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sim.fu.paf.R
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sim.fu.paf.R
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## Packages
library("methods")
suppressMessages(library("EpiModelHIV"))
suppressMessages(library("EpiModelHPC"))
## Environmental Arguments
simno <- as.numeric(Sys.getenv("SIMNO"))
jobno <- as.numeric(Sys.getenv("PBS_ARRAYID"))
njobs <- as.numeric(Sys.getenv("NJOBS"))
fsimno <- paste(simno, jobno, sep = ".")
syphacq <- as.numeric(Sys.getenv("SYPHACQ"))
rectacq <- as.numeric(Sys.getenv("RECTACQ"))
urethacq <- as.numeric(Sys.getenv("URETHACQ"))
syphtrans <- as.numeric(Sys.getenv("SYPHTRANS"))
gctrans <- as.numeric(Sys.getenv("GCTRANS"))
cttrans <- as.numeric(Sys.getenv("CTTRANS"))
gccttrans <- as.numeric(Sys.getenv("GCCTTRANS"))
ctsyphtrans <- as.numeric(Sys.getenv("CTSYPHTRANS"))
gcsyphtrans <- as.numeric(Sys.getenv("GCSYPHTRANS"))
allstitrans <- as.numeric(Sys.getenv("ALLSTITRANS"))
anngcnegcov <- as.numeric(Sys.getenv("ANNGCNEGCOV"))
anngcposcov <- as.numeric(Sys.getenv("ANNGCPOSCOV"))
annctnegcov <- as.numeric(Sys.getenv("ANNCTNEGCOV"))
annctposcov <- as.numeric(Sys.getenv("ANNCTPOSCOV"))
annsyphnegcov <- as.numeric(Sys.getenv("ANNSYPHNEGCOV"))
annsyphposcov <- as.numeric(Sys.getenv("ANNSYPHPOSCOV"))
hrgcnegcov <- as.numeric(Sys.getenv("HRGCNEGCOV"))
hrgcposcov <- as.numeric(Sys.getenv("HRGCPOSCOV"))
hrctnegcov <- as.numeric(Sys.getenv("HRCTNEGCOV"))
hrctposcov <- as.numeric(Sys.getenv("HRCTPOSCOV"))
hrsyphnegcov <- as.numeric(Sys.getenv("HRSYPHNEGCOV"))
hrsyphposcov <- as.numeric(Sys.getenv("HRSYPHPOSCOV"))
## Parameters
load("est/nwstats.rda")
param <- param_msm(nwstats = st,
ai.scale = 1.04,
ai.scale.pospos = 1.04,
# Correlation
sti.stitx.correlation = "false",
sti.hivdx.correlation = "false",
sti.correlation.time = 12,
# STI acquisition
rgc.tprob = 0.4773,
ugc.tprob = 0.3819,
rct.tprob = 0.2564,
uct.tprob = 0.2091,
syph.tprob = 0.2553,
# HIV acquisition
hiv.rgc.rr = rectacq,
hiv.ugc.rr = urethacq,
hiv.rct.rr = rectacq,
hiv.uct.rr = urethacq,
hiv.syph.rr = syphacq,
# HIV transmission
hiv.trans.gc.rr = gctrans,
hiv.trans.ct.rr = cttrans,
hiv.trans.syph.rr = syphtrans,
hiv.trans.gc.ct.rr = gccttrans,
hiv.trans.gc.syph.rr = gcsyphtrans,
hiv.trans.ct.syph.rr = ctsyphtrans,
hiv.trans.allsti.rr = allstitrans,
syph.incub.sympt.prob = 0,
syph.prim.sympt.prob = 0.70,
syph.seco.sympt.prob = 0.85,
syph.earlat.sympt.prob = 0,
syph.latelat.sympt.prob = 0,
syph.tert.sympt.prob = 1.0,
syph.prim.sympt.prob.tx = 0.80,
syph.seco.sympt.prob.tx = 0.80,
syph.earlat.sympt.prob.tx = 0.10,
