistribution from heterozygous offspring to the homozygous homing endonuclease gene (HEG) behavior. HEG_Model” must be set to GERMLINE_HOMING, EGG_HOMING, DUAL_GERMLINE_HOMING, or DRIVING_Y. | {
"HEG_Model": "EGG_HOMING",
"HEG_Homing_Rate": 0.4
}
|
HEG_Model | enum | NA | NA | OFF | This parameter determines the structure of homing endonuclease gene (HEG) dynamics. Possible values are:
|
{
"HEG_Model": "EGG_HOMING",
"HEG_Homing_Rate": 0.4,
"HEG_Fecundity_Limiting": 0.9
}
|
Vector_Sugar_Feeding_Frequency | enum | NA | NA | VECTOR_SUGAR_FEEDING_NONE | The frequency of sugar feeding by a female mosquito. Used is used in conjunction with the SugarTrap and OvipositionTrap interventions. Vector_Sampling_Type must be set to TRACK_ALL_VECTORS or SAMPLE_IND_VECTORS. Possible values are:
|
{
"Vector_Sugar_Feeding_Frequency": "VECTOR_SUGAR_FEEDING_NONE"
}
|
Wolbachia_Infection_Modification | float | 0 | 100 | 1 | The change in vector susceptibility to infection due to a Wolbachia infection. | {
"Wolbachia_Infection_Modification": 1.0
}
|
Wolbachia_Mortality_Modification | float | 0 | 100 | 1 | The change in vector mortality due to a Wolbachia infection. | {
"Wolbachia_Infection_Modification": 0.0
}
|
Vector life cycle¶
The following parameters determine the characteristics of the vector life cycle. Set the vector species to include in the simulation and the feeding, egg-laying, migration, and larval development habits of each using these parameters. The parameters for larval development related to habitat and climate are described in Larval habitat.
Parameter | Data type | Minimum | Maximum | Default | Description | Example |
---|---|---|---|---|---|---|
Adult_Life_Expectancy | float | 0 | 730 | 10 | The number of days an adult mosquito survives. The daily adult mortality rate is 1 / (value of this parameter). | {
"Vector_Species_Params": {
"arabiensis": {
"Adult_Life_Expectancy": 5.9
}
}
}
|
Anthropophily | float | 0 | 1 | 1 | Mosquito preference for humans over animals, measured as a fraction of blood meals from human hosts. This dimensionless propensity is important in differentiating between mosquito species. | {
"Vector_Species_Params": {
"aegypti": {
"Anthropophily": 0.95
}
}
}
|
Cycle_Arrhenius_1 | float | 0 | 1.00E+15 | 4.09E+10 | The Arrhenius equation, , with T in degrees Kelvin, parameterizes the mosquito feeding cycle rate. This duration is a decreasing function of temperature. The variable a1 is a temperature-independent scale factor on feeding rate. Temperature_Dependent_Feeding_Cycle must be set to ARRHENIUS_DEPENDENCE. | {
"Temperature_Dependent_Feeding_Cycle": "ARRHENIUS_DEPENDENCE",
"Vector_Species_Params": {
"arabiensis": {
"Cycle_Arrhenius_1": 99,
"Cycle_Arrhenius_2": 88
}
}
}
|
Cycle_Arrhenius_2 | float | 0 | 1.00E+15 | 7740 | The Arrhenius equation, , with T in degrees Kelvin, parameterizes the mosquito feeding cycle rate. This duration is a decreasing function of temperature. The variable a2 is a temperature-independent scale factor on feeding rate. Temperature_Dependent_Feeding_Cycle must be set to ARRHENIUS_DEPENDENCE. | {
"Temperature_Dependent_Feeding_Cycle": "ARRHENIUS_DEPENDENCE",
"Vector_Species_Params": {
"arabiensis": {
"Cycle_Arrhenius_1": 99,
"Cycle_Arrhenius_2": 88
}
}
}
|
Cycle_Arrhenius_Reduction_Factor | float | 0 | 1 | 1 | The scale factor applied to cycle duration (from oviposition to oviposition) to reduce the duration when primary follicles are at stage II rather than I in the case of newly emerged females. Temperature_Dependent_Feeding_Cycle must be set to ARRHENIUS_DEPENDENCE. | {
