Demographics parameters¶
The parameters described in this reference section can be added to the JSON (JavaScript Object Notation) formatted demographics file to determine the demographics of the population within each geographic node in a simulation. For example, the number of individuals and the distribution for age, gender, immunity, risk, and mortality. These parameters work closely with the Population dynamics parameters in the configuration file, which are simulation-wide and generally control whether certain events, such as births or deaths, are enabled in a simulation.
Generally, you will download a demographics file and modify it to meet the needs of your simulation. Demographics files for several locations are available on the Institute for Disease Modeling (IDM) GitHub EMOD-InputData repository or you can use COmputational Modeling Platform Service (COMPS) to generate demographics and climate files for a particular region. By convention, these are named using the name of the region appended with “_demographics.json”, but you may name the file anything you like.
Additionally, you can use more than one demographics file, with one serving as the base layer and the one or more others acting as overlays that override the values in the base layer. This can be helpful if you want to experiment with different values in the overlay without modifying your base file. For more information, see Demographics file.
At least one demographics file is required for every simulation unless you set the parameter Enable_Demographics_Builtin to 1 (one) in the configuration file. This setting does not represent a real location and is generally only used for testing and validating code pathways rather than actual modeling of disease.
Demographics files are organized into four main sections: Metadata, NodeProperties, Defaults, and Nodes. The following example shows the skeletal format of a demographics file.
{
"Metadata": {
"DateCreated": "dateTime",
"Tool": "scriptUsedToGenerate",
"Author": "author",
"IdReference": "Gridded world grump2.5arcmin",
"NodeCount": 2
},
"NodeProperties": [
{}
],
"Defaults": {
"NodeAttributes": {},
"IndividualAttributes": {},
"IndividualProperties": {},
"Society": {}
},
"Nodes": [{
"NodeID": 1,
"NodeAttributes": {},
"IndividualAttributes": {},
"IndividualProperties": {},
"Society": {}
}, {
"NodeID": 2,
"NodeAttributes": {},
"IndividualAttributes": {},
"IndividualProperties": {},
"Society": {}
}]
}
All parameters except those in the Metadata and NodeProperties sections below can appear in either the Defaults section or the Nodes section of the demographics file. Parameters under Defaults will be applied to all nodes in the simulation. Parameters under Nodes will be applied to specific nodes, overriding the values in Defaults if they appear in both. Each node in the Nodes section is identified using a unique NodeID.
The tables below contain only parameters available when using the malaria simulation type.
Note
Parameters are case-sensitive. For Boolean parameters, set to 1 for true or 0 for false. Minimum, maximum, or default values of “NA” indicate that those values are not applicable for that parameter.
EMOD does not use true defaults; that is, if the dependency relationships indicate that a parameter is required, you must supply a value for it. However, many of the tools used to work with EMOD will use the default values provided below.
JSON format does not permit comments, but you can add “dummy” parameters to add contextual information to your files. Any keys that are not EMOD parameter names will be ignored by the model.
Contents
Metadata¶
Metadata provides information about data provenance. IdReference is the only parameter used by EMOD, but you are encouraged to include information for your own reference. For example, author, date created, tool used, NodeCount and more are commonly included in the Metadata section. You can include any information you like here provided it is in valid JSON format.
If you generate input files using COMPS, the following IdReference values are possible and indicate how the NodeID values are generated:
- Gridded world grump30arcsec
Nodes are approximately square regions defined by a 30-arc second grid and the NodeID values are generated from the latitude and longitude of the northwest corner.
- Gridded world grump2.5arcmin
Nodes are approximately square regions defined by a 2.5-arc minute grid and the NodeID values are generated from the latitude and longitude of the northwest corner.
- Gridded world grump1degree
Nodes are approximately square regions defined by a 1-degree grid and the NodeID values are generated from the latitude and longitude of the northwest corner.
The algorithm for encoding latitude and longitude into a NodeID is as follows:
unsigned int xpix = math.floor((lon + 180.0) / resolution)
unsigned int ypix = math.floor((lat + 90.0) / resolution)
unsigned int NodeID = (xpix << 16) + ypix + 1
This generates a NodeID that is a 4-byte unsigned integer; the first two bytes represent the longitude of the node and the second two bytes represent the latitude. To reserve 0 to be used as a null value, 1 is added to the NodeID as part of the final calculation.
Parameter |
Data type |
Minimum |
Maximum |
Default |
Description |
Example |
|---|---|---|---|---|---|---|
Author |
string |
NA |
NA |
NA |
The person who created the demographics file. Files generated by COMPS will include this value, but it is not used by EMOD simulations. |
{
"Metadata": {
"DateCreated": "Sun Sep 25 23:19:55 2011",
"Tool": "convertdemog.py",
"Author": "jdoe",
"IdReference": "Gridded world grump2.5arcmin",
"NodeCount": 1
}
}
|
DateCreated |
string |
NA |
NA |
NA |
The date the demographics file was created. Files generated by COMPS will include this value, but it is not used by EMOD simulations. |
{
"Metadata": {
"DateCreated": "09212017",
"IdReference": "Gridded world grump2.5arcmin",
"NodeCount": 23
}
}
|
IdReference |
string |
NA |
NA |
NA |
The identifier for a simulation; all input files (except configuration and campaign files) used in a simulation must have the same IdReference value. The value must be greater than 0. If the input files are generated using COMPS, this indicates the method used for generating the NodeID, the identifier used for each node in the simulation. |
{
"Metadata": {
"IdReference": "Gridded world grump30arcsec"
}
}
|
Metadata |
JSON object |
NA |
NA |
NA |
The structure that contains the metadata for the demographics file. |
{
"Metadata": {
"IdReference": "Gridded world grump30arcsec",
"NodeCount": 20
}
}
|
NodeCount |
integer |
1 |
Depends on available memory |
NA |
The number of nodes to expect in the input files. This parameter is required. |
{
"Metadata": {
"NodeCount": 2
}
}
|
Resolution |
integer |
NA |
NA |
NA |
The spatial resolution of the demographics file. Files generated by COMPS will include this value, but it is not used by EMOD simulations. |
{
"Metadata": {
"Resolution": 150
}
}
|
Tool |
string |
NA |
NA |
NA |
The software tool used to create the demographics file. Files generated by COMPS will include this value, but it is not used by EMOD simulations. |
{
"Metadata": {
"Tool": "convertdemog.py",
"Author": "jdoe",
"IdReference": "Gridded world grump2.5arcmin",
"Resolution": 150,
"NodeCount": 1
}
}
|
NodeProperties and IndividualProperties¶
Node properties and individual properties are set similarly and share many of the same parameters. Properties can be thought of as tags that are assigned to nodes or individuals and can then be used to either target interventions to nodes or individuals with certain properties (or prevent them from being targeted). For example, you could define individual properties for disease risk and then target an intervention to only those at high risk. Similarly, you could define properties for node accessibility and set lower intervention coverage for nodes that are difficult to access.
