Symptoms and diagnosis#

The following parameters determine the characteristics of malaria diagnosis and symptoms as the disease progresses, such as anemia and fever. See Malaria symptoms and diagnostics for more information on malaria diagnostics and symptoms.

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.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Anemia_Mortality_Inverse_Width

float

0.1

1000000

10

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the inverse width relative to threshold value of severe disease turn-on around threshold for anemia.

 
{
    "Anemia_Mortality_Inverse_Width": 150
}

Anemia_Mortality_Threshold

double

NA

NA

3

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the inverse width relative to threshold value of mortality turn-on around threshold for hemoglobin count in grams per deciliter (g/dL) at which 50% of individuals die per day.

 
{
    "Anemia_Mortality_Threshold": 1.5
}

Anemia_Severe_Inverse_Width

float

0.1

1000000

10

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the inverse width relative to threshold value of severe disease turn-on around threshold for anemia.

 
{
    "Anemia_Severe_Inverse_Width": 20
}

Anemia_Severe_Threshold

float

0

100

5

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the severe disease threshold level for anemia. Threshold units are in grams per deciliter (g/dL).

 
{
    "Anemia_Severe_Threshold": 3.0
}

Clinical_Fever_Threshold_High

float

0

15

1

The fever threshold (in degrees Celsius above normal) to start a clinical incident.

 
{
    "Clinical_Fever_Threshold_High": 1.5
}

Clinical_Fever_Threshold_Low

float

0

5

1

The fever threshold (in degrees Celsius above normal) to end a clinical incident.

 
{
    "Clinical_Fever_Threshold_Low": 0.5
}

Erythropoiesis_Anemia_Effect

float

0

1000

3.5

The exponential rate of increased red-blood-cell production from reduced red-blood-cell availability.

 
{
    "Erythropoiesis_Anemia_Effect": 3
}

Fever_Detection_Threshold

float

0.5

5

1

The level of body temperature above normal (defined as 37 C), in degrees Celsius, corresponding to detectable fever.

 
{
    "Fever_Detection_Threshold": 1
}

Fever_IRBC_Kill_Rate

float

0

1000

0.15

The maximum kill rate for infected red blood cells due to the inflammatory innate immune response. As fever increases above 38.5 degrees Celsius, the kill rate becomes successively higher along a sigmoidal curve approaching this rate.

 
{
    "Fever_IRBC_Kill_Rate": 1.4
}

Fever_Mortality_Inverse_Width

float

0.1

1000000

10

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the inverse width relative to threshold value of mortality turn-on around threshold for fever.

 
{
    "Fever_Mortality_Inverse_Width": 1000
}

Fever_Mortality_Threshold

double

NA

NA

3

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the fever mortality threshold, in units of degrees Celsius above normal body temperature (defined as 37 C).

 
{
    "Fever_Mortality_Threshold": 10
}

Fever_Severe_Inverse_Width

float

0.1

1000000

10

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the inverse width relative to threshold value of mortality turn-on around threshold for fever.

 
{
    "Fever_Severe_Inverse_Width": 18.7
}

Fever_Severe_Threshold

float

0

10

1.5

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the threshold (in degrees Celsius above normal) for fever indicating severe disease.

 
{
    "Fever_Severe_Threshold": 2.5
}

Min_Days_Between_Clinical_Incidents

float

0

1000000

3

The number of days with fever below the low-threshold before a new incident can start, when fever again exceeds the high-threshold.

 
{
    "Min_Days_Between_Clinical_Incidents": 14
}

New_Diagnostic_Sensitivity

float

0.0001

100000

0.01

The number of microliters of blood tested to find single parasites in a new diagnostic (corresponds to inverse parasites/microliters sensitivity).

 
{
    "New_Diagnostic_Sensitivity": 0.025
}