"Temperature_Dependent_Feeding_Cycle": "ARRHENIUS_DEPENDENCE",
"Vector_Species_Params": {
"funestus": {
"Cycle_Arrhenius_Reduction_Factor": 0.44
}
}
}
|
Days_Between_Feeds | float | 0 | 730 | 2 | The number of days between female mosquito feeding attempts. In the cohort model, this value is converted to a feeding rate, equal to 1/(value of this parameter), and is used to determine the probability that one of each of the various feeding modes (animal host, human host, indoor, outdoor, etc) occurs. In the individual model, this parameter determines the number of days a vector waits between feeds. | {
"Vector_Species_Params": {
"gambiae": {
"Days_Between_Feeds": 3
}
}
}
|
Drought_Egg_Hatch_Delay | float | 0 | 1 | 0.33 | Proportion of regular egg hatching that still occurs when habitat dries up. Enable_Drought_Egg_Hatch_Delay must be set to 1. | {
"Enable_Drought_Egg_Hatch_Delay": 1,
"Drought_Egg_Hatch_Delay": 0.33
}
|
Egg_Arrhenius1 | float | 0 | 1.00E+10 | 6.16E+07 | The Arrhenius equation, math:a_1^{-a_2/T}, with T in degrees Kelvin, parameterizes the daily rate of mosquito egg hatching. This duration is a decreasing function of temperature. The variable a1 is a temperature-independent scale factor on hatching rate. Enable_Temperature_Dependent_Egg_Hatching must be set to 1. | {
"Enable_Temperature_Dependent_Egg_Hatching": 1,
"Egg_Arrhenius1": 61599956,
"Egg_Arrhenius2": 5754
}
|
Egg_Arrhenius2 | float | 0 | 1.00E+10 | 5754.03 | The Arrhenius equation, , with T in degrees Kelvin, parameterizes the daily rate of mosquito egg hatching. This duration is a decreasing function of temperature. The variable a2 is a temperature-dependent scale factor on hatching rate. Enable_Temperature_Dependent_Egg_Hatching must be set to 1. | {
"Enable_Temperature_Dependent_Egg_Hatching": 1,
"Egg_Arrhenius1": 61599956,
"Egg_Arrhenius2": 5754
}
|
Egg_Batch_Size | float | 0 | 10000 | 100 | Number of eggs laid by one female mosquito that has fed successfully. The value of Egg_Batch_Size is used for both the number of female eggs and for the number of male eggs. For example, the default value of 100 means that there are 100 female eggs and 100 male eggs. | {
"Vector_Species_Params": {
"arabiensis": {
"Egg_Batch_Size": 100
}
}
}
|
Egg_Hatch_Delay_Distribution | enum | NA | NA | NO_DELAY | The distribution of the delay from oviposition to egg hatching. Possible values are:
|
{
"Egg_Hatch_Delay_Distribution": "EXPONENTIAL_DURATION",
"Mean_Egg_Hatch_Delay": 2
}
|
Egg_Hatch_Density_Dependence | enum | NA | NA | NO_DENSITY_DEPENDENCE | The effect of larval density on egg hatching rate. Possible values are:
|
{
"Egg_Hatch_Density_Dependence": "NO_DENSITY_DEPENDENCE"
}
|
Egg_Saturation_At_Oviposition | enum | NA | NA | NO_SATURATION | If laying all eggs from ovipositing females would overflow the larval habitat capacity on a given day, the means by which the viable eggs become saturated. Possible values are:
|
{
"Egg_Saturation_At_Oviposition": "SATURATION_AT_OVIPOSITION"
}
|
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_Temperature_Dependent_Egg_Hatching | boolean | 0 | 1 | 0 | Controls whether or not temperature has an effect on egg hatching, defined by Egg_Arrhenius_1 and Egg_Arrhenius_2. | {
"Enable_Temperature_Dependent_Egg_Hatching": 1,
"Egg_Arrhenius1": 61599956.864,
"Egg_Arrhenius2": 5754.033
}
|
Enable_Vector_Aging | boolean | 0 | 1 | 0 | Controls whether or not vectors undergo senescence as they age. | {
