param_shamp: Epidemic Model Parameters for SHAMP
In dth2/EpiModelHIV_SHAMP: Epidemic Modeling of HIV Transmission among MSM, MSMF and Heterosexual Populations
Description
Usage
Arguments
Value
Description
Sets the epidemic parameters for stochastic network models
simulated with netsim for EpiModelHIV
Usage
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param_shamp(race.method = 1, time.unit = 7, method = 1,
last.neg.test.B.f.int = 1464, last.neg.test.BI.f.int = 1464,
last.neg.test.H.f.int = 1464, last.neg.test.HI.f.int = 1464,
last.neg.test.W.f.int = 1464, last.neg.test.B.msf.int = 1708,
last.neg.test.BI.msf.int = 1708, last.neg.test.H.msf.int = 1708,
last.neg.test.HI.msf.int = 1708, last.neg.test.W.msf.int = 1708,
last.neg.test.B.msm.int = 1037, last.neg.test.BI.msm.int = 1037,
last.neg.test.H.msm.int = 1037, last.neg.test.HI.msm.int = 1037,
last.neg.test.W.msm.int = 1037, last.neg.test.B.msmf.int = 1129,
last.neg.test.BI.msmf.int = 1129, last.neg.test.H.msmf.int = 1129,
last.neg.test.HI.msmf.int = 1129, last.neg.test.W.msmf.int = 1129,
mean.test.B.f.int = 1464, mean.test.BI.f.int = 1464,
mean.test.H.f.int = 1464, mean.test.HI.f.int = 1464,
mean.test.W.f.int = 1464, mean.test.B.msf.int = 1708,
mean.test.BI.msf.int = 1708, mean.test.H.msf.int = 1708,
mean.test.HI.msf.int = 1708, mean.test.W.msf.int = 1708,
mean.test.B.msm.int = 1037, mean.test.BI.msm.int = 1037,
mean.test.H.msm.int = 1037, mean.test.HI.msm.int = 1037,
mean.test.W.msm.int = 1037, mean.test.B.msmf.int = 1129,
mean.test.BI.msmf.int = 1129, mean.test.H.msmf.int = 1129,
mean.test.HI.msmf.int = 1129, mean.test.W.msmf.int = 1129,
testing.pattern = "memoryless", test.window.int = 15,
tt.traj.B.f.prob = c(0.741, 0, 0.053, 0.206), tt.traj.BI.f.prob = c(0.741,
0, 0.053, 0.206), tt.traj.H.f.prob = c(0.741, 0, 0.041, 0.218),
tt.traj.HI.f.prob = c(0.741, 0, 0.041, 0.218), tt.traj.W.f.prob = c(0.741,
0, 0.057, 0.202), tt.traj.B.msf.prob = c(0.741, 0, 0.066, 0.193),
tt.traj.BI.msf.prob = c(0.741, 0, 0.066, 0.193),
tt.traj.H.msf.prob = c(0.741, 0, 0.067, 0.192),
tt.traj.HI.msf.prob = c(0.741, 0, 0.067, 0.192),
tt.traj.W.msf.prob = c(0.741, 0, 0.052, 0.207),
tt.traj.B.msm.prob = c(0.025, 0, 0.065, 0.911),
tt.traj.BI.msm.prob = c(0.025, 0, 0.065, 0.911),
tt.traj.H.msm.prob = c(0.025, 0, 0.065, 0.911),
tt.traj.HI.msm.prob = c(0.025, 0, 0.065, 0.911),
tt.traj.W.msm.prob = c(0.025, 0, 0.065, 0.911),
tt.traj.B.msmf.prob = c(0.741, 0, 0.066, 0.193),
tt.traj.BI.msmf.prob = c(0.741, 0, 0.066, 0.193),
tt.traj.H.msmf.prob = c(0.741, 0, 0.041, 0.218),
tt.traj.HI.msmf.prob = c(0.741, 0, 0.041, 0.218),
tt.traj.W.msmf.prob = c(0.741, 0, 0.052, 0.207),
tx.init.B.f.prob = 0.2331, tx.init.BI.f.prob = 0.2331,
tx.init.H.f.prob = 0.2331, tx.init.HI.f.prob = 0.2331,
tx.init.W.f.prob = 0.2331, tx.init.B.msf.prob = 0.2331,
tx.init.BI.msf.prob = 0.2331, tx.init.H.msf.prob = 0.2331,
tx.init.HI.msf.prob = 0.2331, tx.init.W.msf.prob = 0.2331,
tx.init.B.msm.prob = 0.1467, tx.init.BI.msm.prob = 0.1467,
tx.init.H.msm.prob = 0.1467, tx.init.HI.msm.prob = 0.1467,
tx.init.W.msm.prob = 0.1467, tx.init.B.msmf.prob = 0.2331,
tx.init.BI.msmf.prob = 0.2331, tx.init.H.msmf.prob = 0.2331,
tx.init.HI.msmf.prob = 0.2331, tx.init.W.msmf.prob = 0.2331,
tx.halt.B.f.prob = 1e-04, tx.halt.BI.f.prob = 1e-04,
tx.halt.H.f.prob = 1e-04, tx.halt.HI.f.prob = 1e-04,
tx.halt.W.f.prob = 1e-04, tx.halt.B.msf.prob = 1e-04,
tx.halt.BI.msf.prob = 1e-04, tx.halt.H.msf.prob = 1e-04,
tx.halt.HI.msf.prob = 1e-04, tx.halt.W.msf.prob = 1e-04,
tx.halt.B.msm.prob = 1e-04, tx.halt.BI.msm.prob = 1e-04,
tx.halt.H.msm.prob = 1e-04, tx.halt.HI.msm.prob = 1e-04,
tx.halt.W.msm.prob = 1e-04, tx.halt.B.msmf.prob = 1e-04,
tx.halt.BI.msmf.prob = 1e-04, tx.halt.H.msmf.prob = 1e-04,
tx.halt.HI.msmf.prob = 1e-04, tx.halt.W.msmf.prob = 1e-04,
tx.reinit.B.f.prob = 1, tx.reinit.BI.f.prob = 1, tx.reinit.H.f.prob = 1,
tx.reinit.HI.f.prob = 1, tx.reinit.W.f.prob = 1,
tx.reinit.B.msf.prob = 1, tx.reinit.BI.msf.prob = 1,
tx.reinit.H.msf.prob = 1, tx.reinit.HI.msf.prob = 1,
tx.reinit.W.msf.prob = 1, tx.reinit.B.msm.prob = 1,
tx.reinit.BI.msm.prob = 1, tx.reinit.H.msm.prob = 1,
tx.reinit.HI.msm.prob = 1, tx.reinit.W.msm.prob = 1,
tx.reinit.B.msmf.prob = 1, tx.reinit.BI.msmf.prob = 1,
tx.reinit.H.msmf.prob = 1, tx.reinit.HI.msmf.prob = 1,
tx.reinit.W.msmf.prob = 1, max.time.off.tx.full.int = 520 * 7,
max.time.on.tx.part.int = 52 * 15 * 7, max.time.off.tx.part.int = 520 * 7,
vl.acute.rise.int = 45, vl.acute.peak = 6.886, vl.acute.fall.int = 21,
vl.set.point = 4.5, vl.aids.onset.int = 520 * 7, vl.aids.int = 52 * 2 *
7, vl.fatal = 7, vl.full.supp = 1.5, vl.part.supp = 3.5,
full.supp.down.slope = 0.25, full.supp.up.slope = 0.25,
part.supp.down.slope = 0.25, part.supp.up.slope = 0.25, birth.age = 18,
exit.age = 60, b.method = "fixed", msm.frac = 0, msmf.frac = 0.012,
URAI.prob = 138/10000, UIAI.prob = 11/10000, URVI.prob = 8/10000,
UIVI.prob = 4/10000, acute.rr = 4, circ.rr = 0.4, condom.rr = 0.25,
disc.outset.main.B.f.prob = 0, disc.outset.main.BI.f.prob = 0,
disc.outset.main.H.f.prob = 0, disc.outset.main.HI.f.prob = 0,
disc.outset.main.W.f.prob = 0, disc.outset.main.B.msf.prob = 0,
disc.outset.main.BI.msf.prob = 0, disc.outset.main.H.msf.prob = 0,
disc.outset.main.HI.msf.prob = 0, disc.outset.main.W.msf.prob = 0,
disc.outset.main.B.msm.prob = 0, disc.outset.main.BI.msm.prob = 0,
disc.outset.main.H.msm.prob = 0, disc.outset.main.HI.msm.prob = 0,
disc.outset.main.W.msm.prob = 0, disc.outset.main.B.msmf.prob = 0,
disc.outset.main.BI.msmf.prob = 0, disc.outset.main.H.msmf.prob = 0,
disc.outset.main.HI.msmf.prob = 0, disc.outset.main.W.msmf.prob = 0,
disc.at.diag.main.B.f.prob = 0, disc.at.diag.main.BI.f.prob = 0,
disc.at.diag.main.H.f.prob = 0, disc.at.diag.main.HI.f.prob = 0,
disc.at.diag.main.W.f.prob = 0, disc.at.diag.main.B.msf.prob = 0,
disc.at.diag.main.BI.msf.prob = 0, disc.at.diag.main.H.msf.prob = 0,
disc.at.diag.main.HI.msf.prob = 0, disc.at.diag.main.W.msf.prob = 0,
disc.at.diag.main.B.msm.prob = 0, disc.at.diag.main.BI.msm.prob = 0,
disc.at.diag.main.H.msm.prob = 0, disc.at.diag.main.HI.msm.prob = 0,
disc.at.diag.main.W.msm.prob = 0, disc.at.diag.main.B.msmf.prob = 0,
disc.at.diag.main.BI.msmf.prob = 0, disc.at.diag.main.H.msmf.prob = 0,