Individual properties are also used to simulate health care cascades. For example, you can disqualify an individual who would otherwise receive an intervention; such as treating a segment of the population with a second-line treatment but disqualifying those who haven’t already received the first-line treatment. Then you can change the property value after the treatment has been received.
The NodeProperties section is a top-level section at the same level as Defaults and Nodes that contains parameters that assign properties to nodes in a simulation. The IndividualProperties section is under either Defaults or Nodes and contains parameters that assign properties to individuals in a simulation.
Individual and node properties provides more guidance and Generic model scenarios provides some example scenarios that use properties.
Parameter |
Data type |
Minimum |
Maximum |
Default |
Description |
Example |
|---|---|---|---|---|---|---|
Age_Bin_Edges_In_Years |
array |
NA |
NA |
NA |
An array of integers that represents the ages, in years, at which to demarcate the age groups for individuals. Used only with the Age_Bin property type. The first number must be 0, the last must be -1, and they must be listed in ascending order. Cannot be used with NodeProperties. EMOD automatically create the individual property Age_Bin with values based on the bin edges using the format Age_Bin_Property_From_X_To_Y. These appear in the property reports and can be used to target campaign interventions using Property_Restrictions_Within_Node. See Targeting interventions to nodes or individuals for more information. |
The following example creates three age groups: 0 to 5, older than 5 to 13, and older than 13 to the maximum age. {
"Defaults": {
"IndividualProperties": [
{
"Property": "Age_Bin",
"Age_Bin_Edges_In_Years": [
0,
5,
13,
-1
]
}
]
}
}
|
IndividualProperties |
array of objects |
NA |
NA |
NA |
An array that contains parameters that add properties to individuals in a simulation. For example, you can define values for accessibility, age, geography, risk, and other properties and assign values to different individuals. alues. |
{
"Defaults": {
"IndividualProperties": [
{
"Property": "InterventionStatus",
"Values": [
"None",
"ARTStaging"
],
"Initial_Distribution": [
1,
0
]
},
{
"Property": "Risk",
"Values": [
"High",
"Medium",
"Low"
],
"Initial_Distribution": [
0.2,
0.5,
0.3
]
}
]
}
}
|
Initial_Distribution |
array of floats |
0 |
1 |
1 |
An array of floats that define the proportion of property values to assign to individuals or nodes at the beginning of the simulation and when new individuals are born. Their sum must equal 1 and the number of members in this array must match the number of members in Values. For Age_Bin property types, omit this parameter as the demographics file controls the age distribution. |
{
"NodeProperties": [
{
"Property": "InterventionStatus",
"Values": [
"NONE",
"RECENT_SPRAY"
],
"Initial_Distribution": [
1.0,
0.0
]
}
]
}
{
"Nodes": [
{
"NodeID": 25,
"IndividualProperties": [
{
"Initial_Distribution": [
0.2,
0.4,
0.4
]
}
]
}
]
}
|
NodeProperties |
array of objects |
NA |
NA |
NA |
An array that contains parameters that add properties to nodes in a simulation. Defined in the demographics file at the same level as Nodes and Defaults. For example, you can define values for intervention status, risk, and other properties and assign values to different nodes. |
{
"NodeProperties": [
{
"Property": "Place",
"Values": [
"RURAL",
"URBAN"
],
"Initial_Distribution": [
0.85,
0.15
]
},
{
"Property": "InterventionStatus",
"Values": [
"NONE",
"SPRAYED_A",
"SPRAYED_B",
"FENCE_AND_TRAP"
],
"Initial_Distribution": [
1,
0,
0,
0
]
}
],
"Nodes": [
{
"NodeID": 1,
"NodeAttributes": {
"Latitude": 0,
"Longitude": 0,
"Altitude": 0,
"Airport": 0,
"Region": 1,
"Seaport": 0,
"InitialPopulation": 10000,
"BirthRate": 5.48e-05,
"NodePropertyValues": [
"Place:URBAN"
]
}
}
]
}
|
Property |
enum |
NA |
NA |
NA |
The individual or node property type for which you will assign values to create groups. You can then update the property values assigned to individuals or nodes or target interventions to particular groups. Note that these types, with the exception of Age_Bin, are merely labels that do not affect the simulation unless specified to do so. Possible values are:
|
{
"NodeProperties": [
{
"Property": "InterventionStatus",
"Values": [
"NONE",
"RECENT_SPRAY"
],
"Initial_Distribution": [
1.0,
0.0
]
}
]
}
{
"Defaults": {
"IndividualProperties": [
{
"Property": "Age_Bin",
"Age_Bin_Edges_In_Years": [
0,
6,
10,
20,
-1
]
}
]
}
}
|
Values |
array of strings |
NA |
NA |
NA |
An array of the user-defined values that can be assigned to individuals or nodes for this property. The order of the values corresponds to the order of the Initial_Distribution array. You can have up to 125 values for the Geographic and InterventionStatus property types and up to 5 values for all other types. For Age_Bin property types, omit this parameter and use Age_Bin_Edges_In_Years instead. |
{
"NodeProperties": [
{
"Property": "InterventionStatus",
"Values": [
"NONE",
"RECENT_SPRAY"
],
"Initial_Distribution": [
1.0,
0.0
]
}
]
}
{
"Defaults": {
"IndividualProperties": [
{
"Values": [
"Low",
"Medium",
"High"
]
}
]
}
}
|
NodeAttributes¶
The NodeAttributes section contains parameters that add or modify information regarding the location, migration, habitat, and population of node. Some NodeAttributes depend on values set in the configuration parameters.
