SqlReportMalariaGenetics

The SqlReportMalariaGenetics report extends software-report-sql-malaria to output epidemiological, transmission, and parasite genetics data for simulations where Malaria_Model is set to MALARIA_MECHANISTIC_MODEL_WITH_PARASITE_GENETICS. Because of the quantity and complexity of the data, the report 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.

Seealso

FPG model — For an overview of the FPG model, genome configuration, and the full FPG workflow.

Configuration

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

Parameter	Data type	Min	Max	Default	Description
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.
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.
End_Day	float	0	3.40E+38	3.40E+38	The day to stop collecting data for the report.
Start_Day	float	0	3.40E+38	0	The day to start collecting data.

{
    "Reports": [
        {
            "class": "SqlReportMalariaGenetics",
            "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

Because the output is a relational database, most of the tables have a primary key (highlighted in yellow on the figure below) that is a combination of RunNumber and another value. For example, in the Humans table, the primary key is the combination of RunNumber and HumanID. Because the RunNumber is part of the primary key, you can combine data from multiple runs.

The following chart and tables describe the SQL data tables produced by this report. The "many" and "1" notations in the chart show you which tables have a one-to-many row relationship and which have a many-to-one row relationship with the rows in another table.

Schematic of the SQL data tables produced by this report

Humans table

The Humans table tracks of all the humans in the simulation. It contains one row for each individual in the scenario. This table has a one-to-many relationship with the Infections and Health tables.

Parameter	Data type	Description
RunNumber	integer	This value from the Run_Number parameter is the seed to the model's random number generator.
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 home node where the individual starts out.
InitialAgeDays	float	The age, in days, of the individual when they entered the simulation.
SimTimeAdded	float	The time in the simulation when the individual was added.

Health table

The Health table tracks the health of each individual while they are alive in the simulation. There is one record for each timestep during which an individual was alive. This table has a many-to-one relationship with the Humans table. Query the SevereCaseType table if you want to translate the integer value of SevereCaseTypeID to a text value.

Parameter	Data type	Description
RunNumber	integer	This value from the Run_Number parameter is the seed to the model's random number generator.
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.
SimTime	float	The time in the simulation that this data was collected.
Infectiousness	float	An infectiousness value based on the individual's number of mature female gametocytes and fever status.
RelativeBitingRate	float	A number indicating if this individual is more likely to be bitten by mosquitoes. This can include any biting rates you set and/or a value based on the age/area of the individual.
IsClinicalCase	boolean	A value of true (1) means that the individual has a fever greater than both Clinical_Fever_Threshold_Low and Clinical_Fever_Threshold_High.
IsSevereCase	boolean	A value of true (1) means the individual has a fever greater than Clinical_Fever_Threshold_Low and was probabilistically determined to have severe disease.
SevereCaseTypeID	integer	The unique ID of the type of severe disease.
InvMicrolitersBlood	float	The inverse amount of blood the individual has in microliters.
RedBloodCellCount	float	The actual number of red blood cells the individual has.
Cytokines	float	The number of cytokines that have been stimulated by the presence of all malaria parasites.
HRP2	float	The amount of Histidine Rich Protein 2 (HRP2) in person's blood per microliter. Value used to compare against HRP2 detection thresholds.
PfEMP1VariantFraction	float	The number of PfEMP1 antibodies that an individual has divided by the total number possible in the scenario (Falciparum_PfEMP1_Variants).

SevereCaseType table

This is a small, lookup table for translating the integer value of SevereCaseTypeID in the Health table into the actual name of the case type. The SevereCaseType names are based on the SevereCaseTypesEnum parameter.

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

Infections table

The Infections table tracks the infections that occurred in humans during the simulation. There is one row for each infection that occurred. This table has a many-to-one relationship with the Humans and ParasiteGenomes tables.

Parameter	Data type	Description
RunNumber	integer	This value from the Run_Number parameter is the seed to the model's random number generator.
InfectionID	integer	The unique ID of the infection in the simulation.
HumanID	integer	The unique ID of the individual in the simulation.
GenomeID	integer	The unique ID of the genome derived from a hash code function on the nucleotide sequence of the genome.
SimTimeCreated	float	The time in the simulation that the infection was created.

InfectionData table

The InfectionData table contains data about each infection while it was active in the simulation. This table has a many-to-one relationship with the Infections table.

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

ParasiteGenomes table

The ParasiteGenomes table contains one row of information about each unique parasite genome. This table has a one-to many relationship with the GenomeSequenceData and Infections tables.

Parameter	Data type	Description
RunNumber	integer	This value from the Run_Number parameter is the seed to the model's random number generator.
GenomeID	integer	The unique ID of the genome derived from a hash code function on the nucleotide sequence of the genome.
BarcodeID	integer	The unique ID/hash of the barcode portion of the genome, based just on the barcode. It does not include the allele roots.
Barcode	string	The text representation of the barcode where each allele is A, C, G, or T.

DrugStatus table

The DrugStatus table keeps track of the status of each drug in a person. Each person may have multiple records per time step, so the table may be large. Information on each drug will continue until the drug has expired.

Parameter	Data type	Description
RunNumber	integer	This value from the Run_Number parameter is the seed to the model's random number generator.
HumanID	integer	The unique ID of the person in the simulation.
SimTime	float	The time in the simulation that the data is being collected.
DrugName	string	The name of the drug indicated in the intervention as defined by the configuration parameter Malaria_Drug_Params. Depending on the intervention, this may be a concatenated value when a person takes multiple pills in one dose.
CurrentEfficacy	float	The current efficacy of the drug(s).
NumRemainingDoses	integer	The number of doses that the person has yet to take. Depending on the intervention, the dose may involve multiple pills.

GenomeSequenceData table

This table contains the sequence and allele root information for each genome. The RunNumber and GenomeID indicate the particular genome, and the GenomeLocation indicates the location of the values. The number of rows for a particular genome depend on the number of barcode positions and whether or not the simulation tracked the MSP and PfEMP1 variants in the genome. This table has a many-to-one relationship with the ParasiteGenomes and Locations tables.

Parameter	Data type	Description
RunNumber	integer	This value from the Run_Number parameter is the seed to the model's random number generator.
GenomeID	integer	The unique ID of the genome derived from a hash code function on the nucleotide sequence of the genome.
NucleotideSequence	integer	The value of the allele at the genome location.
AlleleRoots	integer	The Infection ID from where this allele originated.
GenomeLocation	integer	The location in the genome, which is a value from 1 to 22790000.

Locations table

The Locations table tracks what type of data is contained in a particular genome location. This table has a one-to-many relationship with the GenomeSequenceData table and a many-to-one relationship with the LocationType lookup table.

Parameter	Data type	Description
RunNumber	integer	This value from the Run_Number parameter is the seed to the model's random number generator.
GenomeLocation	integer	The location in the genome, which is a value from 1 to 22790000.
LocationTypeID	integer	The unique ID of the location type, which indicates if the location is used in the Barcode, Drug Resistance, HRPstatus, MSP, or Major Epitopes. Query the LocationType table to obtain the actual location name.

LocationType table

This is a small lookup table that provides the full name of the location (via the keys in the Locations and GenomeSequenceData tables) used when querying the ParasiteGenomes table.

Parameter	Data type	Description
LocationTypeID	integer	The unique ID of the location type.
Name	enum	The name of the location. Possible values are BARCODE, DRUG_RESISTANCE, HRP_STATUS, MSP, or PFEMP1_VARIANTS.