disc.at.diag.main.HI.msmf.prob = 0, disc.at.diag.main.W.msmf.prob = 0,
disc.post.diag.main.B.f.prob = 0, disc.post.diag.main.BI.f.prob = 0,
disc.post.diag.main.H.f.prob = 0, disc.post.diag.main.HI.f.prob = 0,
disc.post.diag.main.W.f.prob = 0, disc.post.diag.main.B.msf.prob = 0,
disc.post.diag.main.BI.msf.prob = 0, disc.post.diag.main.H.msf.prob = 0,
disc.post.diag.main.HI.msf.prob = 0, disc.post.diag.main.W.msf.prob = 0,
disc.post.diag.main.B.msm.prob = 0, disc.post.diag.main.BI.msm.prob = 0,
disc.post.diag.main.H.msm.prob = 0, disc.post.diag.main.HI.msm.prob = 0,
disc.post.diag.main.W.msm.prob = 0, disc.post.diag.main.B.msmf.prob = 0,
disc.post.diag.main.BI.msmf.prob = 0, disc.post.diag.main.H.msmf.prob = 0,
disc.post.diag.main.HI.msmf.prob = 0, disc.post.diag.main.W.msmf.prob = 0,
disc.outset.pers.B.f.prob = 0, disc.outset.pers.BI.f.prob = 0,
disc.outset.pers.H.f.prob = 0, disc.outset.pers.HI.f.prob = 0,
disc.outset.pers.W.f.prob = 0, disc.outset.pers.B.msf.prob = 0,
disc.outset.pers.BI.msf.prob = 0, disc.outset.pers.H.msf.prob = 0,
disc.outset.pers.HI.msf.prob = 0, disc.outset.pers.W.msf.prob = 0,
disc.outset.pers.B.msm.prob = 0, disc.outset.pers.BI.msm.prob = 0,
disc.outset.pers.H.msm.prob = 0, disc.outset.pers.HI.msm.prob = 0,
disc.outset.pers.W.msm.prob = 0, disc.outset.pers.B.msmf.prob = 0,
disc.outset.pers.BI.msmf.prob = 0, disc.outset.pers.H.msmf.prob = 0,
disc.outset.pers.HI.msmf.prob = 0, disc.outset.pers.W.msmf.prob = 0,
disc.at.diag.pers.B.f.prob = 0, disc.at.diag.pers.BI.f.prob = 0,
disc.at.diag.pers.H.f.prob = 0, disc.at.diag.pers.HI.f.prob = 0,
disc.at.diag.pers.W.f.prob = 0, disc.at.diag.pers.B.msf.prob = 0,
disc.at.diag.pers.BI.msf.prob = 0, disc.at.diag.pers.H.msf.prob = 0,
disc.at.diag.pers.HI.msf.prob = 0, disc.at.diag.pers.W.msf.prob = 0,
disc.at.diag.pers.B.msm.prob = 0, disc.at.diag.pers.BI.msm.prob = 0,
disc.at.diag.pers.H.msm.prob = 0, disc.at.diag.pers.HI.msm.prob = 0,
disc.at.diag.pers.W.msm.prob = 0, disc.at.diag.pers.B.msmf.prob = 0,
disc.at.diag.pers.BI.msmf.prob = 0, disc.at.diag.pers.H.msmf.prob = 0,
disc.at.diag.pers.HI.msmf.prob = 0, disc.at.diag.pers.W.msmf.prob = 0,
disc.post.diag.pers.B.f.prob = 0, disc.post.diag.pers.BI.f.prob = 0,
disc.post.diag.pers.H.f.prob = 0, disc.post.diag.pers.HI.f.prob = 0,
disc.post.diag.pers.W.f.prob = 0, disc.post.diag.pers.B.msf.prob = 0,
disc.post.diag.pers.BI.msf.prob = 0, disc.post.diag.pers.H.msf.prob = 0,
disc.post.diag.pers.HI.msf.prob = 0, disc.post.diag.pers.W.msf.prob = 0,
disc.post.diag.pers.B.msm.prob = 0, disc.post.diag.pers.BI.msm.prob = 0,
disc.post.diag.pers.H.msm.prob = 0, disc.post.diag.pers.HI.msm.prob = 0,
disc.post.diag.pers.W.msm.prob = 0, disc.post.diag.pers.B.msmf.prob = 0,
disc.post.diag.pers.BI.msmf.prob = 0, disc.post.diag.pers.H.msmf.prob = 0,
disc.post.diag.pers.HI.msmf.prob = 0, disc.post.diag.pers.W.msmf.prob = 0,
disc.inst.B.f.prob = 0, disc.inst.BI.f.prob = 0, disc.inst.H.f.prob = 0,
disc.inst.HI.f.prob = 0, disc.inst.W.f.prob = 0,
disc.inst.B.msf.prob = 0, disc.inst.BI.msf.prob = 0,
disc.inst.H.msf.prob = 0, disc.inst.HI.msf.prob = 0,
disc.inst.W.msf.prob = 0, disc.inst.B.msm.prob = 0,
disc.inst.BI.msm.prob = 0, disc.inst.H.msm.prob = 0,
disc.inst.HI.msm.prob = 0, disc.inst.W.msm.prob = 0,
disc.inst.B.msmf.prob = 0, disc.inst.BI.msmf.prob = 0,
disc.inst.H.msmf.prob = 0, disc.inst.HI.msmf.prob = 0,
disc.inst.W.msmf.prob = 0, circ.B.prob = 0.77, circ.BI.prob = 0.45,
circ.H.prob = 0.48, circ.HI.prob = 0.36, circ.W.prob = 0.91,
ccr5.B.f.prob = c(0, 0), ccr5.BI.f.prob = c(0, 0), ccr5.H.f.prob = c(0,
0), ccr5.HI.f.prob = c(0, 0), ccr5.W.f.prob = c(0.017, 0),
ccr5.B.m.prob = c(0, 0), ccr5.BI.m.prob = c(0, 0), ccr5.H.m.prob = c(0,
0), ccr5.HI.m.prob = c(0, 0), ccr5.W.m.prob = c(0.017, 0),
ccr5.heteroz.rr = 0, num.inst.ai.classes = 1,
base.ai.main.B.rate = 1.379/7, base.ai.main.BI.rate = 1.379/7,
base.ai.main.H.rate = 1.379/7, base.ai.main.HI.rate = 1.379/7,
base.ai.main.W.rate = 1.379/7, base.ai.pers.B.rate = 0.883/7,
base.ai.pers.BI.rate = 0.883/7, base.ai.pers.H.rate = 0.883/7,
base.ai.pers.HI.rate = 0.883/7, base.ai.pers.W.rate = 0.883/7,
base.vi.main.B.rate = 0.25, base.vi.main.BI.rate = 0.19,
base.vi.main.H.rate = 0.26, base.vi.main.HI.rate = 0.24,
base.vi.main.W.rate = 0.22, base.vi.pers.B.rate = 0.12,
base.vi.pers.BI.rate = 0.09, base.vi.pers.H.rate = 0.12,
base.vi.pers.HI.rate = 0.09, base.vi.pers.W.rate = 0.12, ai.scale = 1,
vi.scale = 1, cond.main.B.prob.msm = 0.062,
cond.main.BI.prob.msm = 0.062, cond.main.H.prob.msm = 0.062,
cond.main.HI.prob.msm = 0.062, cond.main.W.prob.msm = 0.062,
cond.pers.always.prob.msm = 0.01, cond.pers.B.prob.msm = 0.0304,
cond.pers.BI.prob.msm = 0.0304, cond.pers.H.prob.msm = 0.0304,
cond.pers.HI.prob.msm = 0.0304, cond.pers.W.prob.msm = 0.0304,
cond.inst.always.prob.msm = 0.01, cond.inst.B.prob.msm = 0.413,
cond.inst.BI.prob.msm = 0.413, cond.inst.H.prob.msm = 0.413,
cond.inst.HI.prob.msm = 0.413, cond.inst.W.prob.msm = 0.413,
cond.always.prob.corr.msm = 0.01, cond.main.B.prob.het = 0.12,
cond.main.BI.prob.het = 0.17, cond.main.H.prob.het = 0.17,
cond.main.HI.prob.het = 0.19, cond.main.W.prob.het = 0.16,
cond.pers.always.prob.het = 1e-04, cond.pers.B.prob.het = 0.54,
cond.pers.BI.prob.het = 0.65, cond.pers.H.prob.het = 0.5,
cond.pers.HI.prob.het = 0.49, cond.pers.W.prob.het = 0.48,
cond.inst.always.prob.het = 1e-04, cond.inst.B.prob.het = 0.85,
cond.inst.BI.prob.het = 0.73, cond.inst.H.prob.het = 0.78,
cond.inst.HI.prob.het = 0.76, cond.inst.W.prob.het = 0.72,
cond.always.prob.corr.het = 1e-04, cond.diag.main.beta.msm = -0.67,
cond.discl.main.beta.msm = -0.85, cond.diag.pers.beta.msm = -0.67,
cond.discl.pers.beta.msm = -0.85, cond.diag.inst.beta.msm = -0.67,
cond.discl.inst.beta.msm = -0.85, cond.diag.main.beta.het = 0,
cond.discl.main.beta.het = 0, cond.diag.pers.beta.het = 0,
cond.discl.pers.beta.het = 0, cond.diag.inst.beta.het = 0,
cond.discl.inst.beta.het = 0, role.B.msm.prob = c(0.242, 0.321, 0.437),
role.BI.msm.prob = c(0.242, 0.321, 0.437), role.H.msm.prob = c(0.242,
0.321, 0.437), role.HI.msm.prob = c(0.242, 0.321, 0.437),
role.W.msm.prob = c(0.242, 0.321, 0.437), role.B.msmf.prob = c(0.242,
0.321, 0.437), role.BI.msmf.prob = c(0.242, 0.321, 0.437),