Parameter |
Data type |
Minimum |
Maximum |
Default |
Description |
Example |
|---|---|---|---|---|---|---|
Airport |
boolean |
0 |
1 |
0 |
Indicates whether or not the node has an airport for air migration from (not to) the node. If set to 1, Enable_Air_Migration in the configuration file must be set to 1 or migration will not occur (see Migration parameters). Primarily used to turn off migration in a particular node. |
{
"Defaults": {
"NodeAttributes": {
"Airport": 0
}
}
}
|
Altitude |
float |
-3.40282e+038 |
3.40282e+038 |
0 |
The altitude, in meters, for the node. Required, but only used when Climate_Model is set to CLIMATE_KOPPEN. |
{
"Defaults": {
"NodeAttributes": {
"Altitude": 250
}
}
}
|
BirthRate |
double |
0 |
1 |
0.00008715 |
The birth rate, in births per person per day. In the configuration file, Enable_Birth must be set to 1 and Birth_Rate_Dependence will affect how this rate is used (see Population dynamics parameters). |
{
"Nodes": [
{
"NodeID": 21,
"NodeAttributes": {
"BirthRate": 0.0001
}
}
]
}
|
InfectivityReservoirEndTime |
float |
InfectivityReservoirStartTime |
3.40282e+038 |
3.40282e+038 |
The ending of the exogeneous reservoir of infectivity. This parameter is conditional upon the configuration parameter, Enable_Infectivity_Reservoir, being enabled (set to 1). |
{
"NodeAttributes": {
"InfectivityReservoirSize": 0.1,
"InfectivityReservoirStartTime": 90,
"InfectivityReservoirEndTime": 365
}
}
|
InfectivityReservoirSize |
float |
0 |
3.40282e+038 |
0 |
The quantity-per-timestep added to the total infectivity present in a node; it is equivalent to the expected number of additional infections in a node, per timestep. For example, if timestep is equal to a day, then setting InfectivityReservoirSize to a value of 0.1 would introduce an infection every 10 days from the exogenous reservoir. This parameter is conditional upon the configuration parameter, Enable_Infectivity_Reservoir, being enabled (set to 1). |
{
"NodeAttributes": {
"InfectivityReservoirSize": 0.1,
"InfectivityReservoirStartTime": 90,
"InfectivityReservoirEndTime": 365
}
}
|
InfectivityReservoirStartTime |
float |
0 |
3.40282e+038 |
0 |
The beginning of the exogeneous reservoir of infectivity. This parameter is conditional upon the configuration parameter, Enable_Infectivity_Reservoir, being enabled (set to 1). |
{
"NodeAttributes": {
"InfectivityReservoirSize": 0.1,
"InfectivityReservoirStartTime": 90,
"InfectivityReservoirEndTime": 365
}
}
|
InitialPopulation |
integer |
0 |
2.15E+0 |
1000 |
The number of people that will be populated into the node at the beginning of the simulation. You can scale this number using Base_Population_Scale_Factor in the configuration file (see Population dynamics parameters). |
{
"Nodes": [
{
"NodeID": 25,
"NodeAttributes": {
"InitialPopulation": 1000
}
}
]
}
|
InitialVectorsPerSpecies |
JSON object |
0 |
2.15e+09 |
10,000 |
The number of vectors per species that will be populated into the node at the beginning of the simulation. Population responds to habitat availability that can be scaled by LarvalHabitatMultiplier. Vector_Sampling_Type in the configuration file must be set to TRACK_ALL_VECTORS or SAMPLE_IND_VECTORS. |
{
"Nodes": [
{
"NodeID": 340461476,
"NodeAttributes": {
"InitialVectorsPerSpecies": {
"aegypti": 100,
"funestus": 0,
"gambiae": 0
}
}
}
]
}
|
LarvalHabitatMultiplier |
float or nested JSON object |
NA |
NA |
NA |
The value by which to scale the larval habitat availability specified in the configuration file with Larval_Habitat_Types across all habitat types, for specific habitat types, or for specific mosquito species within each habitat type. |
The following example scales the larval habitat equally across all habitat types and mosquito species. {
"LarvalHabitatMultiplier": [
{
"Habitat": "ALL_HABITATS",
"Species": "ALL_SPECIES",
"Factor": 0.2
}
]
}
The following example scales the larval habitat only in the temporary rainfall habitat for all mosquito species. {
"LarvalHabitatMultiplier": [
{
"Habitat": "TEMPORARY_RAINFALL",
"Species": "ALL_SPECIES",
"Factor": 0.2
}
]
}
The following example scales the larval habitat independently for A. gambiae in the temporary rainfall habitat and for A. arabiensis in the brackish swamp habitat. {
"LarvalHabitatMultiplier": [
{
"Habitat": "TEMPORARY_RAINFALL",
"Species": "gambiae",
"Factor": 0.1
},
{
"Habitat": "BRACKISH_SWAMP",
"Species": "arabiensis",
"Factor": 0.5
}
]
}
|
Latitude |
float |
3.40282e+038 |
-3.40282e+038 |
-1 |
Latitude of the node in decimal degrees. This can be used for several things, including determining infectiousness by latitude and defining the size of grid cells. |
{
"Nodes": [
{
"NodeID": 25,
"NodeAttributes": {
"Latitude": 12.4,
"Longitude": 9.35
}
}
]
}
|
Longitude |
float |
-3.40282e+38 |
3.40282e+38 |
-1 |
Longitude of the node in decimal degrees. This can be used for several things, including defining the size of grid cells. |
{
"Nodes": [
{
"NodeID": 254,
"NodeAttributes": {
"Latitude": 25.4,
"Longitude": 9.1
}
}
]
}
|
NodeAttributes |
JSON object |
NA |
NA |
NA |
The structure that contains parameters that add or modify information regarding the location, migration, habitat, and population of a simulation. Some NodeAttributes depend on values set in the configuration parameters. |
{
"Nodes": [
{
"NodeID": 1487548419,
"NodeAttributes": {
"Latitude": 12.4208,
"Longitude": 9.15417
}
}
]
}
|
PercentageVectorsBySpecies |
JSON object |
