param_msm_sdiego: Epidemic Model Parameters

In thednainus/HIVepisim: Network-modeling for MSM population in San Diego.

Epidemic Model Parameters

Description

Sets the epidemic parameters for stochastic network models simulated with netsim for EpiModelHIV

Usage

param_msm_sdiego(
  netstats,
  time.unit = 7,
  stage_prog_rate1 = 1/((3.32 * 365)/7),
  stage_prog_rate2 = 1/((2.7 * 365)/7),
  stage_prog_rate3 = 1/((5.5 * 365)/7),
  f1 = 0.76,
  f2 = 0.19,
  f3 = 0.05,
  f4 = 0,
  hiv.test.rate = 0.01325,
  test.window.int = 21/7,
  tx.init.prob = 0.092,
  tx.halt.prob = 0.0102,
  tx.reinit.prob = 0.00066,
  trans.r = 1e-04,
  ws0 = 1,
  ws1 = 0.1,
  ws2 = 0.1,
  ws3 = 0.1,
  ws4 = 0.3,
  wc1 = 1,
  wc2 = 0.5,
  wc3 = 0.05,
  wr1 = 1,
  wr2 = 10,
  aids.mr = 1/((5.06 * 365)/7),
  a.rate = 0.00052,
  arrival.age = 18,
  ...
)

Arguments

netstats	Target statistics and related network initialization data from the standard ARTnet workflow.
time.unit	Unit of time relative to one day.
stage_prog_rate1	Rate per time unit spent in CD4+ compartment for stage 1 of HIV infection (Cori et al. 2015).
stage_prog_rate2	Rate per time unit spent in CD4+ compartment for stage 2 of HIV infection (Cori et al. 2015).
stage_prog_rate3	Rate per time unit spent in CD4+ compartment for stage 3 of HIV infection (Cori et al. 2015).
f1	Probability of an individual entering stage 1 of HIV infection after initial HIV infection (acute and early HIV infection).
f2	Probability of an individual entering stage 2 of HIV infection after initial HIV infection (acute and early HIV infection).
f3	Probability of an individual entering stage 3 of HIV infection after initial HIV infection (acute and early HIV infection).
f4	Probability of an individual entering stage 4 of HIV infection after initial HIV infection (acute and early HIV infection).
hiv.test.rate	Mean probability of HIV testing per week for MSM.
test.window.int	Length of the HIV test window period in weeks.
tx.init.prob	Probability per time step that an MSM who has tested positive will initiate treatment.
tx.halt.prob	Probability per time step that an MSM who have started treatment will stop treatment.
tx.reinit.prob	Probability per time step that an MSM who has stopped treatment will restart treatment.
trans.r	Baseline for transmission rate per act.
ws0	Risk ratio of an individual in acute and early HIV infection (stage 0) will transmit to another individual.
ws1	Risk ratio of an individual in stage 1 will transmit to an HIV negative individual.
ws2	Risk ratio of an individual in stage 2 will transmit to an HIV negative individual.
ws3	Risk ratio of an individual in stage 3 will transmit to an HIV negative individual.
ws4	Risk ratio of an individual in stage 4 will transmit to an HIV negative individual.
wc1	Risk ratio of an undiagnosed HIV + individual will transmit to an HIV negative individual.
wc2	Risk ratio of an diagnosed and untreated HIV + individual will transmit to an HIV negative individual.
wc3	Risk ratio of an diagnosed and treated HIV + individual will transmit to an HIV negative individual.
wr1	Risk ratio of individuals in risk group 1 will transmit to an HIV negative individual.
wr2	Risk ratio of individuals in risk group 2 will transmit to an HIV negative individual.
aids.mr	Mortality rate of persons in the AIDS stage who are currently off ART.
a.rate	Rate at which MSM enter the population.
arrival.age	Age (in years) of new arrivals.
...	Additional arguments passed to the function.

Value

A list object of class param_msm, which can be passed to EpiModel function netsim.

References

Cori A, Pickles M, van Sighem A, et al. CD4+ cell dynamics in untreated HIV-1 infection: overall rates, and effects of age, viral load, sex and calendar time. AIDS. 2015;29(18):2435-2446. doi:10.1097/QAD.0000000000000854

thednainus/HIVepisim documentation built on Nov. 23, 2023, 12:26 a.m.