Testing of Process Schematics

[andsv2]

The below will run through testing of each stage of the CombPrevNet workflow in EpiModelHIV.

[andsv2]

Process Schematic 1: Partner Identification

• Updated output can be found at the associated wiki page.
• Partner unique ID and positional ID are compatible:

  
  param <- param_msm(epistats = epistats,
                 netstats = netstats,
                 part.hiv.test.rate  = c(1, 1, 1),
                 part.ident.main.window =  52,
                 part.ident.casl.window  = 52,
                 part.ident.ooff.window  = 52,
                 part.ident.main.prob = 1,
                 part.ident.casl.prob = 1,
                 part.ident.ooff.prob = 1,
                 part.index.window = Inf,
                 part.ident.start = 1
  )

init <- init_msm()

control3 <- control_msm(simno = 1001, nsteps = 2, ncores = 1, nsims = 1, save.nwstats = FALSE, save.clin.hist = FALSE, tergmLite = TRUE)

set.seed(123)

dat <- initialize_msm(est, param, init, control3, s = 1)

for (at in 2:9) { dat <- aging_msm(dat, at) dat <- departure_msm(dat, at) dat <- arrival_msm(dat, at) dat <- partident_msm(dat, at) dat <- hivtest_msm(dat, at) dat <- hivtx_msm(dat, at) dat <- hivprogress_msm(dat, at) dat <- hivvl_msm(dat, at) dat <- simnet_msm(dat, at) dat <- acts_msm(dat, at) dat <- condoms_msm(dat, at) dat <- position_msm(dat, at) dat <- prep_msm(dat, at) dat <- hivtrans_msm(dat, at) dat <- stitrans_msm(dat, at) dat <- stirecov_msm(dat, at) dat <- stitx_msm(dat, at) dat <- prevalence_msm(dat, at) verbose.net(dat, "progress", at = at) }

at = 10 dat <- aging_msm(dat, at) dat <- departure_msm(dat, at) dat <- arrival_msm(dat, at) dat <- partident_msm(dat, at)

From debug of partident_msm: identified partnership list

head(plist.ident)

#

partnerUID ptype start stop partnerPID

1 6658 1 1 NA 6512

2 14919 1 1 NA 14619

3 14202 1 1 NA 13922

4 5959 1 1 NA 5826

5 19365 1 1 NA 18990

6 19806 1 1 NA 19417

dat$attr$uid[c(6512, 14619, 13922, 5826, 18990, 19417)] [1] 6658 14919 14202 5959 19365 19806

[andsv2]

Process Schematic 2: Identified Partner Testing

• Updated output can be found at the associated wiki page.
• True status of tested individual is queried (continues from above):

  ## From debug of hivtest_msm: true status of identified partners
  eligPart <- which(part.ident == at & (diag.status == 0 | is.na(diag.status)))
  head(eligPart)
  [1] 40 61 67 69 78 81
  status[head(eligPart)]
  [1] 0 0 0 0 0 0

• Individuals who have been screened have their correct screening time updated

  
  ## Update when an individual has been screened through the partner identification
  ## process
  prob.screen <- part.hiv.test.rate[race[eligPart]]
  screened <- eligPart[rbinom(length(eligPart), 1, prob.screen) == 1]
  dat$attr$part.scrnd[screened] <- at

dat$attr$part.scrnd[head(eligPart)] [1] 2 2 2 2 2 2

[andsv2]

Process Schematic 3: PrEP initiation

• Check that partners queried have been identified in the current time step:

  ## From debug of prep_msm
  idsEligStartPart <- which(part.ident == at & diag.status == 0 & 
  prepStat == 0)

  head(idsEligStartPart)
  [1] 40 61 67 69 78 81
  dat$attr$part.ident[head(idsEligStartPart)]
  [1] 2 2 2 2 2 2

• Check that individuals who successfully initiate PrEP services, have their PrEP status updated:

  head(idsStartPart) #ID's of identified partners who started PrEP services
  [1] 40 61 67 78 81 95
  dat$attr$prepStat[head(idsStartPart)]
  [1] 1 1 1 1 1 1
  dat$attr$prepStartTime[head(idsStartPart)]
  [1] 2 2 2 2 2 2