NA |
NA |
NA |
A list of key-value pairs of the vector species and percentage of the total they each make up. |
{
"Defaults": {
"NodeAttributes": {
"PercentageVectorsBySpecies": {
"arabiensis": 0.3,
"funestus": 0.3,
"gambiae": 0.4
}
}
}
}
|
Region |
boolean |
0 |
1 |
0 |
Indicates whether or not the node has a road network for regional migration from (not to) the node. If set to 1, Enable_Regional_Migration in the configuration file must be set to 1 or migration will not occur (see Migration parameters). Primarily used to turn off migration in particular nodes. |
{
"Nodes": [
{
"NodeID": 12,
"NodeAttributes": {
"Region": 1
}
}
]
}
|
Seaport |
boolean |
0 |
1 |
0 |
Indicates whether or not the node is connected by sea migration from (not to) the node. If set to 1, Enable_Sea_Migration in the configuration file must be set to 1 or migration will not occur (see Migration parameters). Primarily used to turn off migration in particular nodes. |
{
"Nodes": [
{
"NodeID": 43,
"NodeAttributes": {
"Seaport": 1
}
}
]
}
|
IndividualAttributes¶
The IndividualAttributes section contains parameters that initialize the distribution of attributes across individuals, such as the age or immunity. An initial value for an individual is a randomly selected value from a given distribution. These distributions can be configured using a simple flag system of three parameters or a complex system of many more parameters. The following table contains the parameters that can be used with either distribution system.
Parameter |
Data type |
Minimum |
Maximum |
Default |
Description |
Example |
|---|---|---|---|---|---|---|
IndividualAttributes |
JSON object |
NA |
NA |
NA |
The structure that contains parameters that add or modify the distribution of attributes across individuals in a simulation. For example, the age or immunity distribution. An initial value for an individual is a randomly selected value from a distribution. For example, if you use a uniform distribution to initialize age, the initial ages of individuals in the simulation will be evenly distributed between some minimum and maximum value. These distributions can be set using Simple distributions or Complex distributions. |
{
"Defaults": {
"IndividualAttributes": {
"AgeDistributionFlag": 0,
"AgeDistribution1": 25550,
"AgeDistribution2": 0
}
}
}
|
PercentageChildren |
float |
0 |
1 |
NA |
The percentage of individuals in the node that are children. Set Minimum_Adult_Age_Years to determine the age at which individuals transition to adults. |
{
"Nodes": {
"NodeID": 45,
"IndividualAttributes": {
"PercentageChildren": 0.7
}
}
}
|
Simple distributions¶
Simple distributions are defined by three parameters where one is a flag for the distribution type and the other two are used to further define the distribution. For example, if you set the age flag to a uniform distribution, the initial ages of individuals in the simulation will be evenly distributed between some minimum and maximum value as defined by the other two parameters.
Parameter |
Data type |
Minimum |
Maximum |
Default |
Description |
Example |
||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
AgeDistribution1 |
float |
-3.40282e+038 |
3.40282e+038 |
0.000118 |
The first value in the age distribution, the meaning of which depends upon the value set in AgeDistributionFlag. The table below shows the flag value and corresponding distribution value.
Age_Initialization_Distribution_Type in the configuration file must be set to DISTRIBUTION_SIMPLE (see Population dynamics parameters). |
{
"IndividualAttributes": {
"AgeDistributionFlag": 0,
"AgeDistribution1": 25550,
"AgeDistribution2": 0
}
}
|
||||||||||||||||||
AgeDistribution2 |
float |
-3.40282e+038 |
3.40282e+038 |
0 |
The second value in the age distribution, the meaning of which depends upon the value set in AgeDistributionFlag. The table below shows the flag value and corresponding distribution value.
Age_Initialization_Distribution_Type in the configuration file must be set to DISTRIBUTION_SIMPLE (see Population dynamics parameters). |
{
"IndividualAttributes": {
"AgeDistributionFlag": 0,
"AgeDistribution1": 25550,
"AgeDistribution2": 0
}
}
|
||||||||||||||||||
AgeDistributionFlag |
integer |
0 |
7 |
3 |
The type of distribution to use for age. Possible values are:
Age_Initialization_Distribution_Type in the configuration file must be set to DISTRIBUTION_SIMPLE (see Population dynamics parameters). |
{
"IndividualAttributes": {
"AgeDistributionFlag": 0,
"AgeDistribution1": 25550,
"AgeDistribution2": 0
}
}
|
||||||||||||||||||
MigrationHeterogeneityDistribution1 |
float |
-3.40282e+38 |
3.40282e+38 |
1 |
The first value in the migration heterogeneity distribution, the meaning of which depends upon the value set in MigrationHeterogeneityFlag. The table below shows the flag value and corresponding distribution value.
Enable_Migration_Heterogeneity in the configuration file must be set to 1 (see Migration parameters). |
{
"IndividualAttributes": {
"MigrationHeterogeneityDistributionFlag": 0,
"MigrationHeterogeneityDistribution1": 1,
"MigrationHeterogeneityDistribution2": 0
}
}
|
||||||||||||||||||
MigrationHeterogeneityDistribution2 |
float |
-3.40282e+038 |
3.40282e+038 |
0 |
The second value in the distribution, the meaning of which depends upon the value set in MigrationHeterogeneityDistributionFlag. The table below shows the flag value and corresponding distribution value.