role.H.msmf.prob = c(0.242, 0.321, 0.437), role.HI.msmf.prob = c(0.242,
0.321, 0.437), role.W.msmf.prob = c(0.242, 0.321, 0.437),
vv.iev.B.prob = 0.47874, vv.iev.BI.prob = 0.47874,
vv.iev.H.prob = 0.47874, vv.iev.HI.prob = 0.47874,
vv.iev.W.prob = 0.47874, prep.start = Inf, prep.elig.model = "base",
prep.class.prob = c(0, 0, 0, 0), prep.class.hr = c(1, 0.69, 0.19, 0.05),
prep.coverage = 0, prep.cov.method = "curr", prep.cov.rate = 1,
prep.tst.int = 90, prep.risk.int = 182, prep.risk.reassess = TRUE,
msm.temp.adjust = 1, fa.temp.adjust = 1, depart.adjust = 1,
return.adjust = 1, immig.depart.BI.f = (1/(42 * 52 * 4)) * depart.adjust,
immig.depart.HI.f = (1/(42 * 52 * 4)) * depart.adjust,
immig.depart.BI.m = (1/(42 * 52 * 4)) * depart.adjust,
immig.depart.HI.m = (1/(42 * 52 * 4)) * depart.adjust,
immig.return.BI.f = (1/4) * return.adjust, immig.return.HI.f = (1/4) *
return.adjust, immig.return.BI.m = (1/4) * return.adjust,
immig.return.HI.m = (1/4) * return.adjust, immig.aq.prob.BI.f = 0.3 * 0.06
* ((base.vi.main.BI.rate + base.vi.pers.BI.rate)/2) * URVI.prob *
fa.temp.adjust, immig.aq.prob.HI.f = 0.3 * 0.005 * ((base.vi.main.HI.rate +
base.vi.pers.HI.rate)/2) * URVI.prob * fa.temp.adjust,
immig.aq.prob.BI.m = 0.3 * 0.06 * ((base.vi.main.BI.rate +
base.vi.pers.BI.rate)/2) * UIVI.prob * fa.temp.adjust,
immig.aq.prob.HI.m = 0.3 * 0.005 * ((base.vi.main.HI.rate +
base.vi.pers.HI.rate)/2) * UIVI.prob * fa.temp.adjust,
msm.aq.prob.B = 7.183e-06 * msm.temp.adjust, msm.aq.prob.BI = 7.183e-06 *
msm.temp.adjust, msm.aq.prob.H = 7.183e-06 * msm.temp.adjust,
msm.aq.prob.HI = 7.183e-06 * msm.temp.adjust, msm.aq.prob.W = 7.183e-06 *
msm.temp.adjust, demog.list = data.params[[1]]$demog.list,
demog.dist = data.params[[1]]$demog.dist,
sex.groups = data.params[[1]]$sex.groups,
race.groups = data.params[[1]]$race.groups,
age.groups = data.params[[1]]$age.groups,
age.adj = data.params[[1]]$age.adj, ...)
Arguments
testing.pattern
Method for HIV testing, with options "memoryless"
for constant hazard without regard to time since previous test, or
"interval" deterministic fixed intervals.
test.window.int
Length of the HIV test window period in days.
max.time.off.tx.full.int
Number of days off treatment for a full
suppressor before onset of AIDS, including time before diagnosis.
max.time.on.tx.part.int
Number of days on treatment for a
partial suppressor beofre onset of AIDS.
max.time.off.tx.part.int
Nnumber of days off treatment for a
partial suppressor before onset of AIDS, including time before
diagnosis.
vl.acute.rise.int
Number of days 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 days 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 days to AIDS for a treatment-naive
patient.
vl.aids.int
Duration of AIDS stage infection in days.
vl.fatal
Viral load in AIDS at which death occurs.
vl.full.supp
Log10 viral load at full suppression on ART.
vl.part.supp
Log10 viral load at partial suppression on ART.
full.supp.down.slope
For full suppressors, number of log10 units that
viral load falls per time step from treatment initiation or re-initiation
until the level in vl.full.supp.
full.supp.up.slope
For full suppressors, number of log10 units that
viral load rises per time step from treatment halting until expected
value.
part.supp.down.slope
For partial suppressors, number of log10 units
that viral load falls per time step from treatment initiation or
re-initiation until the level in vl.part.supp.
part.supp.up.slope
For partial suppressors, number of log10 units that
viral load rises per time step from treatment halting until expected value.
birth.age
Age (in years) of new arrivals.
b.method
Method for calculating the number of expected births at each
time step, with "fixed" based on the number of persons at the
initial time step and "varying" based on the current time step.
msm.frac
The fraction of males entering the population at each time step
as a male that has intercourse exclusivly with other males "msm" -
males not designated as msm or msmf are considered "msf".
msmf.frac
The fraction of males entering the population at each time step as
as a male that has intercourse with both males and females "msmf" -
males not designated as msm or msmf are considered "msf".
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.
URVI.prob
Probability of transmission for a woman having unprotected
receptive vaginal intercourse with an infected man at set point viral
load.
UIVI.prob
Probability of transmission for an uncircumcised man having
unprotected insertive vaginal intercourse with an infected women at set
point viral load.
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.
condom.rr
Relative risk of infection from anal sex when a condom is
used.
ccr5.heteroz.rr
Relative risk of infection for people who are heterozygous
in the CCR5 mutation.
num.inst.ai.classes
Number of quantiles into which men should be
divided in determining their levels of one-off anal intercourse.
ai.scale
General relative scaler for all ai act rates for model
calibration.
vi.scale
General relative scaler for all vi act rates for model
calibration.
cond.pers.always.prob.msm
Fraction of men in male-male casual partnerships who always
use condoms in those partnerships.
cond.inst.always.prob.msm
Fraction of men in male-male one-time partnerships who always
use condoms in those partnerships.
cond.always.prob.corr.msm
Correlation coefficient for probability of always
using condoms in both casual and one-off male-male partnerships
cond.pers.always.prob.het
Fraction of people in heterosexual casual partnerships who always
use condoms in those partnerships.
cond.inst.always.prob.het
Fraction of people in heterosexual one-time partnerships who always
use condoms in those partnerships.
cond.always.prob.corr.het
Correlation coefficient for probability of always
using condoms in both casual and one-off heterosexual partnerships
cond.diag.main.beta.msm
Beta multiplier for the log odds of using a
condom in a male-male main partnership if the HIV-infected man has been
diagnosed.
cond.discl.main.beta.msm
Beta multiplier for the log odds of using a
condom in a male-male main partnership if the HIV-infected man has disclosed.