"Enable_Vector_Aging": 1
}
|
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
}
|
Human_Feeding_Mortality | float | 0 | 1 | 0.1 | The fraction of mosquitoes, for all species, that die while feeding on a human. | {
"Human_Feeding_Mortality": 0.15
}
|
Immature_Duration | float | 0 | 730 | 2 | The number of days for larvae to develop into adult mosquitoes. The value is used to calculate mosquito development rate, which equals 1 / (value of this parameter). Development from immature to adult is not dependent on temperature. | {
"Vector_Species_Params": {
"funestus": {
"Immature_Duration": 4
}
}
}
|
Indoor_Feeding_Fraction | float | 0 | 1 | 1 | The fraction (dimensionless) of feeds in which mosquitoes feed on humans indoors; the fraction of feeds on humans that occur outdoors equals 1 – (value of this parameter). | {
"Vector_Species_Params": {
"arabiensis": {
"Acquire_Modifier": 0.2,
"Adult_Life_Expectancy": 10,
"Anthropophily": 0.95,
"Aquatic_Arrhenius_1": 84200000000,
"Aquatic_Arrhenius_2": 8328,
"Aquatic_Mortality_Rate": 0.1,
"Cycle_Arrhenius_1": 0,
"Cycle_Arrhenius_2": 0,
"Cycle_Arrhenius_Reduction_Factor": 0,
"Days_Between_Feeds": 3,
"Egg_Batch_Size": 100,
"Immature_Duration": 4,
"Indoor_Feeding_Fraction": 0.5,
"Infected_Arrhenius_1": 117000000000,
"Infected_Arrhenius_2": 8336,
"Infected_Egg_Batch_Factor": 0.8,
"Infectious_Human_Feed_Mortality_Factor": 1.5,
"Larval_Habitat_Types": {
"TEMPORARY_RAINFALL": 11250000000
},
"Nighttime_Feeding_Fraction": 1,
"Transmission_Rate": 0.5
}
}
}
|
Infected_Egg_Batch_Factor | float | 0 | 10 | 0.8 | The dimensionless factor used to modify mosquito egg batch size in order to account for reduced fertility effects arising due to infection (e.g. when females undergo sporogony). | {
"Vector_Species_Params": {
"arabiensis": {
"Acquire_Modifier": 0.2,
"Adult_Life_Expectancy": 10,
"Anthropophily": 0.95,
"Aquatic_Arrhenius_1": 84200000000,
"Aquatic_Arrhenius_2": 8328,
"Aquatic_Mortality_Rate": 0.1,
"Cycle_Arrhenius_1": 0,
"Cycle_Arrhenius_2": 0,
"Cycle_Arrhenius_Reduction_Factor": 0,
"Days_Between_Feeds": 3,
"Egg_Batch_Size": 100,
"Immature_Duration": 4,
"Indoor_Feeding_Fraction": 0.5,
"Infected_Arrhenius_1": 117000000000,
"Infected_Arrhenius_2": 8336,
"Infected_Egg_Batch_Factor": 0.8,
"Infectious_Human_Feed_Mortality_Factor": 1.5,
"Larval_Habitat_Types": {
"TEMPORARY_RAINFALL": 11250000000
},
"Nighttime_Feeding_Fraction": 1,
"Transmission_Rate": 0.5
}
}
}
|
Larval_Density_Dependence | enum | NA | NA | UNIFORM_WHEN_OVERPOPULATION | The functional form of mortality and growth delay for mosquito larvae based on population density. Possible values are:
|
{
"Larval_Density_Dependence": "GRADUAL_INSTAR_SPECIFIC"
}
|
Larval_Density_Mortality_Offset | float | 0.0001 | 1000 | 0.1 | An offset factor in the formula determining the larval-age-dependent mortality for the GRADUAL_INSTAR_SPECIFIC and LARVAL_AGE_DENSITY_DEPENDENT_MORTALITY_ONLY models. | {
"Larval_Density_Mortality_Offset": 0.001
}
|
Larval_Density_Mortality_Scalar | float | 0.01 | 1000 | 10 | A scale factor in the formula determining the larval-age-dependent mortality for the GRADUAL_INSTAR_SPECIFIC and LARVAL_AGE_DENSITY_DEPENDENT_MORTALITY_ONLY models. | {
"Larval_Density_Mortality_Scalar": 1.0
}
|
Mean_Egg_Hatch_Delay | float | 0 | 120 | 0 | The mean delay in egg hatch time, in days, from the time of oviposition. Set the delay distribution with Egg_Hatch_Delay_Distribution. | {
"Egg_Hatch_Delay_Distribution": "EXPONENTIAL_DURATION",
"Mean_Egg_Hatch_Delay": 2
}
|