Enable_Migration_Heterogeneity in the configuration file must be set to 1 (see Migration parameters). |
{
"IndividualAttributes": {
"MigrationHeterogeneityDistributionFlag": 0,
"MigrationHeterogeneityDistribution1": 1,
"MigrationHeterogeneityDistribution2": 0
}
}
|
||||||||||||||||||
MigrationHeterogeneityDistributionFlag |
integer |
0 |
7 |
0 |
The type of distribution to use for migration heterogeneity. Possible values are:
Enable_Migration_Heterogeneity in the configuration file must be set to 1 (see Migration parameters). |
{
"IndividualAttributes": {
"MigrationHeterogeneityDistributionFlag": 0,
"MigrationHeterogeneityDistribution1": 1,
"MigrationHeterogeneityDistribution2": 0
}
}
|
||||||||||||||||||
PrevalenceDistribution1 |
float |
-3.40282e+038 |
3.40282e+038 |
1 |
The first value in the prevalence distribution, the meaning of which depends upon the value set in PrevalenceDistributionFlag. The table below shows the flag value and corresponding distribution value.
|
{
"IndividualAttributes": {
"PrevalenceDistributionFlag": 0,
"PrevalenceDistribution1": 0.0,
"PrevalenceDistribution2": 0.0
}
}
|
||||||||||||||||||
PrevalenceDistribution2 |
float |
-3.40282e+038 |
3.40282e+038 |
0 |
The second value in the distribution, the meaning of which depends upon the value set in PrevalenceDistributionFlag. The table below shows the flag value and corresponding distribution value.
|
{
"IndividualAttributes": {
"PrevalenceDistributionFlag": 0,
"PrevalenceDistribution1": 0.0,
"PrevalenceDistribution2": 0.0
}
}
|
||||||||||||||||||
PrevalenceDistributionFlag |
integer |
0 |
7 |
0 |
The type of distribution to use for prevalence. Possible values are:
|
{
"IndividualAttributes": {
"PrevalenceDistributionFlag": 0,
"PrevalenceDistribution1": 0.0,
"PrevalenceDistribution2": 0.0
}
}
|
||||||||||||||||||
RiskDistribution1 |
float |
-3.40282e+038 |
3.40282e+038 |
0 |
The first value in the risk distribution, the meaning of which depends upon the value set in RiskDistributionFlag. The table below shows the flag value and corresponding distribution value.
|
{
"IndividualAttributes": {
"RiskDistributionFlag": 0,
"RiskDistribution1": 1,
"RiskDistribution2": 0
}
}
|
||||||||||||||||||
RiskDistribution2 |
float |
-3.40282e+038 |
3.40282e+038 |
0 |
The second value in the distribution, the meaning of which depends upon the value set in RiskDistributionFlag. The table below shows the flag value and corresponding distribution value.
|
{
"IndividualAttributes": {
"RiskDistributionFlag": 0,
"RiskDistribution1": 1,
"RiskDistribution2": 0
}
}
|
||||||||||||||||||
RiskDistributionFlag |
integer |
0 |
7 |
0 |
The type of distribution to use for risk. Possible values are:
Enable_Demographics_Risk must be set to 1 (see Population dynamics parameters). |
{
"IndividualAttributes": {
"RiskDistributionFlag": 0,
"RiskDistribution1": 1,
"RiskDistribution2": 0
}
}
|
||||||||||||||||||
SusceptibilityDistribution1 |
float |
-3.40282e+038 |
3.40282e+038 |
0 |
The first value in the susceptibility distribution, the meaning of which depends upon the value set in SusceptibilityDistributionFlag. The table below shows the flag value and corresponding distribution value.
In the configuration file, Enable_Immunity must be set to 1 and Susceptibility_Initialization_Distribution_Type must be set to DISTRIBUTION_SIMPLE (see Immunity parameters). |
{
"IndividualAttributes": {
"SusceptibilityDistributionFlag": 0,
"SusceptibilityDistribution1": 1,
"SusceptibilityDistribution2": 0
}
}
|
||||||||||||||||||
SusceptibilityDistribution2 |
float |
-3.40282e+038 |
3.40282e+038 |
0 |
The second value in the susceptibility distribution, the meaning of which depends upon the value set in SusceptibilityDistributionFlag. The table below shows the flag value and corresponding distribution value.
In the configuration file, Enable_Immunity must be set to 1 and Susceptibility_Initialization_Distribution_Type must be set to DISTRIBUTION_SIMPLE (see Immunity parameters). |
{
"IndividualAttributes": {
"SusceptibilityDistributionFlag": 0,
"SusceptibilityDistribution1": 1,
"SusceptibilityDistribution2": 0
}
}
|
||||||||||||||||||
SusceptibilityDistributionFlag |
integer |
0 |
7 |
0 |
The type of distribution to use for determining an individual’s probability of full susceptibility. Possible values are:
In the configuration file, Enable_Immunity must be set to 1 and Susceptibility_Initialization_Distribution_Type must be set to DISTRIBUTION_SIMPLE (see Immunity parameters). |
{
"IndividualAttributes": {
"SusceptibilityDistributionFlag": 0,
"SusceptibilityDistribution1": 1,
"SusceptibilityDistribution2": 0
}
}
|
Complex distributions¶
Complex distributions are more effort to configure, but are useful for representing real-world data where the distribution does not fit a standard. Individual attribute values are drawn from a piecewise linear distribution. The distribution is configured using arrays of axes (such as gender or age) and values at points along each of these axes. This allows you to have different distributions for different groups in the population.