cond.diag.pers.beta.msm
Beta multiplier for the log odds of using a
condom in a male-male casual partnership if the HIV-infected man has been
diagnosed.
cond.discl.pers.beta.msm
Beta multiplier for the log odds of using a
condom in a male-male casual partnership if the HIV-infected man has disclosed
his status.
cond.diag.inst.beta.msm
Beta multiplier for the log odds of using a
condom in a male-male one-off partnership if the HIV-infected man has been
diagnosed.
cond.discl.inst.beta.msm
Beta multiplier for the log odds of using a
condom in a male-male one-off partnership if the HIV-infected man has disclosed
his status.
cond.diag.main.beta.het
Beta multiplier for the log odds of using a
condom in a heterosexual main partnership if the HIV-infected man has been
diagnosed.
cond.discl.main.beta.het
Beta multiplier for the log odds of using a
condom in a heterosexual main partnership if the HIV-infected man has disclosed.
cond.diag.pers.beta.het
Beta multiplier for the log odds of using a
condom in a heterosexual casual partnership if the HIV-infected man has been
diagnosed.
cond.discl.pers.beta.het
Beta multiplier for the log odds of using a
condom in a heterosexual casual partnership if the HIV-infected man has disclosed
his status.
cond.diag.inst.beta.het
Beta multiplier for the log odds of using a
condom in a heterosexual one-off partnership if the HIV-infected man has been
diagnosed.
cond.discl.inst.beta.het
Beta multiplier for the log odds of using a
condom in a heterosexual one-off partnership if the HIV-infected man has disclosed
his status.
prep.start
Time step at which the PrEP intervention should start.
prep.elig.model
Modeling approach for determining who is eligible for
PrEP. Current options are limited to: "all" for all persons who
have never been on PrEP and are disease-susceptible.
prep.class.prob
The probability of adherence class in non-adherent,
low adherence, medium adherence, or high adherence groups (from Liu).
prep.class.hr
The hazard ratio for infection per act associated with each
level of adherence (from Grant).
prep.coverage
The proportion of the eligible population who are start
PrEP once they become eligible.
prep.cov.method
The method for calculating PrEP coverage, with options
of "curr" to base the numerator on the number of people currently
on PrEP and "ever" to base it on the number of people ever on
PrEP.
prep.cov.rate
The rate at which persons initiate PrEP conditional on
their eligibility, with 1 equal to instant start.
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 days.
prep.risk.reassess
If TRUE, reassess eligibility for PrEP at
each testing visit.
age.adj
This value is added to the squareroot of age for females in sqrt.age.adj
so that sex age asymmetry can be captured with an absdiff term
...
Additional arguments passed to the function.
last.neg.test.R.S.int
Time range in days for last negative test for
race group R where R is a charater (B, BI, H, HI or W) and sex group S
where s is a charter (f, msf, msm, msmf).
mean.test.B.int
Mean intertest interval in days for race group R where R
is a charater (B, BI, H, HI or W) and sex group S
where s is a charter (f, msf, msm, msmf) who test.
tt.traj.R.S.prob
Proportion of race group R, where R is a charater (B, BI, H, HI or W),
and sex group S, where s is a charter (f, msf, msm, msmf), who enter one of four
testing/treatment trajectories: never test or treat, test and never
initiate treatment, test and treated with partial viral suppression,
and test and treated with full suppression.
tx.init.R.S.prob
Probability per time step that a person in race group R, where R is a
charater (B, BI, H, HI or W), and sex group S, where s is a charter (f, msf, msm, msmf),
who has tested positive will initiate treatment.
tx.halt.R.S.prob
Probability per time step that a person in race group R, where R is a
charater (B, BI, H, HI or W), and sex group S, where s is a charter (f, msf, msm, msmf),
who is currently on treatment will halt treatment.
tx.reinit.R.S.prob
Probability per time step that a person in race group R, where R is a
charater (B, BI, H, HI or W), and sex group S, where s is a charter (f, msf, msm, msmf),
who is not currently on treatment but who has been in the past will
re-initiate treatment.
b.R.S.rate
Rate at which a person in race group R, where R is a
charater (B, BI, H, HI or W), and sex group S, where s is a charter (f, msf, msm, msmf),
enters the population.
disc.outset.main.R.S.prob
Probability that an HIV-infected person in race group R,
where R is a charater (B, BI, H, HI or W), and sex group S, where s is a charter
(f, msf, msm, msmf), will disclose their status at the start of a main partnership.
disc.at.diag.main.R.S.prob
Probability that a a person in race group R, where R is a
charater (B, BI, H, HI or W), and sex group S, where s is a charter (f, msf, msm, msmf),
already in a main partnership will disclose at the time of diagnosis.
disc.post.diag.main.R.S.prob
Probability that an HIV-infected a person in race group R,
where R is a charater (B, BI, H, HI or W), and sex group S, where s is a charter
(f, msf, msm, msmf), in a main partnership will disclose their status, assuming they didn't
at the start of the partnership or at diagnosis.
disc.outset.pers.R.S.prob
Probability that an HIV-infected a person in race group R,
where R is a charater (B, BI, H, HI or W), and sex group S, where s is a charter
(f, msf, msm, msmf), will disclose their status at the start of a casual partnership.
disc.at.diag.pers.R.S.prob
Probability that a person in race group R, where R is a
charater (B, BI, H, HI or W), and sex group S, where s is a charter (f, msf, msm, msmf),
already in a casual partnership will disclose at the time of diagnosis.
disc.post.diag.pers.R.S.prob
Probability that an HIV-infected person in race group R,
where R is a charater (B, BI, H, HI or W), and sex group S, where s is a charter
(f, msf, msm, msmf), in a casual partnership will disclose their status, assuming they
didn't at the start of the partnership or at diagnosis.
disc.inst.R.S.prob
Probability that an HIV-infected person in race group R,
where R is a charater (B, BI, H, HI or W), and sex group S, where s is a charter
(f, msf, msm, msmf), will disclose ther status to a one-off partner.
circ.R.prob
Probablity that a male in race group R, where R is a
charater (B, BI, H, HI or W), newly arriving in the population
will be circumcised.
ccr5.R.S.prob
Vector of length two of frequencies of the Delta 32
mutation (homozygous and heterozygous, respectively) in the CCR5 gene
among people in race group R, where R is a charater (B, BI, H, HI or W),
and sex group S, where s is a charter (f or m).
base.ai.main.R.rate
Expected coital frequency (for anal intercourse) for males
(msm and msmf) in race group R, where R is a charater (B, BI, H, HI or W),
in main partnerships (acts per day).
base.vi.main.R.rate
Expected coital frequency (for vaginal intercourse) for
males and females in race group R, where R is a charater (B, BI, H, HI or W),
in main partnerships (acts per day).
base.ai.pers.R.rate
Expected coital frequency (for anal intercourse) for males
(msm and msmf) in race group R, where R is a charater (B, BI, H, HI or W),
in casual partnerships (acts per day).
base.vi.pers.R.rate
Expected coital frequency (for vaginal intercourse) for
males and females in race group R, where R is a charater (B, BI, H, HI or W),
in casual partnerships (acts per day).
cond.main.R.prob.msm
Probability of condom use by an male of race group R,
where R is a charater (B, BI, H, HI or W), in a male-male main partnership.
cond.pers.R.prob.msm
Of men who are not consistent condom users, per-act
probability of condom use in a casual male-male partnership by
males of race group R, where R is a charater (B, BI, H, HI or W).
cond.inst.R.prob.msm
Of men who are not consistent condom users, per-act
probability of condom use in a one-time male-male partnership by
males of race group R, where R is a charater (B, BI, H, HI or W).
cond.main.R.prob.het
Probability of condom use by an person of race group R,
where R is a charater (B, BI, H, HI or W), in a heterosexual main partnership.
cond.pers.R.prob.het
Of people who are not consistent condom users, per-act
probability of condom use in a casual heterosexual partnership by
people of race group R, where R is a charater (B, BI, H, HI or W).
cond.inst.R.prob.het
Of people who are not consistent condom users, per-act
probability of condom use in a one-time heterosexual partnership by
males of race group R, where R is a charater (B, BI, H, HI or W).
vv.iev.R.prob
Probability that a person of group R, where R is a charater (B, BI, H, HI or W),
in a male male relationship will engage in intra-event versatility
("flipping") given that they're having AI.
immig.depart.R.S
The probability per time step that a person of group R,
where R is a charater (BI or HI), and sex S, were S is a charater (f or m), leaves the population
being simulated by returning to their home country.
immig.return.R.S
The probability per time step that a person of group R,
where R is a charater (BI or HI), and sex S, were S is a charater (f or m), who has left
the population being simulated by returning to their home country returns to the population
being simulated.
immig.aq.prob.R.S
The probability per time step that a person of group R,
where R is a charater (BI or HI), and sex S, were S is a charater (f or m), who has left
the population being simulated aquires HIV while in their home country.
