param_msm: Epidemic Model Parameters

In statnet/EpiModelHIVmsm: Network-Based Epidemic Modeling of HIV Transmission among MSM and Heterosexual Populations

Description

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

Usage

param_msm(netstats, hiv.test.rate = c(0.01325, 0.0125, 0.0124),
  hiv.test.late.prob = c(0.25, 0.25, 0.25), test.window.int = 21/7,
  tt.part.supp = c(0.2, 0.2, 0.2), tt.full.supp = c(0.4, 0.4, 0.4),
  tt.dur.supp = c(0.4, 0.4, 0.4), tx.init.prob = c(0.092, 0.092,
  0.127), tx.halt.part.prob = c(0.0102, 0.0102, 0.0071),
  tx.halt.full.rr = c(0.9, 0.9, 0.9), tx.halt.dur.rr = c(0.5, 0.5,
  0.5), tx.reinit.part.prob = c(0.00066, 0.00066, 0.00291),
  tx.reinit.full.rr = c(1, 1, 1), tx.reinit.dur.rr = c(1, 1, 1),
  max.time.off.tx.full.int = 52 * 15, max.time.on.tx.part.int = 52 *
  10, max.time.off.tx.part.int = 52 * 10, vl.acute.rise.int = 6.4,
  vl.acute.peak = 6.886, vl.acute.fall.int = 6.4, vl.set.point = 4.5,
  vl.aids.onset.int = 520, vl.aids.int = 104, vl.aids.peak = 7,
  vl.full.supp = 1.5, vl.part.supp = 3.5, vl.tx.down.slope = 0.25,
  vl.tx.aids.down.slope = 0.25, vl.tx.up.slope = 0.25,
  aids.mr = 1/104, a.rate = 0.00052, arrival.age = 15,
  URAI.prob = 0.008938, UIAI.prob = 0.003379, trans.scale = c(1, 1,
  1), acute.rr = 6, circ.rr = 0.4, cond.eff = 0.95,
  cond.fail = c(0.25, 0.25, 0.25), circ.prob = c(0.874, 0.874, 0.918),
  epistats, acts.aids.vl = 5.75, acts.scale = 1, cond.scale = 1,
  rgc.tprob = 0.35, ugc.tprob = 0.25, rct.tprob = 0.2,
  uct.tprob = 0.16, rgc.sympt.prob = 0.16, ugc.sympt.prob = 0.8,
  rct.sympt.prob = 0.14, uct.sympt.prob = 0.58, rgc.ntx.int = 16.8,
  ugc.ntx.int = 16.8, gc.tx.int = 1.4, rct.ntx.int = 32,
  uct.ntx.int = 32, ct.tx.int = 1.4, gc.sympt.prob.tx = c(0.95, 0.95,
  0.95), ct.sympt.prob.tx = c(0.9, 0.9, 0.9),
  gc.asympt.prob.tx = c(0.15, 0.15, 0.15), ct.asympt.prob.tx = c(0.15,
  0.15, 0.15), sti.cond.eff = 0.9, sti.cond.fail = c(0.2, 0.2, 0.2),
  hiv.rgc.rr = 2.78, hiv.ugc.rr = 1.73, hiv.rct.rr = 2.78,
  hiv.uct.rr = 1.73, hiv.dual.rr = 0.2, riskh.start = Inf,
  prep.start = Inf, prep.start.prob = 0.2, prep.adhr.dist = c(0.089,
  0.127, 0.784), prep.adhr.hr = c(0.69, 0.19, 0.01),
  prep.discont.rate = 1 - (2^(-1/(224.4237/7))), prep.tst.int = 90/7,
  prep.risk.int = 182/7, prep.sti.screen.int = 182/7,
  prep.sti.prob.tx = 1, prep.risk.reassess.method = "year",
  prep.require.lnt = TRUE, ...)