Parameter |
Data type |
Minimum |
Maximum |
Default |
Description |
Example |
|---|---|---|---|---|---|---|
AgeDistribution |
JSON object |
NA |
NA |
NA |
The structure defining a complex age distribution. Age_Initialization_Distribution_Type in the configuration file must be set to DISTRIBUTION_COMPLEX. |
The following example shows at age distribution in which 25% of individuals are under age 5, 50% are between 5 and 20, and 25% are between 20 and 35. {
"IndividualAttributes": {
"AgeDistribution": {
"ResultUnits": "years",
"ResultScaleFactor": 365,
"ResultValues": [
0,
0.25,
0.75,
1
],
"DistributionValues": [
0,
5,
20,
35
]
}
}
}
|
AxisNames |
array of strings |
NA |
NA |
NA |
An array of the names used for each axis of a complex distribution. The list below shows the axis names to use (in the order given) for each of the distribution types:
[“age”] is the only value accepted for all malaria-specific distributions:
|
{
"IndividualAttributes": {
"MortalityDistribution": {
"AxisNames": [
"gender",
"age"
],
"AxisUnits": [
"male=0,female=1",
"years"
],
"AxisScaleFactors": [
1,
365
],
"NumPopulationGroups": [
2,
1
],
"PopulationGroups": [
[
0,
1
],
[
0
]
],
"ResultUnits": "annual deaths per 1000 individuals",
"ResultScaleFactor": 2.739726027397e-06,
"ResultValues": [
[
0
],
[
0
]
]
}
}
}
|
AxisScaleFactors |
array of floats |
3.40282e+038 |
-3.40282e+038 |
1 |
A list of the scale factors used to convert axis units to data measurements in a complex distribution. For example, 365 to convert daily mortality to annual mortality. The array must contain one factor for each axis. |
{
"IndividualAttributes": {
"MortalityDistribution": {
"AxisNames": [
"gender",
"age"
],
"AxisUnits": [
"male=0,female=1",
"years"
],
"AxisScaleFactors": [
1,
365
],
"NumPopulationGroups": [
2,
1
],
"PopulationGroups": [
[
0,
1
],
[
0
]
],
"ResultUnits": "annual deaths per 1000 individuals",
"ResultScaleFactor": 2.739726027397e-06,
"ResultValues": [
[
0
],
[
0
]
]
}
}
}
|
AxisUnits |
array of strings |
NA |
NA |
NA |
An array that describes the scale factors used to convert the units for the axes into the units expected by EMOD. For example, when age is provided in years but must be scaled to days. EMOD does not use this value; it is only informational. |
{
"IndividualAttributes": {
"MortalityDistribution": {
"AxisNames": [
"gender",
"age"
],
"AxisUnits": [
"male=0,female=1",
"years"
],
"AxisScaleFactors": [
1,
365
]
}
}
}
|
DistributionValues |
array of floats |
0 |
1 |
1 |
An array of values between 0 and 1 listed in ascending order that defines a complex age distribution. Each value represents the proportion of the population below that age and the difference between two successive values is the proportion of the population in the age bin defined in ResultValues. Age_Initialization_Distribution_Type in the configuration file must be set to DISTRIBUTION_COMPLEX (see Population dynamics parameters). |
The following example shows at age distribution in which 25% of individuals are under age 5, 50% are between 5 and 20, and 25% are between 20 and 35. {
"IndividualAttributes": {
"AgeDistribution": {
"ResultUnits": "years",
"ResultScaleFactor": 365,
"AxisScaleFactors": 1,
"DistributionValues": [
0,
0.25,
0.75,
1
],
"ResultValues": [
0,
5,
20,
35
]
}
}
}
|
FertilityDistribution |
JSON object |
NA |
NA |
NA |
The distribution of the fertility rate in the population. Enable_Birth in the configuration file must be set to 1 (see Population dynamics parameters). |
{
"IndividualAttributes": {
"FertilityDistribution": {
"NumDistributionAxes": 2,
"AxisNames": [
"urban",
"XXX"
],
"AxisUnits": [
"rural=0, urban=1",
"years"
],
"AxisScaleFactors": [
1,
365
],
"NumPopulationGroups": [
2,
9
],
"PopulationGroups": [
[
0,
1
],
[
0,
15,
20,
25,
30,
35,
40,
45,
49
]
],
"ResultUnits": "annual births per 1000 individuals",
"ResultScaleFactor": 2.739726027397e-06,
"ResultValues": [
[
0,
28.4,
190.3,
222.4,
155.4,
68,
21.9,
3.6,
0
],
[
0,
28.4,
190.3,
222.4,
155.4,
68,
21.9,
3.6,
0
]
]
}
}
}
|
ImmunityDistribution |
JSON object |
NA |
NA |
NA |
The structure defining a complex immunity distribution. Immunity_Initialization_Distribution_Type in the configuration file must be set to DISTRIBUTION_COMPLEX (see Immunity parameters). |
{
"IndividualAttributes": {
"ImmunityDistribution": {
"AxisNames": [
"age"
],
"AxisUnits": [
"years"
],
"AxisScaleFactors": [
365
],
"NumPopulationGroups": [
1
],
"PopulationGroups": [
[
0
]
],
"ResultScaleFactor": 3.6952,
"ResultValues": [
[
0
]
]
}
}
}
|
MortalityDistribution |
JSON object |
NA |
NA |
NA |
The distribution of non-disease mortality for a population. Death_Rate_Dependence in the configuration file must be set to NONDISEASE_MORTALITY_BY_AGE_AND_GENDER or NONDISEASE_MORTALITY_BY_YEAR_AND_AGE_FOR_EACH_GENDER (see Mortality and survival parameters). Warning Mortality is sampled every 30 days. To correctly attribute neonatal deaths to days 0-30, you must indicate that the threshold for the first age group in PopulationGroups is less than 30 days. |
{
"IndividualAttributes": {
"MortalityDistribution": {
"AxisNames": [
"gender",
"age"
],
"AxisScaleFactors": [
1,
1
],
"NumDistributionAxes": 2,
"NumPopulationGroups": [
2,
4
],
"PopulationGroups": [
[
0,
1
],
[
0.0,
29.99,
365,
1826
]
],
"ResultScaleFactor": 1,
"ResultValues": [
