How to create migration files#

You can create the JSON metadata and binary migration files needed by EMOD to run simulations from either CSV or JSON data using Python scripts provided by IDM. You can assign the same probability of migration to each individual in a node (vector or human), or you can assign different migration rates based on age and/or gender (human only).

Note

The IdReference must match the value in the demographics file. Each node can be connected a maximum of 100 destination nodes.

For both scripts, use one of the following migration types:

LOCAL_MIGRATION
AIR_MIGRATION
REGIONAL_MIGRATION
SEA_MIGRATION

For regional migration, you may want to set up migration such that if a node is not part of the network, the migration of individuals to and from that node considers the closest road hub city. You can do this by constructing a Voronoi tiling based on road hubs, with each non-hub connected to the hub of its tile.

Create from CSV input#

To use the same average migration rate for every individual in a node, create the migration files from a CSV input file.

Create a CSV file with the following three columns (do not include column headers):

From_Node_ID
The origin node, which must match a node ID in the demographics file. You do not need to have the same number of entries for each From_Node_ID.

To_Node_ID
The destination node, which must match a node ID in the demographics file.

Rate
The average number of trips per day.

Run the ‘convert_txt_to_bin.py’ script using the command format below:

python -m emodpy_malaria.migration.convert_txt_to_bin [input-migration-csv] [output-bin] [migration-type] [idreference]

This will create both the metadata and binary file needed by EMOD.

Example file#

1,2,0.0
1,3,0.0
1,4,0.0
1,9,0.0
2,1,0.0
2,3,0.0
4,3,0.0
4,5,0.0
4,9,0.0
5,1,0.00125
5,2,0.00125
5,3,0.00125
5,4,0.00125
5,6,0.00125
5,7,0.00125

Create from JSON input#

To vary the average migration rate based on age and/or gender, create the migration files from a JSON input file.

Create a JSON file with the structure described in the sections below.

Run the ‘convert_json_to_bin.py’ script using the command format below:

python -m emodpy_malaria.migration.convert_json_to_bin [input-json] [output-bin] [migration-type]

This will create both the metadata and binary file needed by EMOD.

JSON parameters#

The following parameters are used in the JSON file for migration file generation.

Parameter	Data type	Description
IdReference	string	The metadata identifier used to generate the NodeID associated with each node in a simulation. The values for IdReference and NodeID must be the same across all input files used in a simulation.
Interpolation_Type	enum	The method by which to interpolate the age dependent rate data. Accepted values are LINEAR_INTERPOLATION and PIECEWISE_CONSTANT.
Gender_Data_Type	enum	Whether age data is provided for each gender separately or is the same for both. Accepted values are ONE_FOR_BOTH_GENDERS and ONE_FOR_EACH_GENDER.
Ages_Years	array	An array that defines the age bins by which to separate the population and define migration rates. The first value defines the upper bound of a bin starting at zero.
Node_Data	JSON object	The structure that contains the migration rate data for each node.
From_Node_ID	integer	The origin node for which to define migration rate.
Rate_Data	array	The structure that contains migration rate data for a single destination node.
To_Node_ID	integer	The destination node for which to define migration rate.
Avg_Num_Trips_Per_Day_Both	array	The array that lists the average number of trips per day for each age bin defined in Ages_Years (male and female). Used when Gender_Data_Type is set to ONE_FOR_BOTH_GENDERS.
Avg_Num_Trips_Per_Day_Female	array	The array that lists the average number of trips per day for each female age bin defined in Ages_Years. Used when Gender_Data_Type is set to ONE_FOR_EACH_GENDER.
Avg_Num_Trips_Per_Day_Male	array	The array that lists the average number of trips per day for each male age bin defined in Ages_Years. Used when Gender_Data_Type is set to ONE_FOR_EACH_GENDER.

Example files#

{
    "IdReference": "ABC",
    "Interpolation_Type": "PIECEWISE_CONSTANT",
    "Gender_Data_Type": "ONE_FOR_EACH_GENDER",
    "Ages_Years": [14.99, 15, 45, 75, 105],
    "Node_Data": [{
        "From_Node_ID": 1,
        "Rate_Data": [{
            "To_Node_ID": 2,
            "Avg_Num_Trips_Per_Day_Male": [0.0, 0.1, 0.2, 0.3, 0.0],
            "Avg_Num_Trips_Per_Day_Female": [0.0, 0.3, 0.2, 0.1, 0.0]
        }]
    }, {
        "From_Node_ID": 2,
        "Rate_Data": [{
            "To_Node_ID": 1,
            "Avg_Num_Trips_Per_Day_Male": [0.0, 0.2, 0.5, 0.3, 0.0],
            "Avg_Num_Trips_Per_Day_Female": [0.0, 0.5, 0.3, 0.2, 0.0]
        }]
    }]
}

{
    "IdReference": "ABC",
    "Interpolation_Type": "PIECEWISE_CONSTANT",
    "Gender_Data_Type": "ONE_FOR_BOTH_GENDERS",
    "Ages_Years": [14.99, 15, 45, 75, 105],
    "Node_Data": [{
        "From_Node_ID": 1,
        "Rate_Data": [{
            "To_Node_ID": 2,
            "Avg_Num_Trips_Per_Day_Both": [0.0, 0.1, 0.2, 0.3, 0.0]
        }]
    }, {
        "From_Node_ID": 2,
        "Rate_Data": [{
            "To_Node_ID": 1,
            "Avg_Num_Trips_Per_Day_Both": [0.0, 0.2, 0.5, 0.3, 0.0]
        }]
    }]
}