MalariaDiagnostic

The MalariaDiagnostic intervention class is similar to SimpleDiagnostic, but distributes a test for malaria. There are several types of configurable diagnostic tests, and the type selected determines the other parameters used.

You should note that the results of MalariaDiagnostic can be different than what you see in the reports. The intervention takes an independent measurement from the reports. It has its own parameters that control the sensitivity and detection threshold.

Note

Parameters are case-sensitive. For Boolean parameters, set to 1 for true or 0 for false. Minimum, maximum, or default values of “NA” indicate that those values are not applicable for that parameter.

EMOD does not use true defaults; that is, if the dependency relationships indicate that a parameter is required, you must supply a value for it. However, many of the tools used to work with EMOD will use the default values provided below.

JSON format does not permit comments, but you can add “dummy” parameters to add contextual information to your files. Any keys that are not EMOD parameter names will be ignored by the model.

The table below describes all possible parameters with which this class can be configured. The JSON example that follows shows one potential configuration.

Parameter Data type Minimum Maximum Default Description Example
Cost_To_Consumer float 0 3.40282E+38 1 The unit cost assigned to the diagnostic. Setting Cost_To_Consumer to zero for all other interventions, and to a non-zero amount for one intervention, provides a convenient way to track the number of times the intervention has been applied in a simulation.
{
    "Cost_To_Consumer": 0.333
}
Days_To_Diagnosis float 0 3.40282E+38 0 The number of days from test until positive diagnosis. A negative test result is given immediately when the intervention is distributed.
{
    "Days_To_Diagnosis": 0.0
}
Detection_Threshold float 0 1.00E+06 100 The diagnostic detection threshold above which a positive diagnosis will be made. The measurement used depends on the value set in Diagnostic_Type.
{
    "Diagnostic_Type": "BLOOD_SMEAR_PARASITES",
    "Detection_Threshold": 40
}
Diagnostic_Type enum NA NA BLOOD_SMEAR_PARASITES

The type of malaria diagnostic test used. Possible values are:

BLOOD_SMEAR_PARASITES
A sample of blood is viewed under a microscope and the number of parasites per microliter of blood is counted. This diagnostic includes some randomness because real-world smear tests may not perfectly measure parasite levels in a person’s system. Detection_Threshold is the number of parasites per microliter of blood. This setting uses the Measurement_Sensitivity parameter and if measurement is larger than Detection_Threshold in the following equation, a positive diagnosis is made:

measurement = ( 1 / Measurement_Sensitivity ) * Poisson (x) where x = Measurement_Sensitivity * true_parasite_density

BLOOD_SMEAR_GAMETOCYTES
A sample of blood is viewed under a microscope and the number of gametocytes per microliter of blood is counted. This diagnostic includes some randomness because real-world smear tests may not perfectly measure gametocyte levels in a person’s system. Detection_Threshold is the number of gametocytes per microliter of blood. This setting uses the Measurement_Sensitivity parameter and if measurement is larger than Detection_Threshold in the following equation, a positive diagnosis is made:

measurement = ( 1 / Measurement_Sensitivity ) * Poisson (x) where x = Measurement_Sensitivity * true_gametocyte_density

