set.susceptibility: Sets susceptibility to infection for the HIV-negative...

In tfojo1/jheem: Executes the JHEEM (Johns Hopkins Epidemiological and Economic Model) - a compartmental model of HIV

Sets susceptibility to infection for the HIV-negative population

Description

Susceptibility is a characteristic of the HIV-negative population, a multiplier indicating how likely an HIV-negative individual in each stratum is to aquire infection (per partnership) relative to a baseline. ie a value of 1 would not change the susceptibility from the global (baseline) rate

Usage

set.susceptibility(
  jheem,
  susceptibility,
  transmission.route.names = jheem$transmission.routes,
  time = -Inf
)

Arguments

jheem	An initialized JHEEM object
susceptibility	An array of susceptibility rates, whose dimensions match the HIV-negative population [age, race, subpopulation, sex, risk, non.hiv.subset].
transmission.route.names	The names of the transmission routes to which the transmissibility should apply (a subset of the 'transmission.route.names' given to initialize.jheem)
time	The time at which these susceptibilities apply, if time-varying

Details

The transmission rate (for one route of transmission) from stratum a (hiv-positive) to stratum b (hiv-negative) is a product of five components (four of which are set as parameters, and one of which - HIV prevalence - is determined by running the model):

• A global transmission rate - applies to all strata equally (set.global.transmission.rate)

• Transmissibility - all factors which depend only on the characteristics of the HIV-positive stratum a (set.transmissibility)

• Contact rate - all factors which depend on both the general characteristics of the HIV-positive stratum a (ie age, race, subpopulation, sex, risk factor) and the characteristics of the HIV-negative stratum b (set.transmission.contact.array)

• Susceptibility - all factors which depend only on the characteristics of the HIV-negative stratum b (set.susceptibility)

• Prevalence of HIV within the general characteristics of the HIV-positive stratum a (ie age, race, subpopulation, sex, risk factor). This is not set, but is estiated at model run time

See Also

create.susceptibility.array.from.marginals, get.hiv.negative.population.skeleton

Other functions to specify transmission: set.global.transmission.rate(), set.new.infection.proportions(), set.transmissibility(), set.transmission.contact.array()

tfojo1/jheem documentation built on Oct. 7, 2022, 1:24 p.m.