set.transmissibility: Sets transmissibility for the HIV-positive population

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

Sets transmissibility for the HIV-positive population

Description

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

Usage

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

Arguments

jheem	An initialized JHEEM object
transmissibility	An array of transmissibility, whose dimensions match the HIV-positive population <age, race, subpopulation, sex, risk factor, continuum of care, cd4, 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 transmissibilities 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

get.hiv.positive.population.skeleton, create.transmissibility.array.from.marginals

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

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