syph.latelat.sympt.prob.tx = 0.10,
syph.tert.sympt.prob.tx = 1.0,
syph.prim.asympt.prob.tx = 1.0,
syph.seco.asympt.prob.tx = 1.0,
syph.earlat.asympt.prob.tx = 1.0,
syph.latelat.asympt.prob.tx = 1.0,
syph.tert.asympt.prob.tx = 1.0,
gc.asympt.prob.tx = 1.0,
ct.asympt.prob.tx = 1.0,
partnercut = 1,
ept.coverage = 0.0,
stianntest.gc.hivneg.coverage = anngcnegcov,
stianntest.ct.hivneg.coverage = annctnegcov,
stianntest.syph.hivneg.coverage = annsyphnegcov,
stihighrisktest.gc.hivneg.coverage = hrgcnegcov,
stihighrisktest.ct.hivneg.coverage = hrctnegcov,
stihighrisktest.syph.hivneg.coverage = hrsyphnegcov,
stianntest.gc.hivpos.coverage = anngcposcov,
stianntest.ct.hivpos.coverage = annctposcov,
stianntest.syph.hivpos.coverage = annsyphposcov,
stihighrisktest.gc.hivpos.coverage = hrgcposcov,
stihighrisktest.ct.hivpos.coverage = hrctposcov,
stihighrisktest.syph.hivpos.coverage = hrsyphposcov,
prep.coverage = 0,
prep.start = 7000,
stitest.start = 7000,
ept.start = 7000,
stitest.active.int = 364,
sti.highrisktest.int = 182) # adjustable for 3 or 6 months
init <- init_msm(st)
control <- control_msm(simno = fsimno,
start = 5201,
nsteps = 5720,
nsims = 16,
ncores = 16,
initialize.FUN = reinit_msm,
verbose = FALSE)
## Simulation
netsim_hpc("est/stimod.burnin.rda", param, init, control,
compress = TRUE, verbose = FALSE)
process_simfiles(simno = simno, min.n = njobs,
outdir = "data/", compress = TRUE, delete.sub = TRUE,
truncate.at = 5200,
vars =
c("num", "ir100", "incid", "ir100.gc", "incid.gc", "incid.gcct",
"ir100.ct", "incid.ct", "ir100.syph", "incid.syph", "incid.sti",
"ir100.rct", "ir100.uct", "ir100.rgc", "ir100.ugc",
"ir100.sti", "ir100.sti.prep", "ir100.gcct",
"ir100.sti.tttraj1", "ir100.sti.tttraj2",
"ir100.gc.tttraj1", "ir100.gc.tttraj2",
"ir100.ct.tttraj1", "ir100.ct.tttraj2",
"ir100.syph.tttraj1", "ir100.syph.tttraj2",
"ir100.gcct.tttraj1", "ir100.gcct.tttraj2",
"incid.sti.tttraj1", "incid.sti.tttraj2",
"incid.gc.tttraj1", "incid.gc.tttraj2",
"incid.ct.tttraj1", "incid.ct.tttraj2",
"incid.syph.tttraj1", "incid.syph.tttraj2",
"incid.gcct.tttraj1", "incid.gcct.tttraj2",
"incid.gc.hivneg", "incid.gc.hivpos",
"incid.ct.hivneg", "incid.ct.hivpos",
"incid.syph.hivneg", "incid.syph.hivpos",
"ir100.gc.hivneg", "ir100.gc.hivpos",
"ir100.ct.hivneg", "ir100.ct.hivpos",
"ir100.syph.hivneg", "ir100.syph.hivpos",
"prop.edges.negneg", "prop.edges.negpos", "prop.edges.pospos",
"num.acts.negneg", "num.acts.negpos", "num.acts.pospos",
"prop.uai.negneg", "prop.uai.negpos", "prop.uai.pospos",
"prop.acts.negneg", "prop.acts.negpos", "prop.acts.pospos",
"GCasympttests", "uGCasympttests", "rGCasympttests",
