MalariaPatientJSONReport

The malaria patient data report (MalariaPatientJSONReport.json) 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.

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.

{
    "Reports": [
        {
            "class": "MalariaPatientJSONReport",
            "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": "Risk:LOW",
            "Must_Have_Intervention": "UsageDependentBednet"
        }
    ],
    "Use_Defaults": 1
}

Output file data

The report contains the following information:

Parameter	Data type	Description
ntsteps	integer	Number of time steps in the simulation in which the report is active. Each channel for each person has this number of elements. People that are born after the start of the simulation or die before the end will have fewer entries.
patient_array	array of JSON objects	For each patient in patient_array, there will be a dictionary of key:value pairs. Some dictionary entries will contain a single, constant value that does not change through time, such as the individual's birthday. Other dictionary entries will be arrays of daily measures for that individual, such as the count of asexual parasites on each day of the simulation. Please see the example below for an illustration.

Patient data channels

Each of the following statistics has one value for each timestep or day.

Parameter	Data type	Description
id	string	The unique ID of the individual.
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.
birthday	float	The day that the individual was born/created in relation to the start of the report.

Patient array data channels

Each of the following statistics is an array of data, where each entry is the value of that field at the time of the event.

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.
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.
infected_mosquito_fraction	float	The fraction of mosquito bites the patient received from infectious mosquitoes.
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, which includes any drugs in the person's system during that timestep. 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": [
        {
            "id": 1,
            "birthday": -3031.024658203,
            "initial_age": 3031.024658203,
            "asexual_parasites": [[0, 30, 30, 730, 570]],
            "asexual_positive_fields": [[0, 21, 19, 154, 147]],
            "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]],
            "infected_mosquito_fraction": [[0, 0.02632671967149, 0.1359317451715, 0.3907080292702, 2.00230383873]],
            "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]]
        }
    ]
}