param_cl: Epidemic Model Parameters
In statnet/PrEP-for-ASMM-and-adult-MSM: Network-Based Epidemic Modeling of HIV Transmission among MSM and ASMM populations
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
param_cl(nwstats, race.method = 1, FU = FALSE,
last.neg.test.B.int = 301, last.neg.test.W.int = 315,
last.neg.test.B.int.asmm = 2900, last.neg.test.W.int.asmm = 2900,
mean.test.B.int = 301, mean.test.W.int = 315,
mean.test.B.int.asmm = 2900, mean.test.W.int.asmm = 2900,
testing.pattern = "memoryless", test.window.int = 21,
tt.traj.B.prob = c(0.077, 0, 0.356, 0.567), tt.traj.W.prob = c(0.052,
0, 0.331, 0.617), tx.init.B.prob = 0.092, tx.init.W.prob = 0.127,
tx.halt.B.prob = 0.0102, tx.halt.W.prob = 0.0071,
tx.reinit.B.prob = 0.00066, tx.reinit.W.prob = 0.00291,
tx.init.B.prob.asmm = 0.092, tx.init.W.prob.asmm = 0.127,
tx.halt.B.prob.asmm = 0.0102, tx.halt.W.prob.asmm = 0.0071,
tx.reinit.B.prob.asmm = 0.00066, tx.reinit.W.prob.asmm = 0.00291,
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 = 45, 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 = 13, b.B.rate.asmm = 0.0001348571,
b.W.rate.asmm = 0.0001348571, b.method = "fixed",
URAI.prob = 0.0082 * 1.09, UIAI.prob = 0.0031 * 1.09, acute.rr = 6,
circ.rr = 0.4, condom.rr = 0.295, disc.outset.main.B.prob = 0.685,
disc.outset.main.W.prob = 0.889, disc.at.diag.main.B.prob = 1,
disc.at.diag.main.W.prob = 1, disc.post.diag.main.B.prob = 0,
disc.post.diag.main.W.prob = 0, disc.outset.pers.B.prob = 0.527,
disc.outset.pers.W.prob = 0.828, disc.at.diag.pers.B.prob = 1,
disc.at.diag.pers.W.prob = 1, disc.post.diag.pers.B.prob = 0,
disc.post.diag.pers.W.prob = 0, disc.inst.B.prob = 0.445,
disc.inst.W.prob = 0.691, disc.outset.asmm.B.prob.asmm = 0,
disc.outset.asmm.W.prob.asmm = 0, disc.at.diag.asmm.B.prob.asmm = 1,
disc.at.diag.asmm.W.prob.asmm = 1,
disc.post.diag.asmm.B.prob.asmm = 0,
disc.post.diag.asmm.W.prob.asmm = 0, circ.B.prob = 0.874,
circ.W.prob = 0.918, ccr5.B.prob = c(0, 0.034),
ccr5.W.prob = c(0.021, 0.176), ccr5.heteroz.rr = 0.3,
num.inst.ai.classes = 1, base.ai.main.BB.rate = 0.17,
base.ai.main.BW.rate = 0.26, base.ai.main.WW.rate = 0.23,
base.ai.pers.BB.rate = 0.11, base.ai.pers.BW.rate = 0.16,
base.ai.pers.WW.rate = 0.14, base.ai.asmm.BB.rate = 0.0384,
base.ai.asmm.BW.rate = 0.0384, base.ai.asmm.WW.rate = 0.0384,
ai.main.scale = 1, ai.pers.scale = 1, ai.inst.scale = 1,
ai.asmm.scale = 1, cond.main.BB.prob = 0.38,
cond.main.BW.prob = 0.1, cond.main.WW.prob = 0.15,
cond.pers.always.prob = 0.216, cond.pers.BB.prob = 0.26,
cond.pers.BW.prob = 0.26, cond.pers.WW.prob = 0.26,
cond.inst.always.prob = 0.326, cond.inst.BB.prob = 0.27,
cond.inst.BW.prob = 0.27, cond.inst.WW.prob = 0.27,
cond.always.prob.corr = 0.5, cond.asmm.always.prob = 0,
cond.asmm.BB.prob = 0.54, cond.asmm.BW.prob = 0.54,
cond.asmm.WW.prob = 0.54, cond.rr.BB = 1, cond.rr.BW = 1,
cond.rr.WW = 1, cond.diag.main.beta = -0.67,
cond.discl.main.beta = -0.85, cond.diag.pers.beta = -0.67,
cond.discl.pers.beta = -0.85, cond.diag.inst.beta = -0.67,
cond.discl.inst.beta = -0.85, cond.diag.asmm.beta = -0.67,
cond.discl.asmm.beta = -0.85, vv.iev.BB.prob = 0.42,
vv.iev.BW.prob = 0.56, vv.iev.WW.prob = 0.49, prep.start = Inf,
prep.elig.model = "base", prep.class.prob = c(0.211, 0.07, 0.1,
0.619), prep.class.hr = c(1, 0.69, 0.19, 0.05),
prep.coverage.adol.naive = 0.4, prep.coverage.adol.exp = 0.4,
prep.cov.method = "curr", prep.cov.rate = 1, prep.tst.int = 90,
prep.risk.int = 182, prep.risk.reassess = TRUE,
