Malaria transmission report (MalariaTransmissionReport.json)

The malaria transmission report is a JSON-formatted report providing data on malaria transmission, by tracking who transmitted malaria to whom. Further, the ID of each infection is tracked, as well as information about the node individuals were residing in during the transmission event.

The output file is named MalariaTransmissionReport.json, and is produces via the libReportMalariaTransmissions.dll file. See Custom reporters for information on using using dynamic link library (DLL) files.

Configuration

To generate this report, the following parameters must be configured.

Parameter	Data Type	Min	Max	Default	Description
Start_Day	float	0	3.40E+38	0	The day to start collecting data for the report.
Duration_Days	float	0	3.40E+38	3.40E+38	The duration of simulation days over which to report events.
Report_Description	string	NA	NA	NA	Name of the report (it augments the filename of the report). If multiple CSV reports are being generated, this allows the user to distinguish one report from another.
Nodeset_Config	JSON object	NA	NA	NA	An object that specifies in which nodes the interventions will be distributed.
Event_Trigger_List	list of strings	NA	NA	NA	The list of event triggers for the events included in the report.
Pretty_Format	enum	NA	NA	F	Possible values are T (true) and F (false); T will cause the file to be written in pretty JSON format; F will save space.

Output file data

The report will contain information on samples and transmissions.

Samples

This section contains an array of objects that provide information about individuals who have received treatment.

Parameter	Data type	Description
individualId	integer	The ID of the individual that received treatment.
infectionIds	array of integers	The IDs of the infections that the individual currently has.
node_id	integer	The external ID of the node that the individual is currently residing in.
parasiteDensities	array of floats	The true parasite densities of the infections.
sample_event	string	The name of the event.
timestep	integer	The time step of the simulation (i.e. a counter). If dt=1, then this will be the day of the simulation.

Transmissions

This section contains an array of objects that provide information about how the infection was transmitted. There should be one entry for each NewInfectionEvent.

Parameter	Data type	Description
acquireIndividualId	integer	The ID of the individual that got the infection.
acquireInfectionGenome	integer	The ID of the infection genome that the individual got.
acquireInfectionId	integer	The ID of the infection that the individual got.
node_id	integer	The external ID of the node that the person got the infection in.
timestep	integer	The times tep of the simulation (i.e. a counter). If dt=1, then this will be the day of the simulation.
transmitGametocyteDensities	array of floats	The true gametocyte density of the infections the individual transmitted.
transmitIndividualId	integer	The ID of the individual that most likely transmitted the infection.
transmitInfectionIds	array of integers	The IDs of the infections the individual transmitted.

Example

The following is an example of a MalariaSurveyJSONAnalyzer file.

{
    "samples": [{
        "individualId": 619,
        "infectionIds": [
            3405
        ],
        "node_id": 340461476,
        "parasiteDensities": [
            5.3583152592182
        ],
        "sample_event": "Received_Treatment",
        "timestep": 455
    }],
    "transmissions": [{
            "acquireIndividualId": 619,
            "acquireInfectionGenome": 0,
            "acquireInfectionId": 3501,
            "node_id": 340461476,
            "timestep": 426,
            "transmitGametocyteDensities": [
                1201.362304688,
                0.3583152592182
            ],
            "transmitIndividualId": 585,
            "transmitInfectionIds": [
                3405,
                3365
            ]
        },
        {
            "acquireIndividualId": 845,
            "acquireInfectionGenome": 0,
            "acquireInfectionId": 3502,
            "node_id": 340461476,
            "timestep": 426,
            "transmitGametocyteDensities": [
                21.64715957642
            ],
            "transmitIndividualId": 911,
            "transmitInfectionIds": [
                3424
            ]
        }
    ]
}