set.transmission.contact.array: Sets the transmission contact array between HIV-negative and...

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

Sets the transmission contact array between HIV-negative and HIV-positive populations

Description

A contact array is a function of both the hiv-infected population and hiv-negative population

Usage

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

Arguments

jheem	An initialized JHEEM object
contact.array	An contact array, with some subset of dimensions: [age.from, race.from, subpopulation.from, sex.from, risk.from, age.to, race.to, subpopulation.to, sex.to, risk.to, non.hiv.subset.to]. from->to follows the direction of HIV transmission
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.contact.array.from.marginals, get.contact.array.skeleton

Other functions for transmission contact arrays: create.contact.array.from.marginals(), get.contact.array.skeleton(), multiply.contact.array.from(), multiply.contact.array.to()

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

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