prep.start.asmm = Inf, prep.elig.model.asmm = "none",
prep.class.prob.asmm = c(0.209, 0.244, 0.131, 0.416),
prep.coverage.asmm = 0.3, prep.cov.method.asmm = "curr",
prep.cov.rate.asmm = 1, prep.rcomp.asmm = 1,
prep.tst.int.asmm = 90, prep.risk.int.asmm = 182,
prep.risk.reassess.asmm = FALSE, prep.delay.asmm = 26,
prepSpell.asmm = TRUE, prepDrop.asmm = 0.014337,
prep.uaicount.thresh.asmm = 10, rcomp.prob = 0,
rcomp.adh.groups = 0:4, rcomp.main.only = FALSE,
rcomp.discl.only = FALSE, out.age.prob = nwstats$out.age.prob,
debut.entry.prob = nwstats$debut.entry.prob,
debut.prob = nwstats$debut.prob,
role.B.prob.asmm = nwstats$role.B.prob.asmm,
role.W.prob.asmm = nwstats$role.W.prob.asmm,
role.B.prob.msm = nwstats$role.B.prob.msm,
role.W.prob.msm = nwstats$role.W.prob.msm, ...)
Arguments
nwstats
Target statistics for the network model. An object of class
nwstats output from calc_nwstats_msm.
race.method
Number of races in the model, with options of 1 or 2. If
1, then race-specific parameters will be averaged.
last.neg.test.B.int
Time range in days for last negative test for
black men.
last.neg.test.W.int
Time range in days for last negative test for
white men.
mean.test.B.int
Mean intertest interval in days for black MSM who test.
mean.test.W.int
Mean intertest interval in days for white MSM who test.
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.
tt.traj.B.prob
Proportion of black MSM 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.
tt.traj.W.prob
Proportion of white MSM who enter into the four
testing/treatment trajectories, as defined above.
tx.init.B.prob
Probability per time step that a black MSM who has
tested positive will initiate treatment.
tx.init.W.prob
Probability per time step that a white MSM who has
tested positive will initiate treatment.
tx.halt.B.prob
Probability per time step that a black MSM who is
currently on treatment will halt treatment.
tx.halt.W.prob
Probability per time step that a white MSM who is
currently on treatment will halt treatment.
tx.reinit.B.prob
Probability per time step that a black MSM who is
not currently on treatment but who has been in the past will
re-initiate treatment.
tx.reinit.W.prob
Probability per time step that a white MSM who is
not currently on treatment but who has been in the past will
re-initiate treatment.
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.
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.
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.
disc.outset.main.B.prob
Probability that an HIV-infected black MSM will
disclose his status at the start of a main partnership.
disc.outset.main.W.prob
Probability that an HIV-infected white MSM will
disclose his status at the start of a main partnership.
disc.at.diag.main.B.prob
Probability that a black MSM already in a main
partnership will disclose at the time of diagnosis.
disc.at.diag.main.W.prob
Probability that a white MSM already in a main
partnership will disclose at the time of diagnosis.
disc.post.diag.main.B.prob
Probability that an HIV-infected black MSM
in a main partnership will disclose his status, assuming he didn't
at the start of the partnership or at diagnosis.
disc.post.diag.main.W.prob
Probability that an HIV-infected white MSM
in a main partnership will disclose his status, assuming he didn't
at the start of the partnership or at diagnosis.
disc.outset.pers.B.prob
Probability that an HIV-infected black MSM will
disclose his status at the start of a casual partnership.