"CTasympttests", "uCTasympttests", "rCTasympttests",
"syphasympttests", "stiasympttests",
"GCasympttests.pos", "uGCasympttests.pos", "rGCasympttests.pos",
"CTasympttests.pos", "uCTasympttests.pos", "rCTasympttests.pos",
"syphasympttests.pos", "syphearlyasympttests.pos",
"syphlateasympttests.pos", "stiasympttests.pos",
# "GCasympttests.hivneg", "uGCasympttests.hivneg", "rGCasympttests.hivneg",
# "CTasympttests.hivneg", "uCTasympttests.hivneg", "rCTasympttests.hivneg",
# "syphasympttests.hivneg", "stiasympttests.hivneg",
#"GCasympttests.pos.hivneg", "uGCasympttests.pos.hivneg", "rGCasympttests.pos.hivneg",
#"CTasympttests.pos.hivneg", "uCTasympttests.pos.hivneg", "rCTasympttests.pos.hivneg",
#"syphasympttests.pos.hivneg", "syphearlyasympttests.pos.hivneg",
#"syphlateasympttests.pos.hivneg", "stiasympttests.pos.hivneg",
# "GCasympttests.hivpos", "uGCasympttests.hivpos", "rGCasympttests.hivpos",
# "CTasympttests.hivpos", "uCTasympttests.hivpos", "rCTasympttests.hivpos",
#"syphasympttests.hivpos", "stiasympttests.hivpos",
#"GCasympttests.pos.hivpos", "uGCasympttests.pos.hivpos", "rGCasympttests.pos.hivpos",
#"CTasympttests.pos.hivpos", "uCTasympttests.pos.hivpos", "rCTasympttests.pos.hivpos",
#"syphasympttests.pos.hivpos", "syphearlyasympttests.pos.hivpos",
#"syphlateasympttests.pos.hivpos", "stiasympttests.pos.hivpos",
"tt.traj.syph1", "tt.traj.gc1", "tt.traj.ct1",
"tt.traj.syph2", "tt.traj.gc2", "tt.traj.ct2",
"tt.traj.sti1", "tt.traj.sti2",
"GCsympttests", "uGCsympttests", "rGCsympttests",
"CTsympttests", "uCTsympttests", "rCTsympttests",
"syphsympttests", "stisympttests",
"rCTasympttests.tttraj1", "rCTasympttests.tttraj2",
"uCTasympttests.tttraj1", "uCTasympttests.tttraj2",
"CTasympttests.tttraj1", "CTasympttests.tttraj2",
"rGCasympttests.tttraj1", "rGCasympttests.tttraj2",
"uGCasympttests.tttraj1", "uGCasympttests.tttraj2",
"GCasympttests.tttraj1", "GCasympttests.tttraj2",
"syphasympttests.tttraj1", "syphasympttests.tttraj2",
"stiasympttests.tttraj1", "stiasympttests.tttraj2",
"rCTsympttests.tttraj1", "rCTsympttests.tttraj2",
"uCTsympttests.tttraj1", "uCTsympttests.tttraj2",
"CTsympttests.tttraj1", "CTsympttests.tttraj2",
"rGCsympttests.tttraj1", "rGCsympttests.tttraj2",
"uGCsympttests.tttraj1", "uGCsympttests.tttraj2",
"GCsympttests.tttraj1", "GCsympttests.tttraj2",
"syphsympttests.tttraj1", "syphsympttests.tttraj2",
"stisympttests.tttraj1", "stisympttests.tttraj2",
"txGC.tttraj1", "txGC_asympt.tttraj1",
"txGC.tttraj2", "txGC_asympt.tttraj2",
"txCT.tttraj1", "txCT_asympt.tttraj1",
"txCT.tttraj2", "txCT_asympt.tttraj2",
"txsyph.tttraj1", "txsyph_asympt.tttraj1",
