Use demographics overlay files¶
You can use multiple demographic files when setting up a simulation. The “base layer” file contains default parameter settings and one or more overlay files contains additional parameters or different parameter values that override the values in the default file. This topic describes how to set up the base layer and overlay files.
Demographic overlay files allow you to do the following:
- Separate different sets of parameters and values into individual overlays (for example, to separate those that are useful for specific diseases into different overlay files)
- Add new parameters for a simulation into an overlay for easier prototyping
- Override certain parameters of interest in an overlay
- Override certain parameters for a particular sub-region
- Simulating subsets of a larger region for which input data files have been constructed
Select the demographics file to use as the base layer file. All nodes to be included in the simulation must be listed in this file.
In the metadata, make note of the IdReference value.
You may change this value if you desire, but all input files for a simulation must have the same IdReference value. For more information about this parameter and the structure of demographics files in general, see Demographics parameters.
Create one or more overlay files. Keep the following things in mind:
- In the metadata, the value for IdReference must match the value in the base layer file and all other input data files.
- Any nodes listed in an overlay but not in the base layer will not be simulated.
- If the demographics files include any JSON array elements, the entire array is overridden. You cannot add or remove individual elements in an array using an overlay file.
- Overriding a parameter value on a node will not affect the other parameter values applied to that node.
- Values set in the Defaults section of an overlay will be applied to all nodes listed in that file, not all nodes in the entire simulation. Therefore, an overlay file that includes a Defaults section but no Nodes section will not have any effect.
Place all demographics files in the directory where the other input data files are stored.
In the configuration file, set Demographics_Filenames to an array that contains a comma-delimited list of demographics files, listing the base layer file first.
An example base layer demographics file and an overlay file is below. You can see that the overlay adds the TransmissionMatrix for Heterogeneous Intra-Node Transmission (HINT) to only three of the five nodes (which correspond to Washington state counties).
{
"Metadata": {
"Author": "ewenger",
"NodeCount": 5,
"Tool": "table_to_demographics.py",
"IdReference": "SampleContent",
"DateCreated": "2013-08-01 15:37:16.853000"
},
"Defaults": {
"NodeAttributes": {
"BirthRate_DESCRIPTION": "Replacement of stable age distribution: Birth_Rate_Dependence=DEMOGRAPHIC_DEP_RATE (i.e. 14-45 year-old PossibleMothers)",
"BirthRate": 0.00017675,
"Airport": 0,
"Region": 1,
"Altitude": 0,
"Seaport": 0
},
"IndividualAttributes": {
"AgeDistribution_DESCRIPTION": "Box between age 0 and 60 years: Age_Initialization_Distribution_Type=DISTRIBUTION_SIMPLE",
"AgeDistributionFlag": 1,
"AgeDistribution1": 0,
"AgeDistribution2": 21900,
"PrevalenceDistribution_DESCRIPTION": "No initial infections",
"PrevalenceDistributionFlag": 0,
"PrevalenceDistribution1": 0,
"PrevalenceDistribution2": 0,
"RiskDistributionFlag": 0,
"RiskDistribution1": 1,
"RiskDistribution2": 0,
"ImmunityDistributionFlag": 0,
"ImmunityDistribution1": 1,
"ImmunityDistribution2": 0,
"MigrationHeterogeneityDistributionFlag": 0,
"MigrationHeterogeneityDistribution1": 1,
"MigrationHeterogeneityDistribution2": 0,
"MortalityDistribution_DESCRIPTION": "WA state (1999-2010). Source: wonder.cdc.gov",
"MortalityDistribution": {
"NumDistributionAxes": 2,
"AxisNames": [ "gender", "age" ],
"AxisUnits": [ "male=0,female=1", "years" ],
"AxisScaleFactors": [ 1, 365 ],
"NumPopulationGroups": [ 2, 15 ],
"PopulationGroups": [
[ 0, 1 ],
[ 0, 1, 2.5, 7.5, 12.5, 17.5, 22.5, 30, 40, 50, 60, 70, 80, 90, 120 ]
],
"ResultUnits": "annual deaths per 1000 individuals",
"ResultScaleFactor": 0.00000273972602739726027397260273973,
"ResultValues": [
[ 4.8, 0.2, 0.1, 0.2, 0.5, 1.1, 1.1, 1.7, 4.1, 9.2, 19.8, 53.7, 154.2, 1000, 1000 ],
[ 4.2, 0.2, 0.2, 0.2, 0.2, 0.4, 0.5, 1.1, 2.6, 5.5, 14.3, 40.1, 129.3, 1000, 1000 ]
]
}
}
},
"Nodes": [
{
"County": "Adams",
"NodeAttributes": {
"Latitude": 47.1274,
"InitialPopulation": 19200,
"Longitude": -118.38
},
"NodeID": 1
},
{
"County": "Asotin",
"NodeAttributes": {
"Latitude": 46.3393,
"InitialPopulation": 21800,
"Longitude": -117.0482
},
"NodeID": 2
},
{
"County": "Benton",
"NodeAttributes": {
"Latitude": 46.2068,
"InitialPopulation": 183400,
"Longitude": -119.7689
},
"NodeID": 3
},
{
"County": "Chelan",
"NodeAttributes": {
"Latitude": 47.4235,
"InitialPopulation": 73600,
"Longitude": -120.3103
},
"NodeID": 4
},
{
"County": "Clallam",
"NodeAttributes": {
"Latitude": 48.1181,
"InitialPopulation": 72350,
"Longitude": -123.4307
},
"NodeID": 5
}
]
}
{
"Metadata": {
"Author": "cwiswell",
"NodeCount": 10,
"Tool": "table_to_demographics.py",
"IdReference": "SampleContent",
"DateCreated": "2013-08-01 15:37:16.853000"
},
"Defaults": {
"IndividualProperties": [
{
"Property": "Accessibility",
"Values": [ "VaccineTake", "VaccineRefuse"],
"Initial_Distribution": [ 0.85, 0.15],
"Transitions": [],
"TransmissionMatrix": {
"Route": "Contact",
"Matrix": [
[1.1, 0.3],
[0.3, 5.0]
]
}
},
{
"Property": "Age_Bin",
"Age_Bin_Edges_In_Years": [ 0, 5, 13, -1 ],
"Transitions": [],
"TransmissionMatrix": {
"Route": "Contact",
"Matrix": [
[1.4, 1.0, 1.0],
[1.0, 2.5, 0.7],
[1.0, 0.7, 1.0]
]
}
}
]
},
"Nodes": [
{
"NodeID": 1
},
{
"NodeID": 3
},
{
"NodeID": 5
}
]
}