disc.outset.pers.W.prob
Probability that an HIV-infected white MSM will
disclose his status at the start of a casual partnership.
disc.at.diag.pers.B.prob
Probability that a black MSM already in a
casual partnership will disclose at the time of diagnosis.
disc.at.diag.pers.W.prob
Probability that a white MSM already in a
casual partnership will disclose at the time of diagnosis.
disc.post.diag.pers.B.prob
Probability that an HIV-infected black MSM
in a casual partnership will disclose his status, assuming he
didn't at the start of the partnership or at diagnosis.
disc.post.diag.pers.W.prob
Probability that an HIV-infected white MSM
in a casual partnership will disclose his status, assuming he
didn't at the start of the partnership or at diagnosis.
disc.inst.B.prob
Probability that an HIV-infected black MSM will
disclose his status to a one-off partner.
disc.inst.W.prob
Probability that an HIV-infected white MSM will
disclose his status to a one-off partner.
circ.B.prob
Probablity that a black new arrival in the population
will be circumcised.
circ.W.prob
Probablity that a white new arrival in the population
will be circumcised.
ccr5.B.prob
Vector of length two of frequencies of the Delta 32
mutation (homozygous and heterozygous, respectively) in the CCR5 gene
among black MSM.
ccr5.W.prob
Vector of length two of frequencies of the Delta 32
mutation (homozygous and heterozygous, respectively) in the CCR5 gene
among white MSM.
ccr5.heteroz.rr
Relative risk of infection for men 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.
base.ai.main.BB.rate
Expected coital frequency in black-black main
partnerships (acts per day).
base.ai.main.BW.rate
Expected coital frequency in black-white main
partnerships (acts per day).
base.ai.main.WW.rate
Expected coital frequency in white-white main
partnerships (acts per day).
base.ai.pers.BB.rate
Expected coital frequency in black-black casual
partnerships (acts per day).
base.ai.pers.BW.rate
Expected coital frequency in black-white casual
partnerships (acts per day).
base.ai.pers.WW.rate
Expected coital frequency in white-white casual
partnerships (acts per day).
cond.main.BB.prob
Probability of condom use in a black-black main
partnership.
cond.main.BW.prob
Probability of condom use in a black-white main
partnership.
cond.main.WW.prob
Probability of condom use in a white-white main
partnership.
cond.pers.always.prob
Fraction of men in casual partnerships who always
use condoms in those partnerships.
cond.pers.BB.prob
Of men who are not consistent condom users, per-act
probability of condom use in a black-black casual partnerships.
cond.pers.BW.prob
Of men who are not consistent condom users, per-act
probability of condom use in a black-white casual partnerships.
cond.pers.WW.prob
Of men who are not consistent condom users, per-act
probability of condom use in a white-white casual partnerships.
cond.inst.always.prob
Fraction of men in instant partnerships who always
use condoms in those partnerships.
cond.inst.BB.prob
Of men who are not consistent condom users, per-act
probability of condom use in a black-black one-off partnerships.
cond.inst.BW.prob
Of men who are not consistent condom users, per-act
probability of condom use in a black-white one-off partnerships.
cond.inst.WW.prob
Of men who are not consistent condom users, per-act
probability of condom use in a white-white one-off partnerships.
cond.always.prob.corr
Correlation coefficient for probability of always
using condoms in both casual and one-off
cond.rr.BB
Condom probability scaler for black-black partnerships for
model calibration purposes.
cond.rr.BW
Condom probability scaler for black-white partnerships for
model calibration purposes.
cond.rr.WW
Condom probability scaler for white-white partnerships for
model calibration purposes.
cond.diag.main.beta
Beta multiplier for the log odds of using a
condom in a main partnership if the HIV-infected man has been
diagnosed.
cond.discl.main.beta
Beta multiplier for the log odds of using a
condom in a main partnership if the HIV-infected man has disclosed.
cond.diag.pers.beta
Beta multiplier for the log odds of using a
condom in a casual partnership if the HIV-infected man has been
diagnosed.
cond.discl.pers.beta
Beta multiplier for the log odds of using a
condom in a casual partnership if the HIV-infected man has disclosed
his status.
cond.diag.inst.beta
Beta multiplier for the log odds of using a
condom in a one-off partnership if the HIV-infected man has been
diagnosed.
cond.discl.inst.beta
Beta multiplier for the log odds of using a
condom in a one-off partnership if the HIV-infected man has disclosed
his status.
vv.iev.BB.prob
Probability that in a black-black partnership of
two versatile men, they will engage in intra-event versatility
("flipping") given that they're having AI.
vv.iev.BW.prob
Probability that in a black-white partnership of
two versatile men, they will engage in intra-event versatility
("flipping") given that they're having AI.
vv.iev.WW.prob
Probability that in a white-white partnership of
two versatile men, they will engage in intra-event versatility
("flipping") given that they're having AI.
