Parasite dynamics#
The following parameters determine the dynamics of the Plasmodium falciparum parasite life cycle, including dynamics within the host and human population. For more information, see Malaria infection and immune model.
Note
Parameters are casesensitive. 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 

Base_Gametocyte_Fraction_Male 
double 
NA 
NA 
0.2 
Fraction of gametocytes that are male. 
{
"Base_Gametocyte_Fraction_Male": 0.25
}

Base_Gametocyte_Mosquito_Survival_Rate 
float 
0 
1 
0.01 
Average fraction of gametocytes in a blood meal that are successful in infecting the mosquito in the absence of other modulating effects, such as fever. 
{
"Base_Gametocyte_Mosquito_Survival_Rate": 0.015
}

Base_Gametocyte_Production_Rate 
double 
NA 
NA 
0.02 
The fraction of infected red blood cells (IRBCs) producing gametocytes. 
{
"Base_Gametocyte_Mosquito_Survival_Rate": 0.01
}

Base_Sporozoite_Survival_Fraction 
float 
0 
1 
0.25 
The fraction of sporozoites that survive to infect a hepatocyte in the absence of antiCSP protection. 
{
"Base_Sporozoite_Survival_Fraction": 0.25
}

Cytokine_Gametocyte_Inactivation 
float 
0 
1 
0.02 
The strength of inflammatory response inactivation of gametocytes. 
{
"Cytokine_Gametocyte_Inactivation": 0.0167
}

Gametocyte_Stage_Survival_Rate 
double 
0 
1 
1 
The rate of gametocyte survival from one development stage to the next in the absence of drugs or inflammatory immune response. 
{
"Gametocyte_Stage_Survival_Rate": 0.8
}

Mean_Sporozoites_Per_Bite 
float 
0 
1000 
11 
The mean number of sporozoites per infectious mosquito bite. 
{
"Mean_Sporozoites_Per_Bite": 11
}

Merozoites_Per_Hepatocyte 
double 
NA 
NA 
15000 
The number of IRBCs caused by a single infected hepatocyte at the start of infection. 
{
"Merozoites_Per_Hepatocyte": 15000
}

Merozoites_Per_Schizont 
double 
NA 
NA 
16 
The number of merozoites released by a single infected schizont after each asexual cycle. The number of resulting IRBC’s depends on the RBC availability and merozoitespecific immunity. 
{
"Merozoites_Per_Schizont": 16
}

Number_Of_Asexual_Cycles_Without_Gametocytes 
integer 
0 
500 
1 
The number of asexual reproduction cycles that do not produce gametocytes. All later cycles will produce gametocytes according to Base_Gametocyte_Production_Rate. 
{
"Number_Of_Asexual_Cycles_Without_Gametocytes": 1
}

Parasite_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 proinflammatory 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( (thresholdvariable) / (threshold/invwidth) ) ). This parameter configures the inverse width relative to threshold value of mortality turnon around threshold for parasite density. 
{
"Parasite_Mortality_Inverse_Width": 100
}

Parasite_Mortality_Threshold 
double 
NA 
NA 
2000000 
The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a proinflammatory 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( (thresholdvariable) / (threshold/invwidth) ) ) This parameter configures the parasitedensity mortality threshold for a simulation. 
{
"Parasite_Mortality_Threshold": 3000000
}

Parasite_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 proinflammatory 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( (thresholdvariable) / (threshold/invwidth) ) ) This parameter configures the inverse width relative to threshold value of severe disease turnon around threshold for parasite density. 
{
"Parasite_Severe_Inverse_Width": 48.66825295
}

Parasite_Severe_Threshold 
float 
0 
3.40E+38 
1000000 
The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a proinflammatory 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( (thresholdvariable) / (threshold/invwidth) ) ) This parameter configures parasite density threshold level that results in severe disease. 
{
"Parasite_Severe_Threshold": 253871
}

Parasite_Smear_Sensitivity 
float 
0.0001 
100 
0.1 
The number of microliters of blood tested to find single parasites in a traditional smear (corresponds to inverse parasites/microliters sensitivity). 
{
"Parasite_Smear_Sensitivity": 0.1
}

Parasite_Switch_Type 
enum 
NA 
NA 
CONSTANT_SWITCH_RATE_2VARS 
The parasite switch type for erythrocyte surface antigens. Possible values are:

{
"Parasite_Switch_Type": "RATE_PER_PARASITE_7VARS"
}
