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	Type	Min	Max	Default	Description
Acute_Duration_In_Months	float	0	5	2.9	The time since infection, in months, over which the Acute_Stage_Infectivity_Multiplier is applied to coital acts occurring in that time period.
Acute_Stage_Infectivity_Multiplier	float	1	100	26	The multiplier acting on Base_Infectivity to determine the per-act transmission probability of an HIV+ individual during the acute stage.
Base_Infectivity	float	0	1000	0.3	The base infectiousness of individuals before accounting for transmission-blocking effects of acquired immunity and/or campaign interventions. For STI or HIV simulations, this is the probability of transmission when none of the transmission multipliers apply to a particular coital act (or when all multipliers are set to 1).
CD4_At_Death_LogLogistic_Heterogeneity	float	0	100	0	The inverse shape parameter of a Weibull distribution that represents the at-death CD4 cell count.
Condom_Transmission_Blocking_Probability	float	0	1	0.9	The per-act multiplier of the transmission probability when a condom is used.
Enable_Infectivity_Reservoir	boolean	0	1	0	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.
Enable_Maternal_Infection_Transmission	boolean	0	1	0	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.
Enable_Skipping	boolean	0	1	0	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.
Enable_Termination_On_Zero_Total_Infectivity	boolean	0	1	0	Controls whether or not the simulation should be ended when total infectivity falls to zero. Supported only in single-node simulations.
Heterogeneous_Infectiousness_LogNormal_Scale	float	0	10	0	Scale parameter of a log normal distribution that governs an infectiousness multiplier. The multiplier represents heterogeneity in infectivity and adjusts Base_Infectivity.
Infection_Updates_Per_Timestep	integer	0	144	1	The number of infection updates executed during each timestep; note that a timestep defaults to one day.
Male_To_Female_Relative_Infectivity_Ages	array of floats	NA	NA	0	The vector of ages governing the susceptibility of females relative to males, by age. Used with Male_To_Female_Relative_Infectivity_Multipliers. See example.
Male_To_Female_Relative_Infectivity_Multipliers	array of floats	NA	NA	1	An array of scale factors governing the susceptibility of females relative to males, by age. Used with Male_To_Female_Relative_Infectivity_Ages. Scaling is linearly interpolated between ages. The first value is used for individuals younger than the first age in Male_To_Female_Relative_Infectivity_Ages and the last value is used for individuals older than the last age. See example.
Maternal_Infection_Transmission_Probability	float	0	1	0	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.
Maternal_Transmission_ART_Multiplier	float	0	1	0.1	The maternal transmission multiplier for on-ART mothers.
Population_Density_C50	float	0	3.40E+38	10	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.
Population_Density_Infectivity_Correction	enum	NA	NA	CONSTANT_INFECTIVITY	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.
Relative_Sample_Rate_Immune	float	0.001	1	0.1	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.
STI_Coinfection_Acquisition_Multiplier	float	0	100	10	The per-act HIV acquisition probability multiplier for individuals with the STI coinfection flag.
STI_Coinfection_Transmission_Multiplier	float	0	100	10	The per-act HIV transmission probability multiplier for individuals with the STI coinfection flag.
Susceptibility_Type	enum	NA	NA	FRACTIONAL	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.