Infectivity and transmission

The following parameters determine aspects of infectivity and disease transmission. For example, how infectious individuals are and the length of time for which they remain infectious, whether the disease can be maternally transmitted, and how population density affects infectivity.

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
Base_Infectivity	link	The base infectiousness of individuals before accounting for transmission-blocking effects of acquired immunity and/or campaign interventions. For generic simulations, this is the average number of individuals per time step who will be exposed to infection by one infectious individual. In the case of super-infection, the infectiousness is summed over all infections.	float	0	1000	0.3
Enable_Heterogeneous_Intranode_Transmission	link	Controls whether or not individuals experience heterogeneous disease transmission within a node. When set to true (1), individual property definitions and the \(\beta\) matrix must be specified in the demographics file (see parameters). The \(\beta\) values are multiplied with the \(\beta\) 0 value configured by Base_Infectivity. This is used only in generic, environmental, and typhoid simulations, but must be set to false (0) for all other simulation types. Heterogeneous transmission for other diseases uses other mechanistic parameters included with the simulation type.	boolean	0	1	0
Enable_Infectivity_Reservoir	link	Controls whether or not an exogeneous reservoir of infectivity will be included in the simulation and allows for the infectivity in a node to be increased additively. When set to 1 (true), the demographics parameter InfectivityReservoirSize is expected in NodeAtttributes for each node. .. warning:: Do not set both Enable_Infectivity_Reservoir and Enable_Strain_Tracking to true (1) - as this combination will cause an exception error.	boolean	0	1	0
Enable_Initial_Prevalence	link	Controls whether or not parameters in the demographics file are used to define a distribution for the number of infected people per node at the beginning of the simulation. Set the distribution under using PrevalenceDistributionFlag, PrevalenceDistribution1, and PrevalenceDistribution2.	boolean	0	1	0
Enable_Maternal_Infection_Transmission	link	Controls whether or not infectious mothers infect infants at birth. Enable_Birth must be set to 1 (true). .. warning:: Do not set both Enable_Maternal_Infection_Transmission and Enable_Strain_Tracking to true (1) - as this combination will cause an exception error.	boolean	0	1	0
Enable_Skipping	link	Controls whether or not the simulation uses an optimization that can increase performance by up to 50% in some cases by probabilistically exposing individuals rather than exposing every single person. Useful in low-prevalence, high-population scenarios.	boolean	0	1	0
Enable_Termination_On_Zero_Total_Infectivity	link	Controls whether or not the simulation should be ended when total infectivity falls to zero. Supported only in single-node simulations.	boolean	0	1	0
Infection_Updates_Per_Timestep	link	The number of infection updates executed during each timestep; note that a timestep defaults to one day.	integer	0	144	1
Infectious_Period_Constant	link	The infectious period to use for all individuals, in days, when Infectious_Period_Distribution is set to CONSTANT_DISTRIBUTION.	float	0	3.40282e+38	-1
Infectious_Period_Distribution	link	The distribution type to use for assigning the infectious period to each individual in the population. Each individual's value is a random draw from the distribution. Possible values are: NOT_INITIALIZED No distribution set. CONSTANT_DISTRIBUTION Use the same value for each individual. Set Infectious_Period_Constant. UNIFORM_DISTRIBUTION Use a uniform distribution with a given minimum and maximum. Set Infectious_Period_Max and Infectious_Period_Min. GAUSSIAN_DISTRIBUTION The distribution is Gaussian (or normal). Values are resampled to ensure >= 0. Set Infectious_Period_Gaussian_Mean and Infectious_Period_Gaussian_Std_Dev. EXPONENTIAL_DISTRIBUTION The distribution is exponential with a given mean. Set Infectious_Period_Exponential. WEIBULL_DISTRIBUTION Use a Weibull distribution with a given shape and scale. Set Infectious_Period_Kappa and Infectious_Period_Lambda. LOG_NORMAL_DISTRIBUTION Use a log-normal distribution with a given mean and standard deviation of the natural log. Set Infectious_Period_Log_Normal_Mu and Infectious_Period_Log_Normal_Sigma. POISSON_DISTRIBUTION Use a Poisson distribution with a given mean. Set Infectious_Period_Poisson_Mean. DUAL_CONSTANT_DISTRIBUTION Use a distribution where some individuals are set to a value of zero and the rest to a given value. Set Infectious_Period_Proportion_0 and Peak_2_Value. This distribution does not use the parameters set for CONSTANT_DISTRIBUTION. DUAL_EXPONENTIAL_DISTRIBUTION Use two exponential distributions with given means. Set Infectious_Period_Mean_1, Infectious_Period_Mean_2, and Infectious_Period_Proportion_1. This distribution does not use the parameters set for EXPONENTIAL_DISTRIBUTION. .. _Gaussian: https://en.wikipedia.org/wiki/Normal_distribution .. _exponential: https://en.wikipedia.org/wiki/Exponential_distribution .. _Weibull: https://en.wikipedia.org/wiki/Weibull_distribution .. _log-normal: https://en.wikipedia.org/wiki/Log-normal_distribution .. _uniform: https://en.wikipedia.org/wiki/Uniform_distribution(continuous) .. _Poisson: https://en.wikipedia.org/wiki/Poisson_distribution	enum	nan	nan	NOT_INITIALIZED
Infectious_Period_Exponential	link	The mean infectious period, in days, when Infectious_Period_Distribution is set to EXPONENTIAL_DISTRIBUTION.	float	0	3.40282e+38	-1
