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	Example	Description	Type	Min	Max	Default
Acquisition_Blocking_Immunity_Decay_Rate	link	The rate at which acquisition-blocking immunity decays after the initial period indicated by the base acquisition-blocking immunity offset. Only used when Enable_Immunity and Enable_Immune_Decay parameters are set to true (1).	float	0	1	0.001
Acquisition_Blocking_Immunity_Duration_Before_Decay	link	The number of days after infection until acquisition-blocking immunity begins to decay. Enable_Immunity and Enable_Immune_Decay must be set to true (1).	float	0	45000	0
Enable_Immune_Decay	link	Controls whether or not immunity decays after an infection clears. Set to true (1) if immunity decays; set to false (0) if recovery from the disease confers complete immunity for life. Enable_Immunity must be set to true (1).	boolean	0	1	1
Enable_Immunity	link	Controls whether or not an individual has protective immunity after an infection clears.	boolean	0	1	1
Enable_Initial_Susceptibility_Distribution	link	Controls whether or not individuals in the population have immunity at the beginning of the simulation. If set to 0, individuals are not initialized with immunity but may acquire immunity. If set to 1, you must indicate the type of distribution to use for immunity in the configuration parameter Immunity_Initialization_Distribution_Type and the distribution values in the demographics file. Enable_Immunity must be set to 1.	boolean	0	1	0
Enable_Maternal_Protection	link	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).	boolean	0	1	0
Immune_Threshold_For_Downsampling	link	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.	float	0	1	0
Maternal_Linear_Slope	link	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.	float	0.0001	1	0.01
Maternal_Linear_SusZero	link	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.	float	0	1	0.2
Maternal_Protection_Type	link	The type of maternal protection afforded to infants. Enable_Maternal_Protection must be set to 1 (true). Possible values are: NONE No immune protection is passed on to infants. LINEAR Susceptibility is a function of age and governed by a linear equation. Susceptibility = Maternal_Linear_Slope * age + Maternal_Linear_SusZero SIGMOID Susceptibility is a function of age and governed by a sigmoidal equation. Susceptibility = Maternal_Sigmoid_SusInit + (1.0 - Maternal_Sigmoid_SusInit) / * (1.0 + EXP(( Maternal_Sigmoid_HalfMaxAge - age) / Maternal_Sigmoid_SteepFac)) 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.	enum	nan	nan	NONE
Maternal_Sigmoid_HalfMaxAge	link	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.	float	-270	3650	180
Maternal_Sigmoid_SteepFac	link	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.	float	0.1	1000	30
Maternal_Sigmoid_SusInit	link	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.	float	0	1	0
Mortality_Blocking_Immunity_Decay_Rate	link	The rate at which mortality-blocking immunity decays after the mortality-blocking immunity offset period. Enable_Immune_Decay must be set to 1.	float	0	1	0.001
Mortality_Blocking_Immunity_Duration_Before_Decay	link	The number of days after infection until mortality-blocking immunity begins to decay. Enable_Immunity and Enable_Immune_Decay must be set to 1.	float	0	45000	0
Post_Infection_Acquisition_Multiplier	link	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).	float	0	1	0
Post_Infection_Mortality_Multiplier	link	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).	float	0	1	0
Post_Infection_Transmission_Multiplier	link	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).	float	0	1	0
Susceptibility_Initialization_Distribution_Type	link	The method for initializing the susceptibility distribution in the simulated population. Enable_Initial_Susceptibility_Distribution must be set to 1 (true). Possible values are: DISTRIBUTION_OFF All individuals default to no susceptibility. DISTRIBUTION_SIMPLE Individual susceptibilities are drawn from a distribution whose functional form and parameters are specified in the demographics file in IndividualAttributes using SusceptibilityDistributionFlag, SusceptibilityDistribution1, and SusceptibilityDistribution2 (see parameters). DISTRIBUTION_COMPLEX Individual susceptibilities are drawn from an age-dependent piecewise linear function for each specific antibody in the demographics file (see parameters).	enum	nan	nan	DISTRIBUTION_OFF
Susceptibility_Type	link	Controls implementation of an individual's susceptibility. Currently only relevant to Maternal_Protection_Type parameter. Possible values are: FRACTIONAL All agents are assigned equal values between 0 and 1 according to a governing equation as specified by Maternal_Protection_Type. BINARY Agents receive a value of either 0 or 1 (complete immunity or susceptibility) with the probability determined by a governing equation as specified by Maternal_Protection_Type.	enum	nan	nan	FRACTIONAL
Transmission_Blocking_Immunity_Decay_Rate	link	The rate at which transmission-blocking immunity decays after the base transmission-blocking immunity offset period. Used only when Enable_Immunity and Enable_Immune_Decay parameters are set to true (1).	float	0	1000	0.001
Transmission_Blocking_Immunity_Duration_Before_Decay	link	The number of days after infection until transmission-blocking immunity begins to decay. Only used when Enable_Immunity and Enable_Immune_Decay parameters are set to true (1).	float	0	45000	0