MalariaImmunityReport

The malaria immunity report (MalariaImmunityReport.json) is a JSON-formatted file that provides statistics for several antibody types for specified age bins over a specified reporting duration. Specifically, the report tracks the average and standard deviation in the fraction of observed antibodies for merozoite surface protein (MSP), Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), and non-specific (and less immunogenic) minor surface epitopes. The total amount possible is determined by the parameters Falciparum_MSP_Variants, Falciparum_PfEMP1_Variants, and Falciparum_Nonspecific_Types. The greater the fraction, the more antibodies the individual has against possible new infections. The smaller the fraction, the more naive the individual’s immune system is to malaria.

Configuration

To generate this report, the following parameters must be configured in the custom_reports.json file:

Parameter name	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.
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	boolean	0	1	0	True (1) sets pretty JSON formatting. The default, false (0), saves space.
Age_Bins	array of integers	0	125	[ ]	The age bins (in years, in ascending order) to aggregate within and report. An empty array does not stratify by age.

{
    "Reports": [
        {
            "class": "MalariaImmunityReport",
            "Age_Bins": [
                10,
                20,
                30,
                40,
                50,
                60,
                70,
                80,
                90,
                100,
                125
            ],
            "Start_Day": 365,
            "End_Day": 465,
            "Filename_Suffix": "Node1",
            "Node_IDs_Of_Interest": [ 1 ],
            "Reporting_Interval": 10,
            "Max_Number_Reports": 1,
            "Pretty_Format": 1
        }
    ],
    "Use_Defaults": 1
}

Output file data

The report contains the following output data.

Parameter name	Data type	Description
Age Bins	array of integers	The array of age bins used in the report (in years).
MSP Mean by Age Bin	float	The average fraction of merozoite surface protein (MSP) antibodies over the total possible (Falciparum_MSP_Variants) an individual has for each age bin for each reporting interval.
Non-Specific Mean by Age Bin	float	The average fraction of less-immunogenic minor surface epitopes (non-specific) an individual has developed antibodies for over the total possible (Falciparum_Nonspecific_Types) for each age bin for each reporting interval.
PfEMP1 Mean by Age Bin	float	The average fraction of Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) antigens for which an individual has developed antibodies for over the total possible (Falciparum_PfEMP1_Variants) for each age bin for each reporting interval.
MSP StdDev by Age Bin	float	TThe standard deviation for the fraction of merozoite surface protein (MSP) seen by an individual for each age bin for each reporting interval.
Non-Specific StdDev by Age Bin	float	The standard deviation for the fraction of less-immunogenic minor surface epitopes (non-specific) seen by an individual for each age bin for each reporting interval.
PfEMP1 StdDev by Age Bin	float	The standard deviation for the fraction of Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) seen by the individual for each age bin for each reporting interval.

Example

The following is an example of MalariaImmunityReport.json. Notice there are five age bins and two reporting intervals.

{
    "Age Bins": [
        25,
        50,
        75,
        100,
        125
    ],
    "MSP Mean by Age Bin": [
        [
            0.8632667310552,
            0.8663234088753,
            0.8725000023842,
            0.857499986887,
            0.8826284248331
        ],
        [
            0.8624046362191,
            0.8712405961259,
            0.873493152122,
            0.857499986887,
            0.8831850525747
        ]
    ],
    "Non-Specific Mean by Age Bin": [
        [
            0.7913650278989,
            0.9880864695119,
            0.9972526126973,
            1,
            1
        ],
        [
            0.7751695395588,
            0.9881515987902,
            0.9972555594525,
            1,
            1
        ]
    ],
    "PfEMP1 Mean by Age Bin": [
        [
            0.9790955765201,
            0.979491552852,
            0.9802499935031,
            0.9786335564639,
            0.9819375015795
        ],
        [
            0.9790281954887,
            0.979908272019,
            0.9804023946189,
            0.9790821977674,
            0.9818309637788
        ]
    ],
    "MSP StdDev by Age Bin": [
        [
            0.03146989378593,
            0.03586982024275,
            0.01299036866778,
            0.02046338790071,
            0.02644183223304
        ],
        [
            0.03046207382119,
            0.036680426133,
            0.01342621718435,
            0.02046338790071,
            0.02496969378762
        ]
    ],
    "Non-Specific StdDev by Age Bin": [
        [
            0.2602374122976,
            0.01315735830347,
            0.00446382233485,
            0,
            0
        ],
        [
            0.2789481711119,
            0.01310852104812,
            0.004462334073195,
            0,
            0
        ]
    ],
    "PfEMP1 StdDev by Age Bin": [
        [
            0.005103897532884,
            0.005738237822243,
            0.002277617507036,
            0.002825865931333,
            0.004145300627574
        ],
        [
            0.005032654177563,
            0.005761350326143,
            0.002171759356921,
            0.002869313618544,
            0.004228758281701
        ]
    ]
}