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.adol.naive
The proportion of the eligible MSM population who did
not use prep as an asmm that 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.
prep.start.asmm
Time step at which the PrEP intervention should start.
prep.elig.model.asmm
Modeling approach for determining who is eligible for
PrEP. Current options are limited to: none, adol.entry, adol.debuted,
adol.AI, adol.entry.older, adol.debuted.older, adol.AI.older,
adol.entry.time, adol.debuted.time, adol.AI.time, adol.entry.older.time,
adol.debuted.older.time, adol.AI.older.time, adol.riskhist,
adol.riskhist.older, adol.riskhist.time, adol.riskhist.older.time
for all persons who have never been on PrEP or those who have cycled off
see: prepSpell if TRUE and are disease-susceptible.
prep.cov.method.asmm
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 for asmm.
prep.tst.int.asmm
Testing interval for asmm who are actively on PrEP. This
overrides the mean testing interval parameters.
prep.risk.int.asmm
Time window for assessment of risk eligibility for PrEP
in days.
prep.risk.reassess.asmm
If TRUE, reassess eligibility for PrEP at
each testing visit.
prepSpell.asmm
If TRUE, there is a constant hazard from dropping PrEP.
rcomp.prob
Level of risk compensation from 0 to 1, where 0 is no risk
compensation, 0.5 is a 50
per act, and 1 is a complete cessation of condom use following PrEP
initiation.
rcomp.adh.groups
PrEP adherence groups for whom risk compensation
occurs, as a vector with values 0, 1, 2, 3 corresponding to non-adherent,
low adherence, medium adherence, and high adherence to PrEP.
rcomp.main.only
Logical, if risk compensation is limited to main
partnerships only, versus all partnerships.
rcomp.discl.only
Logical, if risk compensation is limited known-discordant
partnerships only, versus all partnerships.
...
Additional arguments passed to the function.
b.B.rate
Rate at which black MSM enter the population.
b.W.rate
Rate at which white MSM enter the population.
ai.scale
General relative scaler for all act rates for model
calibration.
prep.coverage
The proportion of the eligible MSM population who used PrEP as an ASMM
and start PrEP once they become eligible.
prep.efficacy.asmm
The per-contact efficacy of PrEP to prevent infection if
used (parameter not currently used).
prep.class.prob.b.asmm
The frequency of being in a low, medium, or high class
of adherence to PrEP for black asmm.
prep.class.prob.w.asmm
The frequency of being in a low, medium, or high class
of adherence to PrEP for white asmm.
prep.class.effect.asmm
The functional effectiveness of PrEP conditional on
PrEP class.
prep.coverage.b.asmm
The proportion of the eligible population who are start
PrEP once they become eligible for black asmm.
prep.coverage.w.asmm
The proportion of the eligible population who are start
PrEP once they become eligible for white asmm.
prep.cov.rate.b.asmm
The rate at which persons initiate PrEP conditional on
their eligibility, with 1 equal to instant start for black asmm.
prep.cov.rate.w.asmm
The rate at which persons initiate PrEP conditional on
their eligibility, with 1 equal to instant start for white asmm.
prep.delay.b.asmm
The number of timesteps between becomeing eligible for PreP and starting PrEP for black asmm.
prep.delay.w.asmm
The number of timesteps between becomeing eligible for PreP and starting PrEP for white asmm.
PrepDrop.b.asmm
The hazard for dropping PrEP for black asmm given prepSpell.asmm==TRUE.
PrepDrop.w.asmm
The hazard for dropping PrEP for white asmm given prepSpell.asmm==TRUE.
prep.uaicount.thresh.b.asmm
The number of UAI a black asmm must have to initiate prep
if PreP eligibility is based on UAI counts.
prep.uaicount.thresh.w.asmm
The number of UAI a white asmm must have to initiate prep
if PreP eligibility is based on UAI counts.