[
0.0016,
0.000107,
6.3e-05,
100.0
],
[
0.0016,
0.000107,
6.3e-05,
100.0
]
]
}
}
}
|
MSP_mean_antibody_distribution |
JSON object |
NA |
NA |
NA |
The mean of the fraction of the antigenic variants of the anti-MSP antibody that the immune system has been exposed to, binned by age using PopulationGroups. ResultValues are bounded between 0 and 1, typically increasing with age. Immunity_Initialization_Distribution_Type in the configuration file must be set to DISTRIBUTION_COMPLEX. |
{
"IndividualAttributes": {
"MSP_mean_antibody_distribution": {
"AxisNames": [
"age"
],
"AxisUnits": [
"years"
],
"AxisScaleFactors": [
365
],
"NumPopulationGroups": [
11
],
"PopulationGroups": [
[
0,
0.5,
1.5,
2.5,
3.5,
4.5,
7.5,
15,
25,
35,
60
]
],
"ResultUnits": "mean fraction of antibody variants",
"ResultScaleFactor": 1,
"ResultValues": [
0,
0.0668,
0.1499,
0.2279,
0.2988,
0.3743,
0.5576,
0.8248,
0.8866,
0.8748,
0.8723
]
}
}
}
|
MSP_variance_antibody_distribution |
JSON object |
NA |
NA |
NA |
The variance of the fraction of the antigenic variants of the anti-MSP antibody that the immune system has been exposed to, binned by age using PopulationGroups. ResultValues are bounded between 0 and 1, typically increasing with age. Immunity_Initialization_Distribution_Type in the configuration file must be set to DISTRIBUTION_COMPLEX. |
{
"IndividualAttributes": {
"MSP_variance_antibody_distribution": {
"AxisNames": [
"age"
],
"AxisUnits": [
"years"
],
"AxisScaleFactors": [
365
],
"NumPopulationGroups": [
11
],
"PopulationGroups": [
[
0,
0.5,
1.5,
2.5,
3.5,
4.5,
7.5,
15,
25,
35,
60
]
],
"ResultUnits": "mean fraction of antibody variants",
"ResultScaleFactor": 1,
"ResultValues": [
0,
0.027,
0.029,
0.0271,
0.0309,
0.0323,
0.0899,
0.0726,
0.0285,
0.0267,
0.0279
]
}
}
}
|
nonspec_mean_antibody_distribution |
JSON object |
NA |
NA |
NA |
The mean of the fraction of the antigenic variants of non-specific malaria antibodies that the immune system has been exposed to, binned by age using PopulationGroups. ResultValues are bounded between 0 and 1, typically increasing with age. Immunity_Initialization_Distribution_Type in the configuration file must be set to DISTRIBUTION_COMPLEX. |
{
"IndividualAttributes": {
"nonspec_mean_antibody_distribution": {
"AxisNames": [
"age"
],
"AxisUnits": [
"years"
],
"AxisScaleFactors": [
365
],
"NumPopulationGroups": [
11
],
"PopulationGroups": [
[
0,
0.5,
1.5,
2.5,
3.5,
4.5,
7.5,
15,
25,
35,
60
]
],
"ResultUnits": "mean fraction of antibody variants",
"ResultScaleFactor": 1,
"ResultValues": [
0,
0.272,
0.5547,
0.7226,
0.8429,
0.9186,
0.9782,
0.9991,
1.0,
1.0,
1.0
]
}
}
}
|
nonspec_variance_antibody_distribution |
JSON object |
NA |
NA |
NA |
The variance of the fraction of the antigenic variants of non-specific malaria antibodies that the immune system has been exposed to, binned by age using PopulationGroups. ResultValues are bounded between 0 and 1, typically increasing with age. Immunity_Initialization_Distribution_Type in the configuration file must be set to DISTRIBUTION_COMPLEX. |
{
"IndividualAttributes": {
"nonspec_variance_antibody_distribution": {
"AxisNames": [
"age"
],
"AxisUnits": [
"years"
],
"AxisScaleFactors": [
365
],
"NumPopulationGroups": [
11
],
"PopulationGroups": [
[
0,
0.5,
1.5,
2.5,
3.5,
4.5,
7.5,
15,
25,
35,
60
]
],
"ResultUnits": "mean fraction of antibody variants",
"ResultScaleFactor": 1,
"ResultValues": [
0,
0.1146,
0.1008,
0.0795,
0.0781,
0.055,
0.0337,
0.0067,
0,
0,
0
]
}
}
}
|
NumDistributionAxes |
integer |
1 |
NA |
NA |
The number of axes to use for a complex distribution. EMOD does not use this value; it is only informational. |
{
"IndividualAttributes": {
"MortalityDistribution": {
"NumDistributionAxes": 2,
"AxisNames": [
"gender",
"age"
],
"AxisScaleFactors": [
1,
365
]
}
}
}
|
NumPopulationGroups |
array of integers |
NA |
NA |
NA |
An array of population groupings for each independent variable for a complex distribution. This variable defines the number of columns for each row in the population group table. The number of values in the array is often two, representing the values for gender and number of age bins. EMOD does not use this value; it is only informational. |
{
"IndividualAttributes": {
"MortalityDistribution": {
"AxisNames": [
"gender",
"age"
],
"AxisUnits": [
"male=0,female=1",
"years"
],
"AxisScaleFactors": [
1,
365
],
"NumPopulationGroups": [
2,
1
],
"PopulationGroups": [
[
0,
1
],
[
0
]
],
"ResultUnits": "annual deaths per 1000 individuals",
"ResultScaleFactor": 2.739726027397e-06,
"ResultValues": [
[
0
],
[
0
]
]
}
}
}
|
PfEMP1_mean_antibody_distribution |
JSON object |
NA |
NA |
NA |
The mean of the fraction of the antigenic variants of the PfEMP1 antibody that the immune system has been exposed to, binned by age using PopulationGroups. ResultValues are bounded between 0 and 1, typically increasing with age. Immunity_Initialization_Distribution_Type in the configuration file must be set to DISTRIBUTION_COMPLEX. |
{
"IndividualAttributes": {
"PfEMP1_mean_antibody_distribution": {
"NumDistributionAxes": 1,
"AxisNames": [
"age"
],
"AxisUnits": [
"years"
],
"AxisScaleFactors": [
365
],
"NumPopulationGroups": [
11
],
"PopulationGroups": [
[
0,
0.5,
1.5,
2.5,
3.5,
4.5,
7.5,
15,
25,
35,
60
]
],
"ResultUnits": "mean fraction of antibody variants",
"ResultScaleFactor": 1,