Value
A list object of class param_shamp, which can be passed to
EpiModel function netsim.
dth2/EpiModelHIV_SHAMP documentation built on May 15, 2019, 4:56 p.m.
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Description Usage Arguments Value
Description
Sets the epidemic parameters for stochastic network models
simulated with netsim for EpiModelHIV
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 | param_shamp(race.method = 1, time.unit = 7, method = 1,
last.neg.test.B.f.int = 1464, last.neg.test.BI.f.int = 1464,
last.neg.test.H.f.int = 1464, last.neg.test.HI.f.int = 1464,
last.neg.test.W.f.int = 1464, last.neg.test.B.msf.int = 1708,
last.neg.test.BI.msf.int = 1708, last.neg.test.H.msf.int = 1708,
last.neg.test.HI.msf.int = 1708, last.neg.test.W.msf.int = 1708,
last.neg.test.B.msm.int = 1037, last.neg.test.BI.msm.int = 1037,
last.neg.test.H.msm.int = 1037, last.neg.test.HI.msm.int = 1037,
last.neg.test.W.msm.int = 1037, last.neg.test.B.msmf.int = 1129,
last.neg.test.BI.msmf.int = 1129, last.neg.test.H.msmf.int = 1129,
last.neg.test.HI.msmf.int = 1129, last.neg.test.W.msmf.int = 1129,
mean.test.B.f.int = 1464, mean.test.BI.f.int = 1464,
mean.test.H.f.int = 1464, mean.test.HI.f.int = 1464,
mean.test.W.f.int = 1464, mean.test.B.msf.int = 1708,
mean.test.BI.msf.int = 1708, mean.test.H.msf.int = 1708,
mean.test.HI.msf.int = 1708, mean.test.W.msf.int = 1708,
mean.test.B.msm.int = 1037, mean.test.BI.msm.int = 1037,
mean.test.H.msm.int = 1037, mean.test.HI.msm.int = 1037,
mean.test.W.msm.int = 1037, mean.test.B.msmf.int = 1129,
mean.test.BI.msmf.int = 1129, mean.test.H.msmf.int = 1129,
mean.test.HI.msmf.int = 1129, mean.test.W.msmf.int = 1129,
testing.pattern = "memoryless", test.window.int = 15,
tt.traj.B.f.prob = c(0.741, 0, 0.053, 0.206), tt.traj.BI.f.prob = c(0.741,
0, 0.053, 0.206), tt.traj.H.f.prob = c(0.741, 0, 0.041, 0.218),
tt.traj.HI.f.prob = c(0.741, 0, 0.041, 0.218), tt.traj.W.f.prob = c(0.741,
0, 0.057, 0.202), tt.traj.B.msf.prob = c(0.741, 0, 0.066, 0.193),
tt.traj.BI.msf.prob = c(0.741, 0, 0.066, 0.193),
tt.traj.H.msf.prob = c(0.741, 0, 0.067, 0.192),
tt.traj.HI.msf.prob = c(0.741, 0, 0.067, 0.192),
tt.traj.W.msf.prob = c(0.741, 0, 0.052, 0.207),
tt.traj.B.msm.prob = c(0.025, 0, 0.065, 0.911),
tt.traj.BI.msm.prob = c(0.025, 0, 0.065, 0.911),
tt.traj.H.msm.prob = c(0.025, 0, 0.065, 0.911),
tt.traj.HI.msm.prob = c(0.025, 0, 0.065, 0.911),
tt.traj.W.msm.prob = c(0.025, 0, 0.065, 0.911),
tt.traj.B.msmf.prob = c(0.741, 0, 0.066, 0.193),
tt.traj.BI.msmf.prob = c(0.741, 0, 0.066, 0.193),
tt.traj.H.msmf.prob = c(0.741, 0, 0.041, 0.218),
tt.traj.HI.msmf.prob = c(0.741, 0, 0.041, 0.218),
tt.traj.W.msmf.prob = c(0.741, 0, 0.052, 0.207),
tx.init.B.f.prob = 0.2331, tx.init.BI.f.prob = 0.2331,
tx.init.H.f.prob = 0.2331, tx.init.HI.f.prob = 0.2331,
tx.init.W.f.prob = 0.2331, tx.init.B.msf.prob = 0.2331,
tx.init.BI.msf.prob = 0.2331, tx.init.H.msf.prob = 0.2331,
tx.init.HI.msf.prob = 0.2331, tx.init.W.msf.prob = 0.2331,
tx.init.B.msm.prob = 0.1467, tx.init.BI.msm.prob = 0.1467,
tx.init.H.msm.prob = 0.1467, tx.init.HI.msm.prob = 0.1467,
tx.init.W.msm.prob = 0.1467, tx.init.B.msmf.prob = 0.2331,
tx.init.BI.msmf.prob = 0.2331, tx.init.H.msmf.prob = 0.2331,
tx.init.HI.msmf.prob = 0.2331, tx.init.W.msmf.prob = 0.2331,
tx.halt.B.f.prob = 1e-04, tx.halt.BI.f.prob = 1e-04,
tx.halt.H.f.prob = 1e-04, tx.halt.HI.f.prob = 1e-04,
tx.halt.W.f.prob = 1e-04, tx.halt.B.msf.prob = 1e-04,
tx.halt.BI.msf.prob = 1e-04, tx.halt.H.msf.prob = 1e-04,
tx.halt.HI.msf.prob = 1e-04, tx.halt.W.msf.prob = 1e-04,
tx.halt.B.msm.prob = 1e-04, tx.halt.BI.msm.prob = 1e-04,
tx.halt.H.msm.prob = 1e-04, tx.halt.HI.msm.prob = 1e-04,
tx.halt.W.msm.prob = 1e-04, tx.halt.B.msmf.prob = 1e-04,
tx.halt.BI.msmf.prob = 1e-04, tx.halt.H.msmf.prob = 1e-04,
tx.halt.HI.msmf.prob = 1e-04, tx.halt.W.msmf.prob = 1e-04,
tx.reinit.B.f.prob = 1, tx.reinit.BI.f.prob = 1, tx.reinit.H.f.prob = 1,
tx.reinit.HI.f.prob = 1, tx.reinit.W.f.prob = 1,
tx.reinit.B.msf.prob = 1, tx.reinit.BI.msf.prob = 1,
tx.reinit.H.msf.prob = 1, tx.reinit.HI.msf.prob = 1,
tx.reinit.W.msf.prob = 1, tx.reinit.B.msm.prob = 1,
tx.reinit.BI.msm.prob = 1, tx.reinit.H.msm.prob = 1,
tx.reinit.HI.msm.prob = 1, tx.reinit.W.msm.prob = 1,
tx.reinit.B.msmf.prob = 1, tx.reinit.BI.msmf.prob = 1,
tx.reinit.H.msmf.prob = 1, tx.reinit.HI.msmf.prob = 1,
tx.reinit.W.msmf.prob = 1, max.time.off.tx.full.int = 520 * 7,
max.time.on.tx.part.int = 52 * 15 * 7, max.time.off.tx.part.int = 520 * 7,
vl.acute.rise.int = 45, vl.acute.peak = 6.886, vl.acute.fall.int = 21,
vl.set.point = 4.5, vl.aids.onset.int = 520 * 7, vl.aids.int = 52 * 2 *
7, vl.fatal = 7, vl.full.supp = 1.5, vl.part.supp = 3.5,
full.supp.down.slope = 0.25, full.supp.up.slope = 0.25,
part.supp.down.slope = 0.25, part.supp.up.slope = 0.25, birth.age = 18,
exit.age = 60, b.method = "fixed", msm.frac = 0, msmf.frac = 0.012,
URAI.prob = 138/10000, UIAI.prob = 11/10000, URVI.prob = 8/10000,
UIVI.prob = 4/10000, acute.rr = 4, circ.rr = 0.4, condom.rr = 0.25,
disc.outset.main.B.f.prob = 0, disc.outset.main.BI.f.prob = 0,
disc.outset.main.H.f.prob = 0, disc.outset.main.HI.f.prob = 0,
disc.outset.main.W.f.prob = 0, disc.outset.main.B.msf.prob = 0,
disc.outset.main.BI.msf.prob = 0, disc.outset.main.H.msf.prob = 0,
disc.outset.main.HI.msf.prob = 0, disc.outset.main.W.msf.prob = 0,
disc.outset.main.B.msm.prob = 0, disc.outset.main.BI.msm.prob = 0,
disc.outset.main.H.msm.prob = 0, disc.outset.main.HI.msm.prob = 0,
disc.outset.main.W.msm.prob = 0, disc.outset.main.B.msmf.prob = 0,
disc.outset.main.BI.msmf.prob = 0, disc.outset.main.H.msmf.prob = 0,
disc.outset.main.HI.msmf.prob = 0, disc.outset.main.W.msmf.prob = 0,
disc.at.diag.main.B.f.prob = 0, disc.at.diag.main.BI.f.prob = 0,
disc.at.diag.main.H.f.prob = 0, disc.at.diag.main.HI.f.prob = 0,
disc.at.diag.main.W.f.prob = 0, disc.at.diag.main.B.msf.prob = 0,
disc.at.diag.main.BI.msf.prob = 0, disc.at.diag.main.H.msf.prob = 0,
disc.at.diag.main.HI.msf.prob = 0, disc.at.diag.main.W.msf.prob = 0,
disc.at.diag.main.B.msm.prob = 0, disc.at.diag.main.BI.msm.prob = 0,
disc.at.diag.main.H.msm.prob = 0, disc.at.diag.main.HI.msm.prob = 0,
disc.at.diag.main.W.msm.prob = 0, disc.at.diag.main.B.msmf.prob = 0,
disc.at.diag.main.BI.msmf.prob = 0, disc.at.diag.main.H.msmf.prob = 0,
disc.at.diag.main.HI.msmf.prob = 0, disc.at.diag.main.W.msmf.prob = 0,
disc.post.diag.main.B.f.prob = 0, disc.post.diag.main.BI.f.prob = 0,
disc.post.diag.main.H.f.prob = 0, disc.post.diag.main.HI.f.prob = 0,
disc.post.diag.main.W.f.prob = 0, disc.post.diag.main.B.msf.prob = 0,
disc.post.diag.main.BI.msf.prob = 0, disc.post.diag.main.H.msf.prob = 0,
disc.post.diag.main.HI.msf.prob = 0, disc.post.diag.main.W.msf.prob = 0,
disc.post.diag.main.B.msm.prob = 0, disc.post.diag.main.BI.msm.prob = 0,
disc.post.diag.main.H.msm.prob = 0, disc.post.diag.main.HI.msm.prob = 0,
disc.post.diag.main.W.msm.prob = 0, disc.post.diag.main.B.msmf.prob = 0,
disc.post.diag.main.BI.msmf.prob = 0, disc.post.diag.main.H.msmf.prob = 0,