FEVER
The fever detection threshold is defined as the number of degrees Celsius above a normal body temperature of 37 degrees. If a person’s body temperature is above this threshold, a positive diagnosis is made. For example, a Detection_Threshold of 2 would result in a positive diagnosis for temperatures above 39 degrees. Fever as a diagnostic uses a model of cytokines based on the paper Innate immunity to malaria.
PCR_PARASITES
The intervention models a quantitative nucleic acid sequence-based amplification (QT-NASBA) type measurement of parasite density and draws a value from a random Gaussian distribution. Detection_Threshold is the number of parasites per microliter of blood. This measurement is based on the paper Improving statistical inference on pathogen densities estimated by quantitative molecular methods: malaria gametocytaemia as a case study.
PCR_GAMETOCYTES
The intervention models a quantitative nucleic acid sequence-based amplification (QT-NASBA) type measurement of gametocyte density and draws a value from a random Gaussian distribution. Detection_Threshold is the number of gametocytes per microliter of blood. This measurement is based on the paper Improving statistical inference on pathogen densities estimated by quantitative molecular methods: malaria gametocytaemia as a case study.
PF_HRP2
Measures the number of picograms of histidine-rick protein 2 (HRP2) in a microliter of blood. Detection_Threshold is in picograms of HRP2 per microliter of blood. This is modeled with boost and decay parameters and is based on the paper Modelling the dynamics of Plasmodium falciparum histidine-rich protein 2 in human malaria to better understand malaria rapid diagnostic test performance.
TRUE_PARASITE_DENSITY
A true measure of the number of parasites per microliter of blood. Detection_Threshold is in parasites per microliter of blood.
{
    "Diagnostic_Type": "BLOOD_SMEAR_PARASITES",
    "Detection_Threshold": 40,
    "Measurement_Sensitivity": 5
}
Disqualifying_Properties array of strings NA NA [] A list of IndividualProperty key:value pairs that cause an intervention to be aborted (persistent interventions will stop being distributed to individuals with these values). See NodeProperties and IndividualProperties parameters for more information. Generally used to control the flow of health care access. For example, to prevent the same individual from accessing health care via two different routes at the same time.
{
    "Disqualifying_Properties": [
        "InterventionStatus:LostForever"
    ]
}
Dont_Allow_Duplicates boolean NA NA 0 If an individual’s container has an intervention, set to true (1) to prevent them from receiving another copy of the intervention. Supported by all intervention classes.
{
    "Dont_Allow_Duplicates": 0
}
Event_Or_Config enum NA NA Config

Specifies whether the current intervention (or a positive diagnosis, depending on the intervention class) distributes a nested intervention (the Config option) or an event will be broadcast which may trigger other interventions in the campaign file (the Event option). Possible values are:

