Immunity#
The following parameters determine the immune system response for the disease being modeled, including waning immunity after an infection clears.
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 |
|---|---|---|---|---|---|---|
Enable_Maternal_Protection |
boolean |
0 |
1 |
0 |
Controls whether or not mothers pass immunity on to their infants. Setting to 1 (true) enables maternal protection as defined by Maternal_Protection_Type. Enable_Birth must be set to 1 (true). |
{
"Enable_Maternal_Protection": 1,
"Maternal_Protection_Type": "LINEAR_FRACTIONAL"
}
|
Immune_Threshold_For_Downsampling |
float |
0 |
1 |
0 |
The threshold on acquisition immunity at which to apply immunity-dependent downsampling; individuals who are more immune than this this threshold are downsampled. A value of 1 is equivalent to full susceptibility and 0 is equivalent to full immunity. If the acquisition immunity modifier is larger than the threshold, no downsampling occurs. Individual_Sampling_Type must set to ADAPTED_SAMPLING_BY_IMMUNE_STATE. |
{
"Relative_Sample_Rate_Immune": 0.1,
"Immune_Threshold_For_Downsampling": 0.5,
"Individual_Sampling_Type": "ADAPTED_SAMPLING_BY_IMMUNE_STATE"
}
|
Maternal_Linear_Slope |
float |
0.0001 |
1 |
0.01 |
Slope parameter describing the rate of waning for maternal protection, must be positive. The per-day increase in susceptibility. Maternal_Protection_Type must be set to LINEAR_FRACTIONAL or LINEAR_BINARY. |
{
"Maternal_Protection_Type": "LINEAR_FRACTIONAL",
"Maternal_Linear_SusZero": 0.45,
"Maternal_Linear_Slope": 0.02
}
|
Maternal_Linear_SusZero |
float |
0 |
1 |
0.2 |
The initial level of maternal protection at age 0, given as susceptibility. A value of 0.0 implies total protection, a value of 1.0 implies no protection. Maternal_Protection_Type must be set to LINEAR_FRACTIONAL or LINEAR_BINARY. |
{
"Maternal_Protection_Type": "LINEAR_FRACTIONAL",
"Maternal_Linear_SusZero": 0.45,
"Maternal_Linear_Slope": 0.02
}
|
Maternal_Protection_Type |
enum |
NA |
NA |
NONE |
The type of maternal protection afforded to infants. Enable_Maternal_Protection must be set to 1 (true). Possible values are:
You must set Susceptibility_Type to determine if susceptibility at a particular age is interpreted as a fractional value or the probability of complete immunity or susceptibility. |
{
"Enable_Maternal_Protection": 1,
"Maternal_Protection_Type": "LINEAR_FRACTIONAL"
}
|
Maternal_Sigmoid_HalfMaxAge |
float |
-270 |
3650 |
180 |
The age in days that the level of maternal protection is half of its initial value. Maternal_Protection_Type must be set to SIGMOID_FRACTIONAL or SIGMOID_BINARY. |
{
"Maternal_Protection_Type": "SIGMOID_BINARY",
"Maternal_Sigmoid_SteepFac": 30,
"Maternal_Sigmoid_HalfMaxAge": 365,
"Maternal_Sigmoid_SusInit": 0.0002
}
|
Maternal_Sigmoid_SteepFac |
float |
0.1 |
1000 |
30 |
The steepness factor describing the rate of waning for maternal protection, must be positive. Small values imply rapid waning.**Maternal_Protection_Type** must be set to SIGMOID_FRACTIONAL or SIGMOID_BINARY. |
{
"Maternal_Protection_Type": "SIGMOID_BINARY",
"Maternal_Sigmoid_SteepFac": 30,
"Maternal_Sigmoid_HalfMaxAge": 365,
"Maternal_Sigmoid_SusInit": 0.0002
}
|
Maternal_Sigmoid_SusInit |
float |
0 |
1 |
0 |
The initial level of maternal protection at age -INF, given as susceptibility. A value of 0.0 implies total protection, a value of 1.0 implies no protection. Maternal_Protection_Type must be set to SIGMOID_FRACTIONAL or SIGMOID_BINARY. |
{
"Maternal_Protection_Type": "SIGMOID_BINARY",
"Maternal_Sigmoid_SteepFac": 30,
"Maternal_Sigmoid_HalfMaxAge": 365,
"Maternal_Sigmoid_SusInit": 0.0002
}
|
Post_Infection_Acquisition_Multiplier |
float |
0 |
1 |
0 |
The multiplicative reduction in the probability of reacquiring disease. At the time of recovery, the immunity against acquisition is multiplied by Acquisition_Blocking_Immunity_Decay_Rate x (1 - Post_Infection_Acquisition_Multiplier). Enable_Immunity must be set to 1 (true). |
{
"Enable_Immunity": 1,
"Enable_Immune_Decay": 1,
"Post_Infection_Acquisition_Multiplier": 0.9
}
|
Post_Infection_Mortality_Multiplier |
float |
0 |
1 |
0 |
The multiplicative reduction in the probability of dying from infection after getting reinfected. At the time of recovery, the immunity against mortality is multiplied by Mortality_Blocking_Immunity_Decay_Rate x (1 - Post_Infection_Mortality_Multiplier). Enable_Immunity must be set to 1 (true). |
{
"Enable_Immunity": 1,
"Enable_Immune_Decay": 1,
"Post_Infection_Mortality_Multiplier": 0.5
}
|
Post_Infection_Transmission_Multiplier |
float |
0 |
1 |
0 |
The multiplicative reduction in the probability of transmitting infection after getting reinfected. At the time of recovery, the immunity against transmission is multiplied by Transmission_Blocking_Immunity_Decay_Rate x (1 - Post_Infection_Transmission_Multiplier). Enable_Immunity must be set to 1 (true). |
{
"Enable_Immunity": 1,
"Enable_Immunity_Decay": 1,
"Post_Infection_Transmission_Multiplier": 0.9
}
|
Susceptibility_Type |
enum |
NA |
NA |
FRACTIONAL |
Controls implementation of an individual’s susceptibility. Currently only relevant to Maternal_Protection_Type parameter. Possible values are:
|
{
"Susceptibility_Type": "FRACTIONAL",
"Enable_Maternal_Protection": 1,
"Maternal_Protection_Type": "LINEAR_FRACTIONAL"
}
|