"ResultValues": [
0,
0.1265,
0.3071,
0.4547,
0.568,
0.6627,
0.809,
0.9405,
0.9772,
0.9796,
0.9801
]
}
}
}
|
PfEMP1_variance_antibody_distribution |
JSON object |
NA |
NA |
NA |
The variance of the fraction of the antigenic variants of the PfEMP1 antibody that the immune system has been exposed to, binned by age using PopulationGroups. ResultValues are bounded between 0 and 1, typically increasing with age. Immunity_Initialization_Distribution_Type in the configuration file must be set to DISTRIBUTION_COMPLEX. |
{
"IndividualAttributes": {
"PfEMP1_variance_antibody_distribution": {
"AxisNames": [
"age"
],
"AxisUnits": [
"years"
],
"AxisScaleFactors": [
365
],
"NumPopulationGroups": [
11
],
"PopulationGroups": [
[
0,
0.5,
1.5,
2.5,
3.5,
4.5,
7.5,
15,
25,
35,
60
]
],
"ResultUnits": "mean fraction of antibody variants",
"ResultScaleFactor": 1,
"ResultValues": [
0,
0.0606,
0.0509,
0.0386,
0.0334,
0.0274,
0.0575,
0.0261,
0.005,
0.0045,
0.0044
]
}
}
}
|
PopulationGroups |
matrix of integers |
NA |
NA |
NA |
An array in which each row represents one of the distribution axes and contains the values that the independent variable can take. The values must be listed in ascending order and each defines the left edge of the bin. Warning Mortality is sampled every 30 days. To correctly attribute neonatal deaths to days 0-30, you must indicate that the threshold for the first age group in PopulationGroups is less than 30 days. |
The following example configures relatively high infant mortality and lower mortality at ages 10 and 40, with everyone dead by age 120. {
"IndividualAttributes": {
"MortalityDistribution": {
"AxisNames": [
"gender",
"age"
],
"AxisUnits": [
"male=0,female=1",
"years"
],
"AxisScaleFactors": [
1,
365
],
"NumPopulationGroups": [
2,
1
],
"PopulationGroups": [
[
0,
1
],
[
0,
10,
40,
120
]
],
"ResultUnits": "annual deaths per 1000 individuals",
"ResultScaleFactor": 2.739726027397e-06,
"ResultValues": [
[
51.6,
3.7,
5.3,
1000
],
[
60.1,
4.1,
4.8,
1000
]
]
}
}
}
|
ResultScaleFactor |
float |
-3.40282e+038 |
3.40282e+038 |
1 |
The scale factor used to convert ResultUnits to number of births, deaths, or another variable per individual per day. |
{
"IndividualAttributes": {
"AgeDistribution": {
"AxisScaleFactors": 1,
"DistributionValues": [
0.99,
1.0
],
"ResultScaleFactor": 365,
"ResultUnits": "years",
"ResultValues": [
0.0027,
0.0027
]
}
}
}
|
ResultUnits |
string |
NA |
NA |
NA |
A string that indicates the units used for the ResultValues parameter of a complex distribution. EMOD does not use this value; it is only informational. The values here are scaled by the value in ResultScaleFactor before being passed to EMOD as a daily rate. |
{
"IndividualAttributes": {
"MortalityDistribution": {
"NumPopulationGroups": [
2,
1
],
"PopulationGroups": [
[
0,
1
],
[
0
]
],
"ResultUnits": "annual deaths per 1000 individuals",
"ResultScaleFactor": 2.739726027397e-06,
"ResultValues": [
[
0
],
[
0
]
]
}
}
}
|
ResultValues |
array of floats |
NA |
NA |
NA |
An array in which each row represents one of the distribution axes and contains the dependent variable values. The units are configurable; the values are scaled by the value in ResultScaleFactor before being passed to EMOD in units of days. For age distributions, it lists in ascending order the ages at which to bin the population. The corresponding values in DistributionValues represent the proportion of the population that is below that age. If the first member of the array is non-zero, the first bin is defined as those with that exact value (EMOD does not assume the bins start at zero). For all other distributions, an array in which each row represents the values for a combination of axes. For example, a mortality distribution that includes both gender and age axes will have a row for males and a row for females that each contain the mortality rate at various ages set in PopulationGroups. |
The following example shows an age distribution in which 10% of individuals are newborn, 25% are under age 5, 50% are between 5 and 20, and 25% are between 20 and 35. {
"IndividualAttributes": {
"AgeDistribution": {
"DistributionValues": [
0.1,
0.25,
0.75,
1
],
"ResultValues": [
0,
5,
20,
35
]
}
}
}
The following example configures relatively high infant mortality and lower mortality at ages 10 and 40, with everyone dead by age 120. {
"IndividualAttributes": {
"MortalityDistribution": {
"AxisNames": [
"gender",
"age"
],
"AxisUnits": [
"male=0,female=1",
"years"
],
"AxisScaleFactors": [
1,
365
],
"NumPopulationGroups": [
2,
1
],
"PopulationGroups": [
[
0,
1
],
[
0,
10,
40,
120
]
],
"ResultUnits": "annual deaths per 1000 individuals",
"ResultScaleFactor": 2.739726027397e-06,
"ResultValues": [
[
51.6,
3.7,
5.3,
1000
],
[
60.1,
4.1,
4.8,
1000
]
]
}
}
}
|
SusceptibilityDistribution |
JSON object |
NA |
NA |
NA |
The structure defining a complex immunity/susceptibility distribution. Susceptibility_Initialization_Distribution_Type in the configuration file must be set to DISTRIBUTION_COMPLEX (see Immunity parameters). |
{
"IndividualAttributes": {
"SusceptibilityDistribution": {
"AxisNames": [
"age"
],
"AxisScaleFactors": [
365
],
"AxisUnits": [
"years"
],
"NumPopulationGroups": [
1
],
"PopulationGroups": [
[
0
]
],
"ResultScaleFactor": 3.6952,
"ResultValues": [
[
0
]
]
}
}
}
|