Detailed malaria survey report (MalariaSurveyJSONAnalyzer.json)

The malaria survey report is a JSON-formatted report that provides detailed information on an individual for each event that occurs during the reporting interval. Multiple files can be created for each reporting interval.

The output file is named MalariaSurveyJSONAnalyzer.json, and is produced via the libmalariasurveyJSON_analyzer_plugin.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.
Reporting_Interval	integer	1	1000000	1000000	Defines the cadence of the report by specifying how many time steps to collect data before writing to the file. This will limit system memory usage and is advised when large output files are expected.
Max_Number_Reports	integer	0	1000000	1	The maximum number of report output files that will be produced for a given campaign.
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.
IP_Key_To_Collect	string	NA	NA	(empty string)	The name of the IndividualProperty Key whose value to collect; an empty string means collect values for all IPs.

Output file data

The report contains the following information:

Parameter	Data type	Description
ntsteps	integer	Number of time steps in the simulation. It should equal the reporting interval unless the simulation ended before the reporting interval.
patient_array	array of strings	An array where there is an entry for each individual that experiences the specified event(s) during the reporting interval. If no events are listed, information will be collected on every individual in the simulation. Each element of the array has numerous channels, listed in the table below.

Patient_array channels

Parameter	Data type	Description
id	string	The individual ID of the person.
node_id	string	The External ID of the node that the person is currently in on the first event.
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.
local_birthday	float	The day that the individual was born/created, in relation to the start of the report.

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

Parameter	Description
strain_ids	The antigen/clade ID and the genome ID of the individual’s current infection.
ip_data	If an ‘IP_Key_To_Collect’ was specified, this will be that value. If it was not specified, this will show the value for all of the IPs.
true_asexual_parasites	The actual parasite density of the individual.
true_gametocytes	The actual gametocyte density of the individual.
smeared_true_asexual_parasites	The actual parasite density, smeared using NASBADensityWithUncertainty.
smeared_true_gametocytes	The actual gametocyte density, smeared using NASBADensityWithUncertainty.
asexual_parasites	The parasite density measured using the BLOOD_SMEAR_PARASITES diagnostic.
gametocytes	The gametocyte density measured using the BLOOD_SMEAR_GAMETOCYTES diagnostic.
pcr_parasites	The parasite density measured using the PCR_PARASITES diagnostic.
pcr_gametocytes	The gametocyte density measured using the PCR_GAMETOCYTES diagnostic.
pfhrp2	The HRP2 measured using the PF_HRP2 diagnostic.
smeared_asexual_parasites	Positive fields of view (pos_asexual_fields) with parasite density.
smeared_gametocytes	Positive fields of view (pos_gametocyte_fields) with gametocyte density.
infectiousness	Infectious of the individual at the time of the event.
infectiousness_smeared	Binomial infectiousness smearing.
infectiousness_age_scaled	Infectiousness adjusted for age dependent Surface Area Biting.
pos_asexual_fields	The number of positive fields of view for parasite smears.
pos_gametocyte_fields	The number of positive fields of view for gametocyte smears.
temps	The individual’s body temperature in Celsius if they have a fever, otherwise it is -1.

Example

The following is a sample of a MalariaSurveyJSONAnalyzer file.

{
    "ntsteps": 73,
    "patient_array": [{
            "id": 5,
            "node_id": 340461476,
            "initial_age": 2497.267822266,
            "local_birthday": -2466.267822266,
            "strain_ids": [
                [
                    0,
                    9947867
                ]
            ],
            "ip_data": [
                ""
            ],
            "true_asexual_parasites": [
                392.6246337891
            ],
            "true_gametocytes": [
                0
            ],
            "smeared_true_asexual_parasites": [
                48.01840209961
            ],
            "smeared_true_gametocytes": [
                0
            ],
            "asexual_parasites": [
                380
            ],
            "gametocytes": [
                0
            ],
            "pcr_parasites": [
                98.8094329834
            ],
            "pcr_gametocytes": [
                0
            ],
            "pfhrp2": [
                9.302060127258
            ],
            "smeared_asexual_parasites": [
                397.7009277344
            ],
            "smeared_gametocytes": [
                0
            ],
            "infectiousness": [
                0
            ],
            "infectiousness_smeared": [
                0
            ],
            "infectiousness_age_scaled": [
                0
            ],
            "pos_asexual_fields": [
                126
            ],
            "pos_gametocyte_fields": [
                0
            ],
            "temps": [
                38.01483154297
            ]
        },
        {
            "id": 11,
            "node_id": 340461476,
            "initial_age": 1387.354614258,
            "local_birthday": -1315.354614258,
            "strain_ids": [
                [
                    0,
                    505461
                ],
                [
                    0,
                    0
                ]
            ],
            "ip_data": [
                ""
            ],
            "true_asexual_parasites": [
                444.5673217773
            ],
            "true_gametocytes": [
                0
            ],
            "smeared_true_asexual_parasites": [
                1481.205932617
            ],
            "smeared_true_gametocytes": [
                0
            ],
            "asexual_parasites": [
                490
            ],
            "gametocytes": [
                0
            ],
            "pcr_parasites": [
                463.1502380371
            ],
            "pcr_gametocytes": [
                0
            ],
            "pfhrp2": [
                10.62057304382
            ],
            "smeared_asexual_parasites": [
                449.572052002
            ],
            "smeared_gametocytes": [
                0
            ],
            "infectiousness": [
                0
            ],
            "infectiousness_smeared": [
                0
            ],
            "infectiousness_age_scaled": [
                0
            ],
            "pos_asexual_fields": [
                135
            ],
            "pos_gametocyte_fields": [
                0
            ],
            "temps": [
                38.0454750061
            ]
        }
    ]
}