disc.post.diag.main.HI.msmf.prob = 0, disc.post.diag.main.W.msmf.prob = 0,
disc.outset.pers.B.f.prob = 0, disc.outset.pers.BI.f.prob = 0,
disc.outset.pers.H.f.prob = 0, disc.outset.pers.HI.f.prob = 0,
disc.outset.pers.W.f.prob = 0, disc.outset.pers.B.msf.prob = 0,
disc.outset.pers.BI.msf.prob = 0, disc.outset.pers.H.msf.prob = 0,
disc.outset.pers.HI.msf.prob = 0, disc.outset.pers.W.msf.prob = 0,
disc.outset.pers.B.msm.prob = 0, disc.outset.pers.BI.msm.prob = 0,
disc.outset.pers.H.msm.prob = 0, disc.outset.pers.HI.msm.prob = 0,
disc.outset.pers.W.msm.prob = 0, disc.outset.pers.B.msmf.prob = 0,
disc.outset.pers.BI.msmf.prob = 0, disc.outset.pers.H.msmf.prob = 0,
disc.outset.pers.HI.msmf.prob = 0, disc.outset.pers.W.msmf.prob = 0,
disc.at.diag.pers.B.f.prob = 0, disc.at.diag.pers.BI.f.prob = 0,
disc.at.diag.pers.H.f.prob = 0, disc.at.diag.pers.HI.f.prob = 0,
disc.at.diag.pers.W.f.prob = 0, disc.at.diag.pers.B.msf.prob = 0,
disc.at.diag.pers.BI.msf.prob = 0, disc.at.diag.pers.H.msf.prob = 0,
disc.at.diag.pers.HI.msf.prob = 0, disc.at.diag.pers.W.msf.prob = 0,
disc.at.diag.pers.B.msm.prob = 0, disc.at.diag.pers.BI.msm.prob = 0,
disc.at.diag.pers.H.msm.prob = 0, disc.at.diag.pers.HI.msm.prob = 0,
disc.at.diag.pers.W.msm.prob = 0, disc.at.diag.pers.B.msmf.prob = 0,
disc.at.diag.pers.BI.msmf.prob = 0, disc.at.diag.pers.H.msmf.prob = 0,
disc.at.diag.pers.HI.msmf.prob = 0, disc.at.diag.pers.W.msmf.prob = 0,
disc.post.diag.pers.B.f.prob = 0, disc.post.diag.pers.BI.f.prob = 0,
disc.post.diag.pers.H.f.prob = 0, disc.post.diag.pers.HI.f.prob = 0,
disc.post.diag.pers.W.f.prob = 0, disc.post.diag.pers.B.msf.prob = 0,
disc.post.diag.pers.BI.msf.prob = 0, disc.post.diag.pers.H.msf.prob = 0,
disc.post.diag.pers.HI.msf.prob = 0, disc.post.diag.pers.W.msf.prob = 0,
disc.post.diag.pers.B.msm.prob = 0, disc.post.diag.pers.BI.msm.prob = 0,
disc.post.diag.pers.H.msm.prob = 0, disc.post.diag.pers.HI.msm.prob = 0,
disc.post.diag.pers.W.msm.prob = 0, disc.post.diag.pers.B.msmf.prob = 0,
disc.post.diag.pers.BI.msmf.prob = 0, disc.post.diag.pers.H.msmf.prob = 0,
disc.post.diag.pers.HI.msmf.prob = 0, disc.post.diag.pers.W.msmf.prob = 0,
disc.inst.B.f.prob = 0, disc.inst.BI.f.prob = 0, disc.inst.H.f.prob = 0,
disc.inst.HI.f.prob = 0, disc.inst.W.f.prob = 0,
disc.inst.B.msf.prob = 0, disc.inst.BI.msf.prob = 0,
disc.inst.H.msf.prob = 0, disc.inst.HI.msf.prob = 0,
disc.inst.W.msf.prob = 0, disc.inst.B.msm.prob = 0,
disc.inst.BI.msm.prob = 0, disc.inst.H.msm.prob = 0,
disc.inst.HI.msm.prob = 0, disc.inst.W.msm.prob = 0,
disc.inst.B.msmf.prob = 0, disc.inst.BI.msmf.prob = 0,
disc.inst.H.msmf.prob = 0, disc.inst.HI.msmf.prob = 0,
disc.inst.W.msmf.prob = 0, circ.B.prob = 0.77, circ.BI.prob = 0.45,
circ.H.prob = 0.48, circ.HI.prob = 0.36, circ.W.prob = 0.91,
ccr5.B.f.prob = c(0, 0), ccr5.BI.f.prob = c(0, 0), ccr5.H.f.prob = c(0,
0), ccr5.HI.f.prob = c(0, 0), ccr5.W.f.prob = c(0.017, 0),
ccr5.B.m.prob = c(0, 0), ccr5.BI.m.prob = c(0, 0), ccr5.H.m.prob = c(0,
0), ccr5.HI.m.prob = c(0, 0), ccr5.W.m.prob = c(0.017, 0),
ccr5.heteroz.rr = 0, num.inst.ai.classes = 1,
base.ai.main.B.rate = 1.379/7, base.ai.main.BI.rate = 1.379/7,
base.ai.main.H.rate = 1.379/7, base.ai.main.HI.rate = 1.379/7,
base.ai.main.W.rate = 1.379/7, base.ai.pers.B.rate = 0.883/7,
base.ai.pers.BI.rate = 0.883/7, base.ai.pers.H.rate = 0.883/7,
base.ai.pers.HI.rate = 0.883/7, base.ai.pers.W.rate = 0.883/7,
base.vi.main.B.rate = 0.25, base.vi.main.BI.rate = 0.19,
base.vi.main.H.rate = 0.26, base.vi.main.HI.rate = 0.24,
base.vi.main.W.rate = 0.22, base.vi.pers.B.rate = 0.12,
base.vi.pers.BI.rate = 0.09, base.vi.pers.H.rate = 0.12,
base.vi.pers.HI.rate = 0.09, base.vi.pers.W.rate = 0.12, ai.scale = 1,
vi.scale = 1, cond.main.B.prob.msm = 0.062,
cond.main.BI.prob.msm = 0.062, cond.main.H.prob.msm = 0.062,
cond.main.HI.prob.msm = 0.062, cond.main.W.prob.msm = 0.062,
cond.pers.always.prob.msm = 0.01, cond.pers.B.prob.msm = 0.0304,
cond.pers.BI.prob.msm = 0.0304, cond.pers.H.prob.msm = 0.0304,
cond.pers.HI.prob.msm = 0.0304, cond.pers.W.prob.msm = 0.0304,
cond.inst.always.prob.msm = 0.01, cond.inst.B.prob.msm = 0.413,
cond.inst.BI.prob.msm = 0.413, cond.inst.H.prob.msm = 0.413,
cond.inst.HI.prob.msm = 0.413, cond.inst.W.prob.msm = 0.413,
cond.always.prob.corr.msm = 0.01, cond.main.B.prob.het = 0.12,
cond.main.BI.prob.het = 0.17, cond.main.H.prob.het = 0.17,
cond.main.HI.prob.het = 0.19, cond.main.W.prob.het = 0.16,
cond.pers.always.prob.het = 1e-04, cond.pers.B.prob.het = 0.54,
cond.pers.BI.prob.het = 0.65, cond.pers.H.prob.het = 0.5,
cond.pers.HI.prob.het = 0.49, cond.pers.W.prob.het = 0.48,
cond.inst.always.prob.het = 1e-04, cond.inst.B.prob.het = 0.85,
cond.inst.BI.prob.het = 0.73, cond.inst.H.prob.het = 0.78,
cond.inst.HI.prob.het = 0.76, cond.inst.W.prob.het = 0.72,
cond.always.prob.corr.het = 1e-04, cond.diag.main.beta.msm = -0.67,
cond.discl.main.beta.msm = -0.85, cond.diag.pers.beta.msm = -0.67,
cond.discl.pers.beta.msm = -0.85, cond.diag.inst.beta.msm = -0.67,
cond.discl.inst.beta.msm = -0.85, cond.diag.main.beta.het = 0,
cond.discl.main.beta.het = 0, cond.diag.pers.beta.het = 0,
cond.discl.pers.beta.het = 0, cond.diag.inst.beta.het = 0,
cond.discl.inst.beta.het = 0, role.B.msm.prob = c(0.242, 0.321, 0.437),
role.BI.msm.prob = c(0.242, 0.321, 0.437), role.H.msm.prob = c(0.242,
0.321, 0.437), role.HI.msm.prob = c(0.242, 0.321, 0.437),
role.W.msm.prob = c(0.242, 0.321, 0.437), role.B.msmf.prob = c(0.242,
0.321, 0.437), role.BI.msmf.prob = c(0.242, 0.321, 0.437),
role.H.msmf.prob = c(0.242, 0.321, 0.437), role.HI.msmf.prob = c(0.242,
0.321, 0.437), role.W.msmf.prob = c(0.242, 0.321, 0.437),
vv.iev.B.prob = 0.47874, vv.iev.BI.prob = 0.47874,
vv.iev.H.prob = 0.47874, vv.iev.HI.prob = 0.47874,
vv.iev.W.prob = 0.47874, prep.start = Inf, prep.elig.model = "base",
prep.class.prob = c(0, 0, 0, 0), prep.class.hr = c(1, 0.69, 0.19, 0.05),
prep.coverage = 0, prep.cov.method = "curr", prep.cov.rate = 1,
prep.tst.int = 90, prep.risk.int = 182, prep.risk.reassess = TRUE,
msm.temp.adjust = 1, fa.temp.adjust = 1, depart.adjust = 1,
return.adjust = 1, immig.depart.BI.f = (1/(42 * 52 * 4)) * depart.adjust,
immig.depart.HI.f = (1/(42 * 52 * 4)) * depart.adjust,
immig.depart.BI.m = (1/(42 * 52 * 4)) * depart.adjust,
immig.depart.HI.m = (1/(42 * 52 * 4)) * depart.adjust,
immig.return.BI.f = (1/4) * return.adjust, immig.return.HI.f = (1/4) *
return.adjust, immig.return.BI.m = (1/4) * return.adjust,
immig.return.HI.m = (1/4) * return.adjust, immig.aq.prob.BI.f = 0.3 * 0.06
* ((base.vi.main.BI.rate + base.vi.pers.BI.rate)/2) * URVI.prob *
fa.temp.adjust, immig.aq.prob.HI.f = 0.3 * 0.005 * ((base.vi.main.HI.rate +
base.vi.pers.HI.rate)/2) * URVI.prob * fa.temp.adjust,
immig.aq.prob.BI.m = 0.3 * 0.06 * ((base.vi.main.BI.rate +
base.vi.pers.BI.rate)/2) * UIVI.prob * fa.temp.adjust,
immig.aq.prob.HI.m = 0.3 * 0.005 * ((base.vi.main.HI.rate +
base.vi.pers.HI.rate)/2) * UIVI.prob * fa.temp.adjust,
msm.aq.prob.B = 7.183e-06 * msm.temp.adjust, msm.aq.prob.BI = 7.183e-06 *
msm.temp.adjust, msm.aq.prob.H = 7.183e-06 * msm.temp.adjust,
