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 diagnosis (which is done when the intervention is distributed) until a positive response is performed. The response to a negative diagnosis is done immediately when the diagnosis is made (at distribution of the intervention).

{
  "Days_To_Diagnosis": 0.0
}

Detection_Threshold

float

0

1e+06

100

The diagnostic detection threshold for parasites, in units of microliters of blood. Used when Diagnostic_Type is set to Other.

{
  "Detection_Threshold": 40
}

Diagnostic_Type

enum

NA

NA

BLOOD_SMEAR_PARASITES

The type of malaria diagnostic 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

0

1

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

“”

An optional IndividualProperty key:value pair that will be assigned when the intervention is applied. 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": {
    "Intervention_List": [
      {
        "Cost_To_Consumer": 0.333,
        "Secondary_Decay_Time_Constant": 1,
        "Vaccine_Take": 1,
        "Vaccine_Type": "AcquisitionBlocking",
        "Waning_Config": {
          "Box_Duration": 3650,
          "Initial_Effect": 0.1,
          "class": "WaningEffectBox"
        },
        "class": "SimpleVaccine"
      }
    ],
    "class": "MultiInterventionDistributor"
  }
}

Positive_Diagnosis_Event

enum

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.

{
  "Event_Or_Config": "Event",
  "Positive_Diagnosis_Event": "TestedPositive_CureMeNow"
}

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.

{
  "class": "MalariaDiagnostic",
  "Treatment_Fraction": 1
}
{
    "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
}