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
            ]
        }
    ]
}