SqlReportMalaria

The SqlReportMalaria report extends software-report-sql with malaria-specific health and infection data. It is only available when Simulation_Type is MALARIA_SIM. The output is a multi-table SQLite relational database (see DB Browser for SQLite for more information). Use the configuration parameters to manage the size of the database.

SqlReportMalariaGenetics extends this report with parasite genetics data for FPG simulations. See software-report-sql-malaria-genetics.

Configuration

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

Parameter	Data type	Min	Max	Default	Description
`Include_Health_Table`	boolean	NA	NA	1	A true value (1) includes the Health table which has data for each time step for the health of an individual.
`Include_Infection_Data_Table`	boolean	NA	NA	1	A true value (1) includes the InfectionData table which has data for each time step for each active infection.
`Include_Individual_Properties`	boolean	NA	NA	0	Include a table with all the possible IPs and include the IP data for each person in the Health table.
`Include_Drug_Status_Table`	boolean	NA	NA	0	A true value (1) includes the table that provides data at each time step for each drug the person has.
`Start_Day`	float	0	3.40E+38	0	The day to start collecting data.
`End_Day`	float	0	3.40E+38	3.40E+38	The day to stop collecting data.

{
    "Reports": [
        {
            "class": "SqlReportMalaria",
            "Include_Drug_Status_Table": 1,
            "Include_Health_Table": 1,
            "Include_Infection_Data_Table": 1,
            "Start_Day": 100,
            "End_Day": 900
        }
    ],
    "Use_Defaults": 1
}

SQL database and table structures

The report produces all tables from software-report-sql. The Health and InfectionData tables are extended with malaria-specific columns, and two new tables are added.

Humans table

The Humans table records all individuals in the simulation. It contains one row per individual and has a one-to-many relationship with the Infections and Health tables.

Parameter	Data type	Description
`RunNumber`	integer	The seed to the random number generator from the Run_Number parameter.
`HumanID`	integer	The unique ID of the individual in the simulation.
`Gender`	text	The gender of the individual. Possible values are M or F.
`HomeNodeID`	integer	The external ID (NodeID in demographics) of the individual's home node.
`InitialAgeDays`	float	The age of the individual in days when they entered the simulation.
`SimTimeAdded`	float	The simulation time when the individual was added.

Health table

The Health table records the health state of each individual at each time step. There is one row per individual per time step. This table has a many-to-one relationship with the Humans table. Omitted when Include_Health_Table is false. Query the SevereCaseType table to translate SevereCaseTypeID values to text names.

Parameter	Data type	Description
`RunNumber`	integer	The seed to the random number generator from the Run_Number parameter.
`HumanID`	integer	The unique ID of the individual in the simulation.
`NodeID`	integer	The external ID of the node the individual is in at this time step.
`SimTime`	float	The simulation time when this data was collected.
`Infectiousness`	float	The individual's infectiousness to vectors at this time step.
`RelativeBitingRate`	float	The relative rate at which this individual is bitten by mosquitoes, based on age and other factors.
`IsClinicalCase`	boolean	1 if the individual has a fever exceeding both Clinical_Fever_Threshold_Low and Clinical_Fever_Threshold_High.
`IsSevereCase`	boolean	1 if the individual has a fever exceeding Clinical_Fever_Threshold_Low and was probabilistically determined to have severe disease.
`SevereCaseTypeID`	integer	The unique ID of the severe case type. Query the SevereCaseType table for the text name.
`InvMicrolitersBlood`	float	The inverse of the individual's blood volume in microliters.
`RedBloodCellCount`	float	The number of red blood cells the individual has.
`Cytokines`	float	The cytokine level stimulated by the presence of malaria parasites.
`HRP2`	float	The amount of Histidine Rich Protein 2 (HRP2) in the individual's blood per microliter. Used to compare against HRP2 detection thresholds.
`PfEMP1VariantFraction`	float	The fraction of PfEMP1 variants for which the individual has antibodies, out of Falciparum_PfEMP1_Variants total.

SevereCaseType table

A small lookup table that maps SevereCaseTypeID values in the Health table to text names.

Parameter	Data type	Description
`SevereCaseTypeID`	integer	The unique ID of the severe case type.
`Name`	enum	The name of the severe case type. Possible values are NONE, ANEMIA, PARASITES, or FEVER.

Infections table

The Infections table records each infection that occurs in the simulation. There is one row per infection. This table has a many-to-one relationship with the Humans table.

Parameter	Data type	Description
`RunNumber`	integer	The seed to the random number generator from the Run_Number parameter.
`InfectionID`	integer	The unique ID of the infection in the simulation.
`HumanID`	integer	The unique ID of the individual who acquired the infection.
`SimTimeCreated`	float	The simulation time when the infection was created.

InfectionData table

The InfectionData table records data for each active infection at each time step. There is one row per infection per time step. This table has a many-to-one relationship with the Infections table. Omitted when Include_Infection_Data_Table is false.

Parameter	Data type	Description
`RunNumber`	integer	The seed to the random number generator from the Run_Number parameter.
`InfectionID`	integer	The unique ID of the infection in the simulation.
`SimTime`	float	The simulation time when this data was collected.
`InfectedRedBloodCells`	integer	The number of infected red blood cells due to this infection at this time step.
`NumMatureGametocytesFemale`	integer	The number of mature female gametocytes in this infection at this time step.
`NumMatureGametocytesMale`	integer	The number of mature male gametocytes in this infection at this time step.

DrugStatus table

The DrugStatus table records the status of each active drug for each individual at each time step. There may be multiple rows per individual per time step — one per active drug. Only present when Include_Drug_Status_Table is true.

Parameter	Data type	Description
`RunNumber`	integer	The seed to the random number generator from the Run_Number parameter.
`HumanID`	integer	The unique ID of the individual in the simulation.
`SimTime`	float	The simulation time when this data was collected.
`DrugName`	string	The name of the drug as defined by Malaria_Drug_Params.
`CurrentEfficacy`	float	The current efficacy of the drug.
`NumRemainingDoses`	integer	The number of doses the individual has yet to take.

IndividualProperties table

A lookup table mapping individual property key-value IDs to their text names. Only present when Include_Individual_Properties is true.

Parameter	Data type	Description
`RunNumber`	integer	The seed to the random number generator from the Run_Number parameter.
`KeyValueID`	integer	The unique ID of the IP key-value pair.
`Key`	text	The name of the individual property key.
`Value`	text	The value of the individual property.