ReportSimpleMalariaTransmission

The simple malaria transmission report (ReportSimpleMalariaTransmission.csv) is a CSV-formatted report that provides data on malaria transmission, by tracking who transmitted malaria to whom. The report can only be used when the simulation setup parameter Malaria_Model is set to MALARIA_MECHANISTIC_MODEL_WITH_CO_TRANSMISSION. This report is typically used as input to the GenEpi model. See the Output file data section for more details.

..To do: need section on co-transmission!

Configuration

To generate this report, the following parameters must be configured in the custom_reports.json file:

Parameter	Data Type	Min	Max	Default	Description
Filename_Suffix	string	NA	NA	(empty string)	Augments the filename of the report. If multiple reports are being generated, this allows you to distinguish among the multiple reports.
Start_Day	float	0	3.40282e+38	0	The day of the simulation to start collecting data.
End_Day	float	0	3.40282e+38	3.40282e+38	The day of the simulation to stop collecting data.
Node_IDs_Of_Interest	array of integers	0	2.14748e+09	[]	Data will be collected for the nodes in this list. Empty list implies all nodes.
Min_Age_Years	float	0	9.3228e+35	0	Minimum age in years of people to collect data on.
Max_Age_Years	float	0	9.3228e+35	9.3228e+35	Maximum age in years of people to collect data on.
Must_Have_IP_Key_Value	string	NA	NA	(empty string)	A Key:Value pair that the individual must have in order to be included. Empty string means to not include IPs in the selection criteria.
Must_Have_Intervention	string	NA	NA	(empty string)	The name of the intervention that the person must have in order to be included. Empty string means to not include interventions in the selection criteria.
Pretty_Format	boolean	0	1	0	True (1) sets pretty JSON formatting. The default, false (0), saves space.
Start_Day	float	0	3.40E+38	0	The day to start collecting data for the report.
Include_Human_To_Vector_Transmission	boolean	NA	NA	0	If set to true (1), Human-to-Vector transmission events will be included. One can identify these events because the ‘acquireIndividualId’=0 and transmitTime=acquireTime. WARNING: This can make the file size quite large.

{
    "Reports": [{
        "class": "ReportSimpleMalariaTransmissionJSON",
        "Filename_Suffix": "Node1",
        "Start_Day": 365,
        "End_Day": 465,
        "Node_IDs_Of_Interest": [ 1 ],
        "Min_Age_Years": 5,
        "Max_Age_Years": 10,
        "Must_Have_IP_Key_Value": "Accessibility:YES",
        "Must_Have_Intervention": "UsageDependentBednet"
        "Pretty_Format": 1
    }],
    "Use_Defaults": 1
}

Output file data

The report contains transmissions as an array of CoTransmission objects that contain data on where the infection came from. Each object represents a new infection in the specified node. The following is the structure of a CoTransmission object:

Parameter	Data type	Description
acquireIndividualId	integer	The ID of the individual who received an infection from the vector.
acquireInfectionIds	integer	The list of infections created due to a bite from the vector. There is only one entry in this list at this time.
acquireTime	integer	The day the vector infected the individual with acquireIndividualId.
concurrentInfectionIds	array of integers	The IDs of other infections the acquiring individual had when they were infected with this new infection.
node_id	integer	The ID of the node where the infection occurred.
transmitTime	integer	The day when the vector was infected. Can be 0 if the infection was due to OutbreakIndividual.
transmitIndividualId	integer	The ID of the individual that infected the vector. Can be 0 if the infection was due to OutbreakIndividual.
transmitInfectionIds	array of integers	The list of infection IDs of the individuals infecting the vectors. Can be empty if the infection was due to OutbreakIndividual.
transmitGametocyteDensities	array of floats	A parallel list to transmitInfectionIds where each gametocyte density is the density for the corresponding infection. Can be empty if the infection was due to OutbreakIndividual.
vectorId	integer	The ID of the vector that was infected by the transmitIndividualId and who gave it to the acquireIndividualId. Can be 0 if the infection was due to OutbreakIndividual.

Example

The following is an example of a ReportSimpleMalariaTransmission file.

{
    "transmissions": [{
            "node_id": 1,
            "transmitTime": 0,
            "transmitIndividualId": 0,
            "transmitInfectionIds": [],
            "transmitGametocyteDensities": [],
            "vectorId": 0,
            "acquireTime": 100,
            "acquireIndividualId": 6,
            "acquireInfectionIds": [
                1
            ],
            "concurrentInfectionIds": []
        },
        {
            "node_id": 1,
            "transmitTime": 231,
            "transmitIndividualId": 62,
            "transmitInfectionIds": [
                579,
                625,
                693,
                715,
                747,
                785,
                819,
                865,
                935,
                965
            ],
            "transmitGametocyteDensities": [
                1154.381591797,
                935.8335571289,
                1806.419799805,
                60.45545959473,
                59.96842575073,
                57.74061584473,
                3.254687070847,
                2.291612148285,
                0.1661687344313,
                0.005024351645261
            ],
            "vectorId": 204416,
            "acquireTime": 249,
            "acquireIndividualId": 50,
            "acquireInfectionIds": [
                1557
            ],
            "concurrentInfectionIds": [
                603,
                645,
                667,
                691,
                739,
                769,
                807,
                849,
                1551
            ]
        }
    ]
}