Value
A list object of class param_msm, which can be passed to
EpiModel function netsim.
statnet/PrEP-for-ASMM-and-adult-MSM documentation built on June 22, 2019, 12:45 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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 | param_cl(nwstats, race.method = 1, FU = FALSE,
last.neg.test.B.int = 301, last.neg.test.W.int = 315,
last.neg.test.B.int.asmm = 2900, last.neg.test.W.int.asmm = 2900,
mean.test.B.int = 301, mean.test.W.int = 315,
mean.test.B.int.asmm = 2900, mean.test.W.int.asmm = 2900,
testing.pattern = "memoryless", test.window.int = 21,
tt.traj.B.prob = c(0.077, 0, 0.356, 0.567), tt.traj.W.prob = c(0.052,
0, 0.331, 0.617), tx.init.B.prob = 0.092, tx.init.W.prob = 0.127,
tx.halt.B.prob = 0.0102, tx.halt.W.prob = 0.0071,
tx.reinit.B.prob = 0.00066, tx.reinit.W.prob = 0.00291,
tx.init.B.prob.asmm = 0.092, tx.init.W.prob.asmm = 0.127,
tx.halt.B.prob.asmm = 0.0102, tx.halt.W.prob.asmm = 0.0071,
tx.reinit.B.prob.asmm = 0.00066, tx.reinit.W.prob.asmm = 0.00291,
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 = 45, 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 = 13, b.B.rate.asmm = 0.0001348571,
b.W.rate.asmm = 0.0001348571, b.method = "fixed",
URAI.prob = 0.0082 * 1.09, UIAI.prob = 0.0031 * 1.09, acute.rr = 6,
circ.rr = 0.4, condom.rr = 0.295, disc.outset.main.B.prob = 0.685,
disc.outset.main.W.prob = 0.889, disc.at.diag.main.B.prob = 1,
disc.at.diag.main.W.prob = 1, disc.post.diag.main.B.prob = 0,
disc.post.diag.main.W.prob = 0, disc.outset.pers.B.prob = 0.527,
disc.outset.pers.W.prob = 0.828, disc.at.diag.pers.B.prob = 1,
disc.at.diag.pers.W.prob = 1, disc.post.diag.pers.B.prob = 0,
disc.post.diag.pers.W.prob = 0, disc.inst.B.prob = 0.445,
disc.inst.W.prob = 0.691, disc.outset.asmm.B.prob.asmm = 0,
disc.outset.asmm.W.prob.asmm = 0, disc.at.diag.asmm.B.prob.asmm = 1,
disc.at.diag.asmm.W.prob.asmm = 1,
disc.post.diag.asmm.B.prob.asmm = 0,
disc.post.diag.asmm.W.prob.asmm = 0, circ.B.prob = 0.874,
circ.W.prob = 0.918, ccr5.B.prob = c(0, 0.034),
ccr5.W.prob = c(0.021, 0.176), ccr5.heteroz.rr = 0.3,
num.inst.ai.classes = 1, base.ai.main.BB.rate = 0.17,
base.ai.main.BW.rate = 0.26, base.ai.main.WW.rate = 0.23,
base.ai.pers.BB.rate = 0.11, base.ai.pers.BW.rate = 0.16,
base.ai.pers.WW.rate = 0.14, base.ai.asmm.BB.rate = 0.0384,
base.ai.asmm.BW.rate = 0.0384, base.ai.asmm.WW.rate = 0.0384,
ai.main.scale = 1, ai.pers.scale = 1, ai.inst.scale = 1,
ai.asmm.scale = 1, cond.main.BB.prob = 0.38,
cond.main.BW.prob = 0.1, cond.main.WW.prob = 0.15,
cond.pers.always.prob = 0.216, cond.pers.BB.prob = 0.26,
cond.pers.BW.prob = 0.26, cond.pers.WW.prob = 0.26,
cond.inst.always.prob = 0.326, cond.inst.BB.prob = 0.27,
cond.inst.BW.prob = 0.27, cond.inst.WW.prob = 0.27,
cond.always.prob.corr = 0.5, cond.asmm.always.prob = 0,
cond.asmm.BB.prob = 0.54, cond.asmm.BW.prob = 0.54,
cond.asmm.WW.prob = 0.54, cond.rr.BB = 1, cond.rr.BW = 1,
cond.rr.WW = 1, cond.diag.main.beta = -0.67,
cond.discl.main.beta = -0.85, cond.diag.pers.beta = -0.67,
cond.discl.pers.beta = -0.85, cond.diag.inst.beta = -0.67,
cond.discl.inst.beta = -0.85, cond.diag.asmm.beta = -0.67,
cond.discl.asmm.beta = -0.85, vv.iev.BB.prob = 0.42,
vv.iev.BW.prob = 0.56, vv.iev.WW.prob = 0.49, prep.start = Inf,
prep.elig.model = "base", prep.class.prob = c(0.211, 0.07, 0.1,
0.619), prep.class.hr = c(1, 0.69, 0.19, 0.05),
prep.coverage.adol.naive = 0.4, prep.coverage.adol.exp = 0.4,
prep.cov.method = "curr", prep.cov.rate = 1, prep.tst.int = 90,
prep.risk.int = 182, prep.risk.reassess = TRUE,
prep.start.asmm = Inf, prep.elig.model.asmm = "none",
prep.class.prob.asmm = c(0.209, 0.244, 0.131, 0.416),
prep.coverage.asmm = 0.3, prep.cov.method.asmm = "curr",
prep.cov.rate.asmm = 1, prep.rcomp.asmm = 1,
prep.tst.int.asmm = 90, prep.risk.int.asmm = 182,
prep.risk.reassess.asmm = FALSE, prep.delay.asmm = 26,
prepSpell.asmm = TRUE, prepDrop.asmm = 0.014337,
prep.uaicount.thresh.asmm = 10, rcomp.prob = 0,
rcomp.adh.groups = 0:4, rcomp.main.only = FALSE,