Infectious_Period_Gaussian_Mean	link	The mean infectious period, in days, when Infectious_Period_Distribution is set to GAUSSIAN_DISTRIBUTION.	float	0	3.40282e+38	-1
Infectious_Period_Gaussian_Std_Dev	link	The standard deviation of the infectious period, in days, when Infectious_Period_Distribution is set to GAUSSIAN_DISTRIBUTION.	float	1.17549e-38	3.40282e+38	-1
Infectious_Period_Kappa	link	The shape value for the infectious period, in days, when Infectious_Period_Distribution is set to WEIBULL_DISTRIBUTION.	float	1.17549e-38	3.40282e+38	-1
Infectious_Period_Lambda	link	The scale value for the infectious period, in days, when Infectious_Period_Distribution is set to WEIBULL_DISTRIBUTION.	float	1.17549e-38	3.40282e+38	-1
Infectious_Period_Log_Normal_Mu	link	The mean of the natural log of the infectious period, in days, when Infectious_Period_Distribution is set to LOG_NORMAL_DISTRIBUTION.	float	-3.40282e+38	1.70141e+38	3.40282e+38
Infectious_Period_Log_Normal_Sigma	link	The standard deviation of the natural log of the infectious period, in days, when Infectious_Period_Distribution is set to LOG_NORMAL_DISTRIBUTION.	float	-3.40282e+38	1.70141e+38	3.40282e+38
Infectious_Period_Max	link	The maximum infectious period, in days, when Infectious_Period_Distribution is set to UNIFORM_DISTRIBUTION.	float	0	3.40282e+38	-1
Infectious_Period_Mean_1	link	The mean of the first exponential distribution, in days, when Infectious_Period_Distribution is set to DUAL_EXPONENTIAL_DISTRIBUTION.	float	1.17549e-38	3.4e+38	-1
Infectious_Period_Mean_2	link	The mean of the second exponential distribution, in days, when Infectious_Period_Distribution is set to DUAL_EXPONENTIAL_DISTRIBUTION.	float	1.17549e-38	3.40282e+38	-1
Infectious_Period_Min	link	The minimum infectious period, in days, when Infectious_Period_Distribution is set to UNIFORM_DISTRIBUTION.	float	0	3.40282e+38	-1
Infectious_Period_Peak_2_Value	link	The infectious period value, in days, to assign to the remaining individuals when Infectious_Period_Distribution is set to DUAL_CONSTANT_DISTRIBUTION.	float	0	3.40282e+38	-1
Infectious_Period_Poisson_Mean	link	The mean of the infectious period, in days, when Infectious_Period_Distribution is set to POISSON_DISTRIBUTION.	float	0	3.40282e+38	-1
Infectious_Period_Proportion_0	link	The proportion of individuals to assign a value of zero days infectiousness when Infectious_Period_Distribution is set to DUAL_CONSTANT_DISTRIBUTION.	float	0	1	-1
Infectious_Period_Proportion_1	link	The proportion of individuals in the first exponential distribution when Infectious_Period_Distribution is set to DUAL_EXPONENTIAL_DISTRIBUTION.	float	0	1	-1
Infectivity_Exponential_Baseline	link	The scale factor applied to Base_Infectivity at the beginning of a simulation, before the infectivity begins to grow exponentially. Infectivity_Scale_Type must be set to EXPONENTIAL_FUNCTION_OF_TIME.	float	0	1	0
Infectivity_Exponential_Delay	link	The number of days before infectivity begins to ramp up exponentially. When Enable_Infectivity_Scaling_Exponential configuration parameter is enabled, Infectivity_Exponential_Delay is an expected parameter.	float	0	3.4e+38	0
Infectivity_Exponential_Rate	link	The daily rate of exponential growth to approach to full infectivity after the delay set by Infectivity_Exponential_Delay has passed. When Enable_Infectivity_Scaling_Exponential configuration parameter is enabled, Infectivity_Exponential_Rate is an expected parameter.	float	0	3.4e+38	0
Maternal_Infection_Transmission_Probability	link	The probability of transmission of infection from mother to infant at birth. Enable_Maternal_Infection_Transmission must be set to 1. .. note:: For malaria and vector simulations, set this to 0. Instead, use the Maternal_Antibody_Protection, Maternal_Antibody_Decay_Rate, and Maternal_Antibodies_Type parameters.	float	0	1	0
Population_Density_C50	link	The population density at which R0 for a 2.5-arc minute square reaches half of its initial value. Population_Density_Infectivity_Correction must be set to SATURATING_FUNCTION_OF_DENSITY.	float	0	3.4e+38	10
Population_Density_Infectivity_Correction	link	Correction to alter infectivity by population density set in the Population_Density_C50 parameter. Measured in people per square kilometer. Possible values are: CONSTANT_INFECTIVITY SATURATING_FUNCTION_OF_DENSITY .. note:: Sparsely populated areas have a lower infectivity, while densely populated areas have a higher infectivity, which rises to saturate at the Base_Infectivity value.	enum	nan	nan	CONSTANT_INFECTIVITY
Relative_Sample_Rate_Immune	link	The relative sampling rate for people who have acquired immunity through recovery or vaccination. The immune threshold at which to downsample is set by Immune_Threshold_For_Downsampling. If set to 1, this will have no effect, even if the individual's immunity modifier is below threshold. This can be a useful sanity check while learning this feature. Individual_Sampling_Type must be set to ADAPTED_SAMPLING_BY_IMMUNE_STATE.	float	0.001	1	0.1
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
Symptomatic_Infectious_Offset	link	Amount of time, in days, after the infectious period starts that symptoms appear. Negative values imply an individual is symptomatic before infectious. If this offset is greater than the infectious duration, the infection will not be symptomatic. For example, if Incubation_Period_Constant is set to 10 and Symptomatic_Infectious_Offset is set to 4, then an infected person would become symptomatic 14 days after transmission.	float	-3.40282e+38	3.40282e+38	3.40282e+38
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