msm.aq.prob.HI = 7.183e-06 * msm.temp.adjust, msm.aq.prob.W = 7.183e-06 *
msm.temp.adjust, demog.list = data.params[[1]]$demog.list,
demog.dist = data.params[[1]]$demog.dist,
sex.groups = data.params[[1]]$sex.groups,
race.groups = data.params[[1]]$race.groups,
age.groups = data.params[[1]]$age.groups,
age.adj = data.params[[1]]$age.adj, ...)
|
Arguments
testing.pattern |
Method for HIV testing, with options |
test.window.int |
Length of the HIV test window period in days. |
max.time.off.tx.full.int |
Number of days off treatment for a full suppressor before onset of AIDS, including time before diagnosis. |
max.time.on.tx.part.int |
Number of days on treatment for a partial suppressor beofre onset of AIDS. |
max.time.off.tx.part.int |
Nnumber of days off treatment for a partial suppressor before onset of AIDS, including time before diagnosis. |
vl.acute.rise.int |
Number of days 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 days 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 days to AIDS for a treatment-naive patient. |
vl.aids.int |
Duration of AIDS stage infection in days. |
vl.fatal |
Viral load in AIDS at which death occurs. |
vl.full.supp |
Log10 viral load at full suppression on ART. |
vl.part.supp |
Log10 viral load at partial suppression on ART. |
full.supp.down.slope |
For full suppressors, number of log10 units that
viral load falls per time step from treatment initiation or re-initiation
until the level in |
full.supp.up.slope |
For full suppressors, number of log10 units that viral load rises per time step from treatment halting until expected value. |
part.supp.down.slope |
For partial suppressors, number of log10 units
that viral load falls per time step from treatment initiation or
re-initiation until the level in |
part.supp.up.slope |
For partial suppressors, number of log10 units that viral load rises per time step from treatment halting until expected value. |
birth.age |
Age (in years) of new arrivals. |
b.method |
Method for calculating the number of expected births at each
time step, with |
msm.frac |
The fraction of males entering the population at each time step as a male that has intercourse exclusivly with other males "msm" - males not designated as msm or msmf are considered "msf". |
msmf.frac |
The fraction of males entering the population at each time step as as a male that has intercourse with both males and females "msmf" - males not designated as msm or msmf are considered "msf". |
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. |
URVI.prob |
Probability of transmission for a woman having unprotected receptive vaginal intercourse with an infected man at set point viral load. |
UIVI.prob |
Probability of transmission for an uncircumcised man having unprotected insertive vaginal intercourse with an infected women at set point viral load. |
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. |
condom.rr |
Relative risk of infection from anal sex when a condom is used. |
ccr5.heteroz.rr |
Relative risk of infection for people who are heterozygous in the CCR5 mutation. |
num.inst.ai.classes |
Number of quantiles into which men should be divided in determining their levels of one-off anal intercourse. |
ai.scale |
General relative scaler for all ai act rates for model calibration. |
vi.scale |
General relative scaler for all vi act rates for model calibration. |
cond.pers.always.prob.msm |
Fraction of men in male-male casual partnerships who always use condoms in those partnerships. |
cond.inst.always.prob.msm |
Fraction of men in male-male one-time partnerships who always use condoms in those partnerships. |
cond.always.prob.corr.msm |
Correlation coefficient for probability of always using condoms in both casual and one-off male-male partnerships |
cond.pers.always.prob.het |
Fraction of people in heterosexual casual partnerships who always use condoms in those partnerships. |
cond.inst.always.prob.het |
Fraction of people in heterosexual one-time partnerships who always use condoms in those partnerships. |
cond.always.prob.corr.het |
Correlation coefficient for probability of always using condoms in both casual and one-off heterosexual partnerships |
cond.diag.main.beta.msm |
Beta multiplier for the log odds of using a condom in a male-male main partnership if the HIV-infected man has been diagnosed. |
cond.discl.main.beta.msm |
Beta multiplier for the log odds of using a condom in a male-male main partnership if the HIV-infected man has disclosed. |
cond.diag.pers.beta.msm |
Beta multiplier for the log odds of using a condom in a male-male casual partnership if the HIV-infected man has been diagnosed. |
cond.discl.pers.beta.msm |
Beta multiplier for the log odds of using a condom in a male-male casual partnership if the HIV-infected man has disclosed his status. |
cond.diag.inst.beta.msm |
Beta multiplier for the log odds of using a condom in a male-male one-off partnership if the HIV-infected man has been diagnosed. |
cond.discl.inst.beta.msm |
Beta multiplier for the log odds of using a condom in a male-male one-off partnership if the HIV-infected man has disclosed his status. |
cond.diag.main.beta.het |
Beta multiplier for the log odds of using a condom in a heterosexual main partnership if the HIV-infected man has been diagnosed. |
cond.discl.main.beta.het |
Beta multiplier for the log odds of using a condom in a heterosexual main partnership if the HIV-infected man has disclosed. |
cond.diag.pers.beta.het |
Beta multiplier for the log odds of using a condom in a heterosexual casual partnership if the HIV-infected man has been diagnosed. |
cond.discl.pers.beta.het |
Beta multiplier for the log odds of using a condom in a heterosexual casual partnership if the HIV-infected man has disclosed his status. |
cond.diag.inst.beta.het |
Beta multiplier for the log odds of using a condom in a heterosexual one-off partnership if the HIV-infected man has been diagnosed. |
cond.discl.inst.beta.het |
Beta multiplier for the log odds of using a condom in a heterosexual one-off partnership if the HIV-infected man has disclosed his status. |
prep.start |
Time step at which the PrEP intervention should start. |
prep.elig.model |
Modeling approach for determining who is eligible for
PrEP. Current options are limited to: |
prep.class.prob |
The probability of adherence class in non-adherent, low adherence, medium adherence, or high adherence groups (from Liu). |
prep.class.hr |
The hazard ratio for infection per act associated with each level of adherence (from Grant). |
prep.coverage |
The proportion of the eligible population who are start PrEP once they become eligible. |
prep.cov.method |
The method for calculating PrEP coverage, with options
of |
prep.cov.rate |
The rate at which persons initiate PrEP conditional on their eligibility, with 1 equal to instant start. |
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 days. |
prep.risk.reassess |
If |
age.adj |
This value is added to the squareroot of age for females in sqrt.age.adj so that sex age asymmetry can be captured with an absdiff term |