Arguments

netstats	Target statistics and related network initialization data from the standard ARTnet workflow.
hiv.test.rate	Mean probability of HIV testing per week for black/hispanic/white MSM (vector of length 3).
hiv.test.late.prob	Proportion of black/hispanic/white MSM who test only during AIDS stage infection (vector of length 3).
test.window.int	Length of the HIV test window period in weeks.
tt.part.supp	Proportion of black/hispanic/white MSM who enter partial viral suppression category after ART initiation (vector of length 3).
tt.full.supp	Proportion of black/hispanic/white MSM who enter full viral suppression category after ART initiation (vector of length 3).
tt.dur.supp	Proportion of black/hispanic/white MSM who enter durable viral suppression category after ART initiation (vector of length 3).
tx.init.prob	Probability per time step that a black/hispanic/white MSM who has tested positive will initiate treatment (vector of length 3).
tx.halt.part.prob	Probability per time step that black/hispanic/white MSM who have started treatment and assigned to the partial VL suppression category will stop treatment (vector of length 3).
tx.halt.full.rr	Relative reduction in tx.halt.part.prob for black/hispanic/white MSM in the full VL suppression category (vector of length 3).
tx.halt.dur.rr	Relative reduction in tx.halt.part.prob for black/hispanic/white MSM in the durable VL suppression category (vector of length 3).
tx.reinit.part.prob	Probability per time step that a black/hispanic/white MSM who has stopped treatment and assigned to the partial VL suppression category will restart treatment (vector of length 3).
tx.reinit.full.rr	Relative reduction in tx.reinit.part.prob for black/hispanic/white MSM in the full VL suppression category (vector of length 3).
tx.reinit.dur.rr	Relative reduction in tx.reinit.part.prob for black/hispanic/white MSM in the durable VL suppression category (vector of length 3).
max.time.off.tx.full.int	Number of weeks off treatment for a full suppressor before onset of AIDS, including time before diagnosis.
max.time.on.tx.part.int	Number of weeks on treatment for a partial suppressor beofre onset of AIDS.
max.time.off.tx.part.int	Nnumber of weeks off treatment for a partial suppressor before onset of AIDS, including time before diagnosis.
vl.acute.rise.int	Number of weeks to peak viremia during acute infection.
vl.acute.peak	Peak viral load (in log10 units) at the height of acute infection.
vl.acute.fall.int	Number of weeks from peak viremia to set-point viral load during the acute infection period.
vl.set.point	Set point viral load (in log10 units).
vl.aids.onset.int	Number of weeks to AIDS for a treatment-naive patient.
vl.aids.int	Duration of AIDS stage infection in weeks.
vl.aids.peak	Maximum viral load during AIDS stage.
vl.full.supp	Log10 viral load at full suppression on ART.
vl.part.supp	Log10 viral load at partial suppression on ART.
vl.tx.down.slope	Number of log10 units that viral load falls per time step from treatment initiation or re-initiation until the suppression level is reached (pre-AIDS stages).
vl.tx.aids.down.slope	Number of log10 units that viral load falls per time step from treatment initiation or re-initiation until the suppression level is reached (AIDS stage).
vl.tx.up.slope	Number of log10 units that viral load rises per time step from treatment halting until expected value.
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.
URAI.prob	Probability of transmission for a man having unprotected receptive anal intercourse with an infected man at set point viral load.
UIAI.prob	Probability of transmission for an uncircumcised man having unprotected insertive anal intercourse with an infected man at set point viral load.
trans.scale	Relative scalar on base infection probabilities for model calibration for black/hispanic/white men (vector of length 3).
acute.rr	Relative risk of infection (compared to that predicted by elevated viral load) when positive partner is in the acute stage.
circ.rr	Relative risk of infection from insertive anal sex when the negative insertive partner is circumcised.
