tests/testthat/test-params.R

In dth2/EpiModelHIV_SHAMP: Epidemic Modeling of HIV Transmission among MSM, MSMF and Heterosexual Populations

context("Assigning Epidemic Parameters, Initial Conditions and Model Controls")

test_that("assign.formals testing", {
  time.unit <- 7

  num.B <- 5000
  num.W <- 5000

  deg.mp.B <- matrix(c(0.506, 0.151, 0.053,
                       0.207, 0.061, 0.022),
                     byrow = TRUE, nrow = 2)
  deg.mp.W <- matrix(c(0.435, 0.184, 0.095,
                       0.233, 0.033, 0.020),
                     byrow = TRUE, nrow = 2)

  # Revised rates
  mdeg.inst.B <- matrix(c(0.010402, 0.012954, 0.011485,
                          0.007912, 0.007424, 0.007424),
                        byrow = TRUE, nrow = 2)
  mdeg.inst.W <- matrix(c(0.008186, 0.012017, 0.013024,
                          0.008151, 0.008341, 0.008341),
                        byrow = TRUE, nrow = 2)

  # Quintile distribution of overall AI rates
  qnts.W <- c(0, 0.000450, 0.005102, 0.009680, 0.032970)
  qnts.B <- c(0, 0.001457, 0.005536, 0.010516, 0.030226)

  prop.hom.mpi.B <- c(0.9484, 0.9019, 0.9085)
  prop.hom.mpi.W <- c(0.9154, 0.8509, 0.8944)

  sqrt.adiff.BB <- c(0.417, 0.498, 0.456)
  sqrt.adiff.BW <- c(0.454, 0.629, 0.585)
  sqrt.adiff.WW <- c(0.520, 0.632, 0.590)

  durs.main <- c(421, 662, 963)
  durs.pers <- c(326, 344, 347)

  ages <- 18:39
  asmr.B <- c(rep(0, 17),
              1 - (1 - c(rep(0.00159, 7),
                         rep(0.00225, 10),
                         rep(0.00348, 5))) ^ (1/(365/time.unit)),
              1)

  asmr.W <- c(rep(0, 17),
              1 - (1 - c(rep(0.00103, 7),
                         rep(0.00133, 10),
                         rep(0.00214, 5))) ^ (1/(365/time.unit)),
              1)

  role.B.prob <- c(0.242, 0.321, 0.437)
  role.W.prob <- c(0.228, 0.228, 0.544)

  st <- calc_nwstats_msm(
    time.unit = time.unit,
    method = 2,
    num.B = num.B,
    num.W = num.W,
    deg.mp.B = deg.mp.B,
    deg.mp.W = deg.mp.W,
    mdeg.inst.B = mdeg.inst.B,
    mdeg.inst.W = mdeg.inst.W,
    qnts.B = qnts.B,
    qnts.W = qnts.W,
    prop.hom.mpi.B = prop.hom.mpi.B,
    prop.hom.mpi.W = prop.hom.mpi.W,
    balance = "mean",
    sqrt.adiff.BB = sqrt.adiff.BB,
    sqrt.adiff.WW = sqrt.adiff.WW,
    sqrt.adiff.BW = sqrt.adiff.BW,
    diss.main = ~offset(edges) + offset(nodemix("race", base = 1)),
    diss.pers = ~offset(edges) + offset(nodemix("race", base = 1)),
    durs.main = durs.main,
    durs.pers = durs.pers,
    ages = ages,
    asmr.B = asmr.B,
    asmr.W = asmr.W,
    role.B.prob = role.B.prob,
    role.W.prob = role.W.prob)

  param <- param_msm(nwstats = st, last.neg.test.B.int = 200)
  init <- init_msm(nwstats = st, prev.B = 0.3)
  control <- control_msm(nsteps = 10, new.control = 1)

})