ReportInfectionStatsMalaria

The malaria infection statistics report (ReportInfectionStatsMalaria.csv) provides per-infection parasite burden data for every active infection in the simulation at each reporting interval. For each infection it records the individual's identity and demographics, the infectiousness of the individual, the current age of the infection, and — depending on configuration — the counts of hepatocytes, infected red blood cells (IRBCs), and gametocytes associated with that infection. Because the report produces one row per active infection per individual per reporting interval, the output can be large; use Start_Day, End_Day, and Reporting_Interval to limit its size.

This report is only available for MALARIA_SIM simulations.

Configuration

To generate this report, configure the following parameters in the custom_reports.json file:

Parameter	Data type	Min	Max	Default	Description
Filename_Suffix	string	NA	NA	(empty string)	Suffix appended to the report filename. Required when configuring multiple instances of this report to prevent them from overwriting each other.
Start_Day	float	0	3.40E+38	0	The day of the simulation to start collecting data.
End_Day	float	0	3.40E+38	3.40E+38	The day of the simulation to stop collecting data.
Reporting_Interval	float	1	1000000	1	The number of time steps between data collection periods. Increasing this value reduces output file size.
Include_Column_Hepatocyte	boolean	NA	NA	1	If set to true (1), a column is added to the report with the count of infected hepatocytes for the infection.
Include_Column_IRBC	boolean	NA	NA	1	If set to true (1), a column is added to the report with the number of infected red blood cells (IRBCs) for the infection.
Include_Column_Gametocyte	boolean	NA	NA	1	If set to true (1), a column is added to the report with the total number of mature gametocytes (male and female combined) for the infection.
Include_Data_Threshold_Hepatocytes	float	0	3.40E+38	0	Minimum hepatocyte count an infection must have for its row to be written. Only applies when Include_Column_Hepatocyte is true. A value of 0 disables this threshold. If this threshold is not met, the entire row is omitted even if other thresholds are met.
Include_Data_Threshold_IRBC	float	0	3.40E+38	0	Minimum IRBC count an infection must have for its row to be written. Only applies when Include_Column_IRBC is true. A value of 0 disables this threshold. If this threshold is not met, the entire row is omitted even if other thresholds are met.
Include_Data_Threshold_Gametocytes	float	0	3.40E+38	0	Minimum gametocyte count an infection must have for its row to be written. Only applies when Include_Column_Gametocyte is true. A value of 0 disables this threshold. If this threshold is not met, the entire row is omitted even if other thresholds are met.

Note

A row is only written if every enabled column meets its corresponding threshold. If any enabled threshold is not met, the entire row is omitted.

{
    "Reports": [
        {
            "class": "ReportInfectionStatsMalaria",
            "Start_Day": 3860,
            "End_Day": 3880,
            "Reporting_Interval": 1,
            "Include_Column_Hepatocyte": 1,
            "Include_Column_IRBC": 1,
            "Include_Column_Gametocyte": 1,
            "Include_Data_Threshold_Hepatocytes": 0,
            "Include_Data_Threshold_IRBC": 0,
            "Include_Data_Threshold_Gametocytes": 0
        }
    ],
    "Use_Defaults": 1
}

Output file data

The output file is named ReportInfectionStatsMalaria.csv. The report contains the following columns.

Column	Data type	Description
Time	float	The simulation time in days when the data was collected.
NodeID	integer	The external ID of the node where the individual is currently present.
IndividualID	integer	The unique ID of the individual carrying the infection.
Gender	enum	The gender of the individual. Possible values are M or F.
AgeYears	float	The age of the individual in years at the time of data collection.
InfectionID	integer	The unique ID of the infection.
Infectiousness	float	The infectiousness of the individual — the probability that a feeding mosquito will become infected. This value is based on the total number of gametocytes in the bloodstream contributed by all of the individual's infections.
Duration	float	The duration in days of this infection at the time of data collection.
Hepatocytes	integer	The number of infected hepatocytes associated with this infection. Only present if Include_Column_Hepatocyte is true.
IRBCs	integer	The number of infected red blood cells associated with this infection. Only present if Include_Column_IRBC is true.
Gametocytes	integer	The total number of mature gametocytes (male and female combined) associated with this infection. Only present if Include_Column_Gametocyte is true.

Example

The following is an example of ReportInfectionStatsMalaria.csv.

Parameter	Data type	Min	Max	Default	Description
Filename_Suffix	string	NA	NA	(empty string)	Suffix appended to the report filename. Required when configuring multiple instances of this report to prevent them from overwriting each other.
Start_Day	float	0	3.40E+38	0	The day of the simulation to start collecting data.
End_Day	float	0	3.40E+38	3.40E+38	The day of the simulation to stop collecting data.
Reporting_Interval	float	1	1000000	1	The number of time steps between data collection periods. Increasing this value reduces output file size.
Include_Column_Hepatocyte	boolean	NA	NA	1	If set to true (1), a column is added to the report with the count of infected hepatocytes for the infection.
Include_Column_IRBC	boolean	NA	NA	1	If set to true (1), a column is added to the report with the number of infected red blood cells (IRBCs) for the infection.
Include_Column_Gametocyte	boolean	NA	NA	1	If set to true (1), a column is added to the report with the total number of mature gametocytes (male and female combined) for the infection.
Include_Data_Threshold_Hepatocytes	float	0	3.40E+38	0	Minimum hepatocyte count an infection must have for its row to be written. Only applies when Include_Column_Hepatocyte is true. A value of 0 disables this threshold. If this threshold is not met, the entire row is omitted even if other thresholds are met.
Include_Data_Threshold_IRBC	float	0	3.40E+38	0	Minimum IRBC count an infection must have for its row to be written. Only applies when Include_Column_IRBC is true. A value of 0 disables this threshold. If this threshold is not met, the entire row is omitted even if other thresholds are met.
Include_Data_Threshold_Gametocytes	float	0	3.40E+38	0	Minimum gametocyte count an infection must have for its row to be written. Only applies when Include_Column_Gametocyte is true. A value of 0 disables this threshold. If this threshold is not met, the entire row is omitted even if other thresholds are met.