cond.eff	Relative risk of HIV infection from anal sex when a condom is used properly (biological efficacy).
cond.fail	Condom failure rates for HIV for black/hispanic/white MSM, as a reduction in the cond.eff parameter (vector of length 3).
circ.prob	Probablity that a black/hispanic/white new arrival in the population will be circumcised (vector of length 3).
epistats	GLMs for epidemiological parameter from the standard ARTnet workflow.
acts.aids.vl	Viral load level after which sexual act rate goes to zero.
acts.scale	Scalar for main/casual act rate for model calibration.
cond.scale	Scalar for condom use probability for model calibration.
rgc.tprob	Probability of rectal gonorrhea infection per act.
ugc.tprob	Probability of urethral gonorrhea infection per act.
rct.tprob	Probability of rectal chlamydia infection per act.
uct.tprob	Probability of urethral chlamydia infection per act.
rgc.sympt.prob	Probability of symptoms given infection with rectal gonorrhea.
ugc.sympt.prob	Probability of symptoms given infection with urethral gonorrhea.
rct.sympt.prob	Probability of symptoms given infection with rectal chlamydia.
uct.sympt.prob	Probability of symptoms given infection with urethral chlamydia.
rgc.ntx.int	Average duration in weeks of untreated rectal gonorrhea.
ugc.ntx.int	Average duration in weeks of untreated urethral gonorrhea.
gc.tx.int	Average duration in weeks of treated gonorrhea (both sites).
rct.ntx.int	Average in weeks duration of untreated rectal chlamydia.
uct.ntx.int	Average in weeks duration of untreated urethral chlamydia.
ct.tx.int	Average in weeks duration of treated chlamydia (both sites).
gc.sympt.prob.tx	Probability of treatment for symptomatic gonorrhea for black/hispanic/white men (vector of length 3).
ct.sympt.prob.tx	Probability of treatment for symptomatic chlamydia for black/hispanic/white men (vector of length 3).
gc.asympt.prob.tx	Probability of treatment for asymptomatic gonorrhea for black/hispanic/white men (vector of length 3).
ct.asympt.prob.tx	Probability of treatment for asymptomatic chlamydia for black/hispanic/white men (vector of length 3).
sti.cond.eff	Relative risk of STI infection from anal sex when a condom is used properly (biological efficacy).
sti.cond.fail	Condom failure rates for STI for black/hispanic/white MSM, as a reduction in the cond.eff parameter (vector of length 3).
hiv.rgc.rr	Relative risk of HIV infection given current rectal gonorrhea.
hiv.ugc.rr	Relative risk of HIV infection given current urethral gonorrhea.
hiv.rct.rr	Relative risk of HIV infection given current rectal chlamydia.
hiv.uct.rr	Relative risk of HIV infection given current urethral chlamydia.
hiv.dual.rr	Additive proportional risk, from 0 to 1, for HIV infection given dual infection with both gonorrhea and chlamydia.
riskh.start	Time step at which behavioral risk history assessment occurs.
prep.start	Time step at which the PrEP intervention should start.
prep.start.prob	Probability of starting PrEP given current indications.
prep.adhr.dist	Proportion of men who are low, medium, and high adherent to PrEP.
prep.adhr.hr	The hazard ratio for infection per act associated with each level of adherence (from Grant).
prep.discont.rate	Rate of random discontinuation from PrEP.
prep.tst.int	Testing interval for those who are actively on PrEP. This overrides the mean testing interval parameters.
prep.risk.int	Time window for assessment of risk eligibility for PrEP in weeks.
prep.sti.screen.int	Interval in weeks between STI screening at PrEP visits.
prep.sti.prob.tx	Probability of treatment given positive screening during PrEP visit.
prep.risk.reassess.method	Interval for reassessment of risk indications of active PrEP users, either "none" for no reassessment, "inst" for weekly, or "year" for year.
prep.require.lnt	If TRUE, only start on PrEP if current time step is equal to the last negative test.
...	Additional arguments passed to the function.

Value

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

statnet/EpiModelHIVmsm documentation built on Aug. 28, 2020, 11:07 p.m.