"txsyph.tttraj2", "txsyph_asympt.tttraj2",
"txearlysyph.tttraj1", "txlatesyph.tttraj1",
"txearlysyph.tttraj2", "txlatesyph.tttraj2",
"txSTI.tttraj1", "txSTI.tttraj2",
"txSTI_asympt.tttraj1", "txSTI_asympt.tttraj2",
"hivtests.nprep", "hivtests.pos", "hivtests.prep",
'test.gc.12mo', 'test.gc.12mo.hivpos', 'test.gc.12mo.hivneg',
'test.ct.12mo', 'test.ct.12mo.hivpos', 'test.ct.12mo.hivneg',
'test.syph.12mo', 'test.syph.12mo.hivpos', 'test.syph.12mo.hivneg',
"i.prev", "prev.primsecosyph", "prev.syph", "prev.earlysyph", "prev.latesyph",
"prev.gc", "prev.rgc", "prev.ugc",
"prev.ct", "prev.rct", "prev.uct", "prev.sti",
"prev.dxhiv.dxipssyph",
"prev.primsecosyph.tttraj1", "prev.primsecosyph.tttraj2",
"prev.syph.tttraj1", "prev.syph.tttraj2",
"prev.gcct.tttraj1", "prev.gcct.tttraj2",
"prev.gc.tttraj1", "prev.gc.tttraj2",
"prev.ct.tttraj1", "prev.ct.tttraj2",
"prev.sti.tttraj1", "prev.sti.tttraj2",
"prev.rgc.hivneg.only", "prev.ugc.hivneg.only",
"prev.rct.hivneg.only", "prev.uct.hivneg.only",
"prev.primsecosyph.hivneg.only",
"prev.rgc.hivpos.only","prev.ugc.hivpos.only",
"prev.rct.hivpos.only", "prev.uct.hivpos.only",
"prev.primsecosyph.hivpos.only",
"prev.hivposmultsti", "prev.hivnegmultsti",
"txearlysyph", "txlatesyph", "txsyph", "txGC", "txCT",
"txGC_asympt", "txCT_asympt", "txsyph_asympt", "txSTI", "txSTI_asympt",
"tx.gc.prop", "tx.ct.prop", "tx.gcct.prop", "tx.syph.prop",
"gc.infect.dur", "ct.infect.dur", "gcct.infect.dur", "syph.infect.dur",
"sum_GC", "sum_CT", "sum_syph", "sum_urethral", "sum_rectal",
"cell1_gc", "cell2_gc", "cell3_gc", "cell4_gc",
"cell1_ct", "cell2_ct", "cell3_ct", "cell4_ct",
"cell1_syph", "cell2_syph", "cell3_syph", "cell4_syph",
"cell1_sti", "cell2_sti", "cell3_sti", "cell4_sti",
"deathage", "stiactiveind.prop", "stiactiveind",
"recentpartners", "recentpartners.prop",
"num.newearlydiagsyph",
"num.newlatediagsyph", "early.late.syphratio",
"early.late.diagsyphratio",
"num.asympt.tx", "num.asympt.cases", "num.rect.cases", "num.rect.tx",
"time.hivneg",
"eptCov", "eptpartelig", "eptpartprovided", "eptpartuptake",
"eptTx", "propindexeptElig", "eptprop_provided", "eptprop_tx",
"eptuninfectedprovided","eptuninfecteduptake","eptgcinfectsti",
"eptctinfectsti","eptgcinfecthiv", "eptctinfecthiv",
"stage.time.ar.ndx","stage.time.ar.dx", "stage.time.af.ndx",
"stage.time.af.dx", "stage.time.early.chronic.ndx",
"stage.time.early.chronic.dx.yrone",
"stage.time.early.chronic.dx.yrstwotolate",
"stage.time.early.chronic.art", "stage.time.late.chronic.ndx",
"stage.time.late.chronic.dx", "stage.time.late.chronic.art",
"stage.time.aids.ndx", "stage.time.aids.dx","stage.time.aids.art"))