rcomp.discl.only = FALSE, out.age.prob = nwstats$out.age.prob,
debut.entry.prob = nwstats$debut.entry.prob,
debut.prob = nwstats$debut.prob,
role.B.prob.asmm = nwstats$role.B.prob.asmm,
role.W.prob.asmm = nwstats$role.W.prob.asmm,
role.B.prob.msm = nwstats$role.B.prob.msm,
role.W.prob.msm = nwstats$role.W.prob.msm, ...)
|
Arguments
nwstats |
Target statistics for the network model. An object of class
|
race.method |
Number of races in the model, with options of 1 or 2. If 1, then race-specific parameters will be averaged. |
last.neg.test.B.int |
Time range in days for last negative test for black men. |
last.neg.test.W.int |
Time range in days for last negative test for white men. |
mean.test.B.int |
Mean intertest interval in days for black MSM who test. |
mean.test.W.int |
Mean intertest interval in days for white MSM who test. |
testing.pattern |
Method for HIV testing, with options |
test.window.int |
Length of the HIV test window period in days. |
tt.traj.B.prob |
Proportion of black MSM 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. |
tt.traj.W.prob |
Proportion of white MSM who enter into the four testing/treatment trajectories, as defined above. |
tx.init.B.prob |
Probability per time step that a black MSM who has tested positive will initiate treatment. |
tx.init.W.prob |
Probability per time step that a white MSM who has tested positive will initiate treatment. |
tx.halt.B.prob |
Probability per time step that a black MSM who is currently on treatment will halt treatment. |
tx.halt.W.prob |
Probability per time step that a white MSM who is currently on treatment will halt treatment. |
tx.reinit.B.prob |
Probability per time step that a black MSM who is not currently on treatment but who has been in the past will re-initiate treatment. |
tx.reinit.W.prob |
Probability per time step that a white MSM who is not currently on treatment but who has been in the past will re-initiate treatment. |
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 |
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. |
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. |
disc.outset.main.B.prob |
Probability that an HIV-infected black MSM will disclose his status at the start of a main partnership. |
disc.outset.main.W.prob |
Probability that an HIV-infected white MSM will disclose his status at the start of a main partnership. |
disc.at.diag.main.B.prob |
Probability that a black MSM already in a main partnership will disclose at the time of diagnosis. |
disc.at.diag.main.W.prob |
Probability that a white MSM already in a main partnership will disclose at the time of diagnosis. |
disc.post.diag.main.B.prob |
Probability that an HIV-infected black MSM in a main partnership will disclose his status, assuming he didn't at the start of the partnership or at diagnosis. |
disc.post.diag.main.W.prob |
Probability that an HIV-infected white MSM in a main partnership will disclose his status, assuming he didn't at the start of the partnership or at diagnosis. |
disc.outset.pers.B.prob |
Probability that an HIV-infected black MSM will disclose his status at the start of a casual partnership. |
disc.outset.pers.W.prob |
Probability that an HIV-infected white MSM will disclose his status at the start of a casual partnership. |
disc.at.diag.pers.B.prob |
Probability that a black MSM already in a casual partnership will disclose at the time of diagnosis. |
disc.at.diag.pers.W.prob |
Probability that a white MSM already in a casual partnership will disclose at the time of diagnosis. |
disc.post.diag.pers.B.prob |
Probability that an HIV-infected black MSM in a casual partnership will disclose his status, assuming he didn't at the start of the partnership or at diagnosis. |
disc.post.diag.pers.W.prob |
Probability that an HIV-infected white MSM in a casual partnership will disclose his status, assuming he didn't at the start of the partnership or at diagnosis. |
disc.inst.B.prob |
Probability that an HIV-infected black MSM will disclose his status to a one-off partner. |