... |
Additional arguments passed to the function. |
last.neg.test.R.S.int |
Time range in days for last negative test for race group R where R is a charater (B, BI, H, HI or W) and sex group S where s is a charter (f, msf, msm, msmf). |
mean.test.B.int |
Mean intertest interval in days for race group R where R is a charater (B, BI, H, HI or W) and sex group S where s is a charter (f, msf, msm, msmf) who test. |
tt.traj.R.S.prob |
Proportion of race group R, where R is a charater (B, BI, H, HI or W), and sex group S, where s is a charter (f, msf, msm, msmf), who enter one of four testing/treatment trajectories: never test or treat, test and never initiate treatment, test and treated with partial viral suppression, and test and treated with full suppression. |
tx.init.R.S.prob |
Probability per time step that a person in race group R, where R is a charater (B, BI, H, HI or W), and sex group S, where s is a charter (f, msf, msm, msmf), who has tested positive will initiate treatment. |
tx.halt.R.S.prob |
Probability per time step that a person in race group R, where R is a charater (B, BI, H, HI or W), and sex group S, where s is a charter (f, msf, msm, msmf), who is currently on treatment will halt treatment. |
tx.reinit.R.S.prob |
Probability per time step that a person in race group R, where R is a charater (B, BI, H, HI or W), and sex group S, where s is a charter (f, msf, msm, msmf), who is not currently on treatment but who has been in the past will re-initiate treatment. |
b.R.S.rate |
Rate at which a person in race group R, where R is a charater (B, BI, H, HI or W), and sex group S, where s is a charter (f, msf, msm, msmf), enters the population. |
disc.outset.main.R.S.prob |
Probability that an HIV-infected person in race group R, where R is a charater (B, BI, H, HI or W), and sex group S, where s is a charter (f, msf, msm, msmf), will disclose their status at the start of a main partnership. |
disc.at.diag.main.R.S.prob |
Probability that a a person in race group R, where R is a charater (B, BI, H, HI or W), and sex group S, where s is a charter (f, msf, msm, msmf), already in a main partnership will disclose at the time of diagnosis. |
disc.post.diag.main.R.S.prob |
Probability that an HIV-infected a person in race group R, where R is a charater (B, BI, H, HI or W), and sex group S, where s is a charter (f, msf, msm, msmf), in a main partnership will disclose their status, assuming they didn't at the start of the partnership or at diagnosis. |
disc.outset.pers.R.S.prob |
Probability that an HIV-infected a person in race group R, where R is a charater (B, BI, H, HI or W), and sex group S, where s is a charter (f, msf, msm, msmf), will disclose their status at the start of a casual partnership. |
disc.at.diag.pers.R.S.prob |
Probability that a person in race group R, where R is a charater (B, BI, H, HI or W), and sex group S, where s is a charter (f, msf, msm, msmf), already in a casual partnership will disclose at the time of diagnosis. |
disc.post.diag.pers.R.S.prob |
Probability that an HIV-infected person in race group R, where R is a charater (B, BI, H, HI or W), and sex group S, where s is a charter (f, msf, msm, msmf), in a casual partnership will disclose their status, assuming they didn't at the start of the partnership or at diagnosis. |
disc.inst.R.S.prob |
Probability that an HIV-infected person in race group R, where R is a charater (B, BI, H, HI or W), and sex group S, where s is a charter (f, msf, msm, msmf), will disclose ther status to a one-off partner. |
circ.R.prob |
Probablity that a male in race group R, where R is a charater (B, BI, H, HI or W), newly arriving in the population will be circumcised. |
ccr5.R.S.prob |
Vector of length two of frequencies of the Delta 32 mutation (homozygous and heterozygous, respectively) in the CCR5 gene among people in race group R, where R is a charater (B, BI, H, HI or W), and sex group S, where s is a charter (f or m). |
base.ai.main.R.rate |
Expected coital frequency (for anal intercourse) for males (msm and msmf) in race group R, where R is a charater (B, BI, H, HI or W), in main partnerships (acts per day). |
base.vi.main.R.rate |
Expected coital frequency (for vaginal intercourse) for males and females in race group R, where R is a charater (B, BI, H, HI or W), in main partnerships (acts per day). |
base.ai.pers.R.rate |
Expected coital frequency (for anal intercourse) for males (msm and msmf) in race group R, where R is a charater (B, BI, H, HI or W), in casual partnerships (acts per day). |
base.vi.pers.R.rate |
Expected coital frequency (for vaginal intercourse) for males and females in race group R, where R is a charater (B, BI, H, HI or W), in casual partnerships (acts per day). |
cond.main.R.prob.msm |
Probability of condom use by an male of race group R, where R is a charater (B, BI, H, HI or W), in a male-male main partnership. |
cond.pers.R.prob.msm |
Of men who are not consistent condom users, per-act probability of condom use in a casual male-male partnership by males of race group R, where R is a charater (B, BI, H, HI or W). |
cond.inst.R.prob.msm |
Of men who are not consistent condom users, per-act probability of condom use in a one-time male-male partnership by males of race group R, where R is a charater (B, BI, H, HI or W). |
cond.main.R.prob.het |
Probability of condom use by an person of race group R, where R is a charater (B, BI, H, HI or W), in a heterosexual main partnership. |
cond.pers.R.prob.het |
Of people who are not consistent condom users, per-act probability of condom use in a casual heterosexual partnership by people of race group R, where R is a charater (B, BI, H, HI or W). |
cond.inst.R.prob.het |
Of people who are not consistent condom users, per-act probability of condom use in a one-time heterosexual partnership by males of race group R, where R is a charater (B, BI, H, HI or W). |
vv.iev.R.prob |
Probability that a person of group R, where R is a charater (B, BI, H, HI or W), in a male male relationship will engage in intra-event versatility ("flipping") given that they're having AI. |
immig.depart.R.S |
The probability per time step that a person of group R, where R is a charater (BI or HI), and sex S, were S is a charater (f or m), leaves the population being simulated by returning to their home country. |
immig.return.R.S |
The probability per time step that a person of group R, where R is a charater (BI or HI), and sex S, were S is a charater (f or m), who has left the population being simulated by returning to their home country returns to the population being simulated. |
immig.aq.prob.R.S |
The probability per time step that a person of group R, where R is a charater (BI or HI), and sex S, were S is a charater (f or m), who has left the population being simulated aquires HIV while in their home country. |
Value
A list object of class param_shamp, which can be passed to
EpiModel function netsim.
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