Nighttime_Feeding_Fraction | float | 0 | 1 | 1 | The fraction of feeds on humans (for a specific mosquito species) that occur during the nighttime. Thus the fraction of feeds on humans that occur during the day equals 1 - (value of this parameter). | {
"Vector_Species_Params": {
"arabiensis": {
"Acquire_Modifier": 0.2,
"Adult_Life_Expectancy": 10,
"Anthropophily": 0.95,
"Aquatic_Arrhenius_1": 84200000000,
"Aquatic_Arrhenius_2": 8328,
"Aquatic_Mortality_Rate": 0.1,
"Cycle_Arrhenius_1": 0,
"Cycle_Arrhenius_2": 0,
"Cycle_Arrhenius_Reduction_Factor": 0,
"Days_Between_Feeds": 3,
"Egg_Batch_Size": 100,
"Immature_Duration": 4,
"Indoor_Feeding_Fraction": 0.5,
"Infected_Arrhenius_1": 117000000000,
"Infected_Arrhenius_2": 8336,
"Infected_Egg_Batch_Factor": 0.8,
"Infectious_Human_Feed_Mortality_Factor": 1.5,
"Larval_Habitat_Types": {
"TEMPORARY_RAINFALL": 11250000000
},
"Nighttime_Feeding_Fraction": 1,
"Transmission_Rate": 0.5
}
}
}
|
Temperature_Dependent_Feeding_Cycle | enum | NA | NA | NO_TEMPERATURE_DEPENDENCE | The effect of temperature on the duration between blood feeds. Possible values are:
|
{
"Temperature_Dependent_Feeding_Cycle": "BOUNDED_DEPENDENCE"
}
|
Vector_Migration_Food_Modifier | float | 0 | 3.40E+38 | 0 | The preference of a vector to migrate toward a node currently occupied by humans, independent of the number of humans in the node. Used only when Vector_Sampling_Type is set to TRACK_ALL_VECTORS. Enable_Vector_Migration must be set to 1. | {
"Vector_Migration_Food_Modifier": 1.0
}
|
Vector_Migration_Modifier_Equation | enum | NA | NA | LINEAR | The functional form of vector migration modifiers. Enable_Vector_Migration must be set to 1. Possible values are: LINEAR EXPONENTIAL | {
"Vector_Migration_Modifier_Equation": "EXPONENTIAL"
}
|
Vector_Migration_Stay_Put_Modifier | float | 0 | 3.40E+38 | 0 | The preference of a vector to remain in its current node rather than migrate to another node. Used only when Vector_Sampling_Type is set to TRACK_ALL_VECTORS. Enable_Vector_Migration must be set to 1. | {
"Vector_Migration_Stay_Put_Modifier": 1.0
}
|
Vector_Species_Names | array of strings | NA | NA | [] | An array of vector species names for all species that are present in the simulation. You may provide any species names you desire, but the same names must be used in Vector_Species_Params. | {
"Vector_Species_Names": [
"arabiensis",
"funestus",
"gambiae"
]
}
|
Vector_Species_Params | JSON object | NA | NA | NA | A JSON object that lists each vector species, as defined in Vector_Species_Names, and the parameters that define them. | {
"Vector_Species_Params": {
"arabiensis": {
"Acquire_Modifier": 1,
"Adult_Life_Expectancy": 10,
"Anthropophily"
"Aquatic_Arrhenius_1": 84200000000,
"Aquatic_Arrhenius_2": 8328,
"Aquatic_Mortality_Rate": 0.1,
"Days_Between_Feeds": 3,
"Egg_Batch_Size": 100,
"Immature_Duration": 4,
"Indoor_Feeding_Fraction": 0.5,
"Infected_Arrhenius_1": 117000000000,
"Infected_Arrhenius_2": 8336,
"Infected_Egg_Batch_Factor": 0.8,
"Infectious_Human_Feed_Mortality_Factor": 1.5,
"Larval_Habitat_Types": {
"TEMPORARY_RAINFALL": 1e10,
"WATER_VEGETATION": 1e6
},
"Transmission_Rate": 0.5
}
}
|
Vector_Sugar_Feeding_Frequency | enum | NA | NA | VECTOR_SUGAR_FEEDING_NONE | The frequency of sugar feeding by a female mosquito. Used is used in conjunction with the SugarTrap and OvipositionTrap interventions. Vector_Sampling_Type must be set to TRACK_ALL_VECTORS or SAMPLE_IND_VECTORS. Possible values are:
|
{
"Vector_Sugar_Feeding_Frequency": "VECTOR_SUGAR_FEEDING_NONE"
}
|