disc.inst.W.prob |
Probability that an HIV-infected white MSM will disclose his status to a one-off partner. |
circ.B.prob |
Probablity that a black new arrival in the population will be circumcised. |
circ.W.prob |
Probablity that a white new arrival in the population will be circumcised. |
ccr5.B.prob |
Vector of length two of frequencies of the Delta 32 mutation (homozygous and heterozygous, respectively) in the CCR5 gene among black MSM. |
ccr5.W.prob |
Vector of length two of frequencies of the Delta 32 mutation (homozygous and heterozygous, respectively) in the CCR5 gene among white MSM. |
ccr5.heteroz.rr |
Relative risk of infection for men 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. |
base.ai.main.BB.rate |
Expected coital frequency in black-black main partnerships (acts per day). |
base.ai.main.BW.rate |
Expected coital frequency in black-white main partnerships (acts per day). |
base.ai.main.WW.rate |
Expected coital frequency in white-white main partnerships (acts per day). |
base.ai.pers.BB.rate |
Expected coital frequency in black-black casual partnerships (acts per day). |
base.ai.pers.BW.rate |
Expected coital frequency in black-white casual partnerships (acts per day). |
base.ai.pers.WW.rate |
Expected coital frequency in white-white casual partnerships (acts per day). |
cond.main.BB.prob |
Probability of condom use in a black-black main partnership. |
cond.main.BW.prob |
Probability of condom use in a black-white main partnership. |
cond.main.WW.prob |
Probability of condom use in a white-white main partnership. |
cond.pers.always.prob |
Fraction of men in casual partnerships who always use condoms in those partnerships. |
cond.pers.BB.prob |
Of men who are not consistent condom users, per-act probability of condom use in a black-black casual partnerships. |
cond.pers.BW.prob |
Of men who are not consistent condom users, per-act probability of condom use in a black-white casual partnerships. |
cond.pers.WW.prob |
Of men who are not consistent condom users, per-act probability of condom use in a white-white casual partnerships. |
cond.inst.always.prob |
Fraction of men in instant partnerships who always use condoms in those partnerships. |
cond.inst.BB.prob |
Of men who are not consistent condom users, per-act probability of condom use in a black-black one-off partnerships. |
cond.inst.BW.prob |
Of men who are not consistent condom users, per-act probability of condom use in a black-white one-off partnerships. |
cond.inst.WW.prob |
Of men who are not consistent condom users, per-act probability of condom use in a white-white one-off partnerships. |
cond.always.prob.corr |
Correlation coefficient for probability of always using condoms in both casual and one-off |
cond.rr.BB |
Condom probability scaler for black-black partnerships for model calibration purposes. |
cond.rr.BW |
Condom probability scaler for black-white partnerships for model calibration purposes. |
cond.rr.WW |
Condom probability scaler for white-white partnerships for model calibration purposes. |
cond.diag.main.beta |
Beta multiplier for the log odds of using a condom in a main partnership if the HIV-infected man has been diagnosed. |
cond.discl.main.beta |
Beta multiplier for the log odds of using a condom in a main partnership if the HIV-infected man has disclosed. |
cond.diag.pers.beta |
Beta multiplier for the log odds of using a condom in a casual partnership if the HIV-infected man has been diagnosed. |
cond.discl.pers.beta |
Beta multiplier for the log odds of using a condom in a casual partnership if the HIV-infected man has disclosed his status. |
cond.diag.inst.beta |
Beta multiplier for the log odds of using a condom in a one-off partnership if the HIV-infected man has been diagnosed. |
cond.discl.inst.beta |
Beta multiplier for the log odds of using a condom in a one-off partnership if the HIV-infected man has disclosed his status. |
vv.iev.BB.prob |
