SimpleDiagnostic#

The SimpleDiagnostic intervention class identifies infected individuals, regardless of disease state, based on specified diagnostic sensitivity and specificity. Diagnostics are a key component of modern disease control efforts, whether used to identify high-risk individuals, infected individuals, or drug resistance. This intervention class distributes a specified intervention to a fraction of individuals who test positive.

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

Base_Sensitivity

float

0

1

1

The sensitivity of the diagnostic. This sets the proportion of the time that individuals with the condition being tested receive a positive diagnostic test. When set to zero, then individuals who have the condition always receive a false-negative diagnostic test.

 
{
    "Base_Sensitivity": 0.8
}

Base_Specificity

float

0

1

1

The specificity of the diagnostic. This sets the proportion of the time that individuals without the condition being tested receive a negative diagnostic test. When set to 1, the diagnostic always accurately reflects the lack of having the condition. When set to zero, then individuals who do not have the condition always receive a false-positive diagnostic test.

 
{
    "Base_Specificity": 0.9
}

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 diagnosis.

 
{
    "Days_To_Diagnosis": 0.0
}

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
}

Enable_IsSymptomatic

boolean

0

1

0

If true (1), requires an infection to be symptomatic to return a positive test.

 
{
    "Enable_IsSymptomatic": 1,
    "Base_Specificity": 0.85,
    "Base_Sensitivity": 0.92
}

Intervention_Name

string

NA

NA

NA

The optional name used to refer to this intervention as a means to differentiate it from others that use the same class.

 
{
    "Intervention_Name": "Diagnostic_Sample"
}

New_Property_Value

string

NA

NA

NA

An optional IndividualProperty key:value pair that will be assigned when the intervention is distributed. 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.

 
{
    "Positive_Diagnosis_Config": {
        "class": "MultiInterventionDistributor",
        "Intervention_List": [
            {
                "Cost_To_Consumer": 0.333,
                "Secondary_Decay_Time_Constant": 1,
                "Vaccine_Take": 1,
                "Vaccine_Type": "AcquisitionBlocking",
                "class": "SimpleVaccine",
                "Waning_Config": {
                    "Box_Duration": 3650,
                    "Initial_Effect": 0.1,
                    "class": "WaningEffectBox"
                }
            }
        ]
    }
}

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.

 
{
    "Intervention_Config": {
        "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,
        "class": "SimpleDiagnostic"
    }
}

Treatment_Fraction

float

0

1

1

The fraction of positive diagnoses that are treated.

 
{
    "Intervention_Config": {
        "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,
        "class": "SimpleDiagnostic"
    }
}

{
    "Events":[{
            "class":"CampaignEvent",
            "Start_Day":200,
            "Nodeset_Config":{
                "class":"NodeSetAll"
            },
            "Event_Coordinator_Config":{
                "class":"StandardInterventionDistributionEventCoordinator",
                "Target_Demographic":"Everyone",
                "Demographic_Coverage": 1.0,
                "Intervention_Config":{
                    "class":"SimpleDiagnostic",
                    "Base_Sensitivity":1.0,
                    "Base_Specificity":1.0,
                    "Cost_To_Consumer":0,
                    "Days_To_Diagnosis":5.0,
                    "Dont_Allow_Duplicates":0,
                    "Event_Or_Config":"Event",
                    "Positive_Diagnosis_Event":"Acorn",
                    "Intervention_Name":"Diagnostic_Sample",
                    "Treatment_Fraction":1.0
                }
            }
        }],
    "Use_Defaults":1
}