  • Event
  • Config
{
    "Event_Or_Config": "Config"
}
Intervention_Name string NA NA MalariaDiagnostic The optional name used to refer to this intervention as a means to differentiate it from others that use the same class.
{
    "Intervention_Config": {
        "class": "MalariaDiagnostic",
        "Intervention_Name": "First round of malaria testing"
    }
}
Measurement_Sensitivity float 0 1000000.0 0.1 The number of microliters of blood tested to find a single parasite or gametocyte in a traditional smear (corresponds to the inverse of parasites/microliters sensitivity). This is similar to Report_Parasite_Smear_Sensitivity and Report_Gametocyte_Smear_Sensitivity in the configuration file used for reports, but this is for this instance of the diagnostic. This parameter is used when Diagnostic_Type is set to BLOOD_SMEAR_PARASITES or BLOOD_SMEAR_GAMETOCYTES.
{
    "Intervention_Config": {
        "class": "MalariaDiagnostic",
        "Diagnostic_Type": "BLOOD_SMEAR_GAMETOCYTES",
        "Detection_Threshold": 10,
        "Measurement_Sensitivity": 0.25
    }
}
Negative_Diagnosis_Config JSON object NA NA NA If Event_Or_Config is set to Config, this defines a new intervention to be given to the person upon a negative test result.
{
    "Event_Or_Config": "Config",
    "Negative_Diagnosis_Config": {
        "class": "SimpleVaccine",
        "Cost_To_Consumer": 1,
        "Vaccine_Take": 1,
        "Vaccine_Type": "AcquisitionBlocking",
        "Waning_Config": {
            "class": "WaningEffectBox",
            "Box_Duration": 40,
            "Initial_Effect": 0.75
        }
    }
}
Negative_Diagnosis_Event string NA NA NA If Event_Or_Config is set to Event, this defines the event that is broadcast upon a negative test result. See Event list for possible values or define custom events by adding to the list for the configuration parameter Custom_Individual_Event.
{
    "Event_Or_Config": "Event",
    "Negative_Diagnosis_Event": "TestedNegative_IamSusceptible"
}
New_Property_Value string NA NA NA An optional IndividualProperty key:value pair that will be assigned when the intervention is first updated. See NodeProperties and IndividualProperties parameters for more information. Generally used to indicate the broad category of health care cascade to which an intervention belongs to prevent individuals from accessing care through multiple pathways. For example, if an individual must already be taking a particular medication to be prescribed a new one.
{
    "New_Property_Value": "InterventionStatus:None"
}
Positive_Diagnosis_Config JSON object NA NA NA The intervention distributed to individuals if they test positive. Only used when Event_Or_Config is set to Config.
{
    "Event_Or_Config": "Config",
    "Positive_Diagnosis_Config": {
        "class": "SimpleVaccine",
        "Cost_To_Consumer": 0.333,
        "Secondary_Decay_Time_Constant": 1,
        "Vaccine_Take": 1,
        "Vaccine_Type": "AcquisitionBlocking",
        "Waning_Config": {
            "class": "WaningEffectBox",
            "Box_Duration": 3650,
            "Initial_Effect": 0.1
        }
    }
}
Positive_Diagnosis_Event enum NA NA NA If the test is positive, this specifies an event that can trigger another intervention when the event occurs. Only used if Event_Or_Config is set to Event. See Event list for possible values or define custom events by adding to the list for the configuration parameter Custom_Individual_Event.
{
    "Intervention_Config": {
        "class": "SimpleDiagnostic",
        "Base_Sensitivity": 1.0,
        "Base_Specificity": 1.0,
        "Cost_To_Consumer": 0.0,
        "Days_To_Diagnosis": 0.0,
        "Event_Or_Config": "Event",
        "Positive_Diagnosis_Event": "TestedPositive_CureMeNow",
        "Treatment_Fraction": 1.0
    }
}
Treatment_Fraction float 0 1 1 The fraction of positive diagnoses that are treated or given the Positive_Diagnosis_Config or Positive_Diagnosis_Event when used in campaign classes that trigger separate interventions or events upon a positive diagnosis.
{
    "Intervention_Config": {
        "class": "SimpleDiagnostic",
        "Base_Sensitivity": 1.0,
        "Base_Specificity": 1.0,
        "Cost_To_Consumer": 0.0,
        "Days_To_Diagnosis": 0.0,
        "Event_Or_Config": "Event",
        "Positive_Diagnosis_Event": "TestedPositive_CureMeNow",
        "Treatment_Fraction": 1.0
    }
}
{
    "Events": [{
        "class": "CampaignEvent",
        "Nodeset_Config": {
            "class": "NodeSetAll"
        },
        "Start_Day": 18050,
        "Event_Coordinator_Config": {
            "class": "StandardInterventionDistributionEventCoordinator",
            "Target_Demographic": "Everyone",
            "Demographic_Coverage": 0.5,
            "Intervention_Config": {
                "class": "NodeLevelHealthTriggeredIV",
                "Trigger_Condition": "TriggerString",
                "Trigger_Condition_String": "Diagnostic_Survey_2",
                "Actual_IndividualIntervention_Config": {
                    "class": "MalariaDiagnostic",
                    "Cost_To_Consumer": 0,
                    "Diagnostic_Type": "BLOOD_SMEAR_PARASITES",
                    "Measurement_Sensitivity": 0.1,
                    "Detection_Threshold": 3,
                    "Event_Or_Config": "Config",
                    "Positive_Diagnosis_Config": {
                        "class": "AntimalarialDrug",
                        "Cost_To_Consumer": 5,
                        "Drug_Type": "Chloroquine"
                    },
                    "Negative_Diagnosis_Config": {
                        "class": "SimpleVaccine",
                        "Cost_To_Consumer": 10,
                        "Vaccine_Take": 1,
                        "Vaccine_Type": "AcquisitionBlocking",
                        "Waning_Config": {
                            "class": "WaningEffectBox",
                            "Box_Duration": 3650,
                            "Initial_Effect": 1
                        }
                    }
                }
            }
        }
    }],
    "Use_Defaults": 1
}