Probability that in a black-black partnership of two versatile men, they will engage in intra-event versatility ("flipping") given that they're having AI. |
vv.iev.BW.prob |
Probability that in a black-white partnership of two versatile men, they will engage in intra-event versatility ("flipping") given that they're having AI. |
vv.iev.WW.prob |
Probability that in a white-white partnership of two versatile men, they will engage in intra-event versatility ("flipping") given that they're having AI. |
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.adol.naive |
The proportion of the eligible MSM population who did not use prep as an asmm that 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 |
prep.start.asmm |
Time step at which the PrEP intervention should start. |
prep.elig.model.asmm |
Modeling approach for determining who is eligible for
PrEP. Current options are limited to: |
prep.cov.method.asmm |
The method for calculating PrEP coverage, with options
of |
prep.tst.int.asmm |
Testing interval for asmm who are actively on PrEP. This overrides the mean testing interval parameters. |
prep.risk.int.asmm |
Time window for assessment of risk eligibility for PrEP in days. |
prep.risk.reassess.asmm |
If |
prepSpell.asmm |
If |
rcomp.prob |
Level of risk compensation from 0 to 1, where 0 is no risk compensation, 0.5 is a 50 per act, and 1 is a complete cessation of condom use following PrEP initiation. |
rcomp.adh.groups |
PrEP adherence groups for whom risk compensation occurs, as a vector with values 0, 1, 2, 3 corresponding to non-adherent, low adherence, medium adherence, and high adherence to PrEP. |
rcomp.main.only |
Logical, if risk compensation is limited to main partnerships only, versus all partnerships. |
rcomp.discl.only |
Logical, if risk compensation is limited known-discordant partnerships only, versus all partnerships. |
... |
Additional arguments passed to the function. |
b.B.rate |
Rate at which black MSM enter the population. |
b.W.rate |
Rate at which white MSM enter the population. |
ai.scale |
General relative scaler for all act rates for model calibration. |
prep.coverage |
The proportion of the eligible MSM population who used PrEP as an ASMM and start PrEP once they become eligible. |
prep.efficacy.asmm |
The per-contact efficacy of PrEP to prevent infection if used (parameter not currently used). |
prep.class.prob.b.asmm |
The frequency of being in a low, medium, or high class of adherence to PrEP for black asmm. |
prep.class.prob.w.asmm |
The frequency of being in a low, medium, or high class of adherence to PrEP for white asmm. |
prep.class.effect.asmm |
The functional effectiveness of PrEP conditional on PrEP class. |
prep.coverage.b.asmm |
The proportion of the eligible population who are start PrEP once they become eligible for black asmm. |
prep.coverage.w.asmm |
The proportion of the eligible population who are start PrEP once they become eligible for white asmm. |
prep.cov.rate.b.asmm |
The rate at which persons initiate PrEP conditional on their eligibility, with 1 equal to instant start for black asmm. |
prep.cov.rate.w.asmm |
The rate at which persons initiate PrEP conditional on their eligibility, with 1 equal to instant start for white asmm. |
prep.delay.b.asmm |
The number of timesteps between becomeing eligible for PreP and starting PrEP for black asmm. |
prep.delay.w.asmm |
The number of timesteps between becomeing eligible for PreP and starting PrEP for white asmm. |
PrepDrop.b.asmm |
The hazard for dropping PrEP for black asmm given prepSpell.asmm==TRUE. |
PrepDrop.w.asmm |
The hazard for dropping PrEP for white asmm given prepSpell.asmm==TRUE. |
prep.uaicount.thresh.b.asmm |
The number of UAI a black asmm must have to initiate prep if PreP eligibility is based on UAI counts. |
prep.uaicount.thresh.w.asmm |
The number of UAI a white asmm must have to initiate prep if PreP eligibility is based on UAI counts. |
Value
A list object of class param_msm, which can be passed to
EpiModel function netsim.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.