Malaria patient data report (MalariaPatientReport.json)

The malaria patient data report is a JSON-formatted report that provides medical data for each individual on each day of the simulation. For example, for a specified number of time steps, each “patient” will have information collected on the temperature of their fever, their parasite counts, treatments they received, and other relevant data.

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

Configuration

No special parameters need to be configured to generate this report.

Output file data

The report contains the following information:

Parameter	Data type	Description
ntsteps	integer	Number of time steps in the simulation. Each channel for each person should have this number of elements.
patient_array	array of strings	An array where there is an entry for each individual in the simulation. Each element of the array has numerous channels, listed in the table below.

Patient_array channels

Parameter	Data type	Description
asexual_parasites	integer	The results of the BLOOD_SMEAR_PARASITES diagnostic that reports the number of parasites detected.
asexual_positive_fields	integer	The count of parasites using positive slide fields.
birthday	float	The day that the individual was born/created.
gametocyte_positive_fields	integer	The count of gametocytes using positive slide fields.
gametocytes	integer	The results of the BLOOD_SMEAR_GAMETOCYTES diagnostic that reports the number of gametocytes detected.
hemoglobin	float	The amount of hemoglobin the individual has based on their red blood cell count.
id	string	The unique ID of the individual.
infected_mosquito_fraction	float	The individual’s infectiousness as a percentage.
initial_age	float	The initial age of the person, in days, when the report started tracking them. This value will be non-zero for individuals created at initialization, but should be zero for the rest of the population.
temps	float	The individual’s body temperature, in Celsius, when they had a fever. It is -1 if they do not have a fever. This is based on their cytokine level.
treatment	string	The list of drug names that the user is currently taking. The names are separated by ‘space+space.’
true_asexual_parasites	float	The actual number of parasites that the individual has.
true_gametocytes	float	The actual number of gametocytes that the individual has.

Example

The following is an example of MalariaPatientReport.json.

{
    "ntsteps": 5,
    "patient_array": [{
        "asexual_parasites": [
            [
                0,
                30,
                30,
                730,
                570

            ]
        ],
        "asexual_positive_fields": [
            [
                0,
                21,
                19,
                154,
                147
            ]
        ],
        "birthday": -3031.024658203,
        "gametocyte_positive_fields": [
            [
                0,
                0,
                0,
                0,
                1
            ]
        ],
        "gametocytes": [
            [
                0,
                0,
                0,
                0,
                10
            ]
        ],
        "hemoglobin": [
            [
                13.95295619965,
                13.94942092896,
                13.94591999054,
                13.94245052338,
                13.93901348114
            ]
        ],
        "id": 1,
        "infected_mosquito_fraction": [
            [
                0,
                0.02632671967149,
                0.1359317451715,
                0.3907080292702,
                2.00230383873
            ]
        ],
        "initial_age": 3031.024658203,
        "temps": [
            [
                -1,
                38.39496612549,
                40.47192382813,
                40.53329849243,
                43.32601165771
            ]
        ],
        "treatment": [
            [
                "",
                "",
                "",
                "",
                ""
            ]
        ],
        "true_asexual_parasites": [
            [
                0,
                0.01264353003353,
                0.2007576525211,
                2.86963891983,
                41.02872848511
            ]
        ],
        "true_gametocytes": [
            [
                0,
                0.3181047737598,
                4.729532718658,
                67.70833587646,
                967.8447875977
            ]
        ]
    }]
}