tests/testthat/test-onevax_xvwv.R

In mrc-ide/gonovax: Deterministic Compartmental Model of Gonorrhoea with Vaccination

context("onevax_xvwv")

test_that("run_onevax_xvwv works correctly", {
  tt <- seq(0, 5)
  gp <- gono_params(1:2)
  y1 <- run_onevax_xvwv(tt, gp, vea = 0, dur = 1e3)[[1]]

  # check no-one is vaccinated with v switched off
  expect_true(all(y1$cum_vaccinated == 0))
  y2 <- run_onevax_xvwv(tt, gp, vea = 0, dur = 1e3, vbe = 1)
  # check 100% vbe vaccinates all new entrants
  expect_equal(diff(rowSums(y2[[1]]$cum_vaccinated[, , 1])), rep(12e3, max(tt)))
  # and no-one else
  expect_equal(sum(y2[[1]]$cum_vaccinated[, , 2:3]), 0)

  # check can restart
  init_params <- lapply(y2, restart_params)
  y3 <- run_onevax_xvwv(seq(max(tt), length.out = 2, by = 1),
                        gp, init_params,
                        vea = 0, dur = 1e3, vbe = 1)
  for (i in seq_along(y2)) {
    expect_equal(y2[[i]]$U[length(tt), , ], y3[[i]]$U[1, , ])
    expect_equal(y2[[i]]$I[length(tt), , ], y3[[i]]$I[1, , ])
    expect_equal(y2[[i]]$A[length(tt), , ], y3[[i]]$A[1, , ])
    expect_equal(y2[[i]]$S[length(tt), , ], y3[[i]]$S[1, , ])
    expect_equal(y2[[i]]$T[length(tt), , ], y3[[i]]$T[1, , ])
  }

  uptake <- c(0.5, 1)
  # check VoD is working correctly
  y3e <- run_onevax_xvwv(tt, gp, vea = 1, dur = 1e3, strategy = "VoD",
                         uptake = uptake)

  for (i in seq_along(y3e)) {
    # no-one in stratum V is vaccinated again
    expect_equal(sum(y3e[[i]]$cum_vaccinated[, , 2]), 0)
    # uptake % of treated are vaccinated
    expect_equal(y3e[[i]]$cum_vaccinated[, , -2] / uptake[i],
                 y3e[[i]]$cum_treated[, , -2])
    # efficacy is perfect
    expect_equal(sum(y3e[[i]]$cum_treated[, , 2]), 0)
    # no-one is lost
    expect_equal(apply(y3e[[i]]$N, 1, sum), rep(6e5, 6), tolerance = 1e-5)
  }

  # check VoA is working correctly
  y4e <- run_onevax_xvwv(tt, gp, vea = 1, dur = 1e3, strategy = "VoA",
                         uptake = uptake)
  for (i in seq_along(y4e)) {
    # no-one in stratum V is vaccinated again
    expect_equal(sum(y4e[[i]]$cum_vaccinated[, , 2]), 0)
    expect_equal(y4e[[i]]$cum_vaccinated[, , -2] / uptake[i],
                 y4e[[i]]$cum_screened[, , -2] + y4e[[i]]$cum_treated[, , -2])
    expect_equal(apply(y4e[[i]]$N, 1, sum), rep(6e5, 6), tolerance = 1e-5)
  }
  # check vaccination targeting
  y5e <- run_onevax_xvwv(tt, gp, vea = 1, dur = 1e3, strategy = "VoD(L)+VoA(H)",
                         uptake = uptake)
  for (i in seq_along(y5e)) {
    # no-one in stratum V is vaccinated again
    expect_equal(sum(y5e[[i]]$cum_vaccinated[, , 2]), 0)
    # only treated L are vaccinated
    expect_equal(y5e[[i]]$cum_vaccinated[, 1, -2] / uptake[i],
                 y5e[[i]]$cum_treated[, 1, -2])
    # all attending H are vaccinated
    expect_equal(y5e[[i]]$cum_vaccinated[, 2, -2] / uptake[i],
                 y5e[[i]]$cum_treated[, 2, -2] + y5e[[i]]$cum_screened[, 2, -2])
  }

  # check length of uptake vector must be 1 or length(gp)
  expect_error(run_onevax_xvwv(tt, gp, vea = 1, dur = 1e3, strategy = "VbE",
                               uptake = c(0, 0.5, 1)))
  expect_error(run_onevax_xvwv(tt, gp, vea = c(0, 1, 2), dur = 1e3,
                               strategy = "VbE", uptake = 1))
  expect_error(run_onevax_xvwv(tt, gp, vea = 1, dur = c(0, 1e2, 1e3),
                               strategy = "VbE", uptake = 1))
})

test_that("vaccine effects work as expected", {

  tt <- seq(0, 5)
  gp <- gono_params(1:2)

  ## check protection against duration works
  # for perfect ved (= 1), the maximum rate of movement A->U is the rate of
  # care seeking (mu)
  # if same number of people start in A as in S and parameters
  # lambda and eta = 0 (i.e other routes into A & S and out of A respectively)
  # the rate of movement of people A -> U and S -> T should be the same

  # replace lambda, eta = 0
  elements_to_replace <- c("eta_l_t", "eta_h_t", "beta_t")
  for (i in 1:2){
    for (element in elements_to_replace) {
      gp[[i]][[element]] <- rep(0, times = length(gp[[1]][[element]]))
    }
  }

  # set starting conditions
  pars <- c(demographic_params(), gp)
  n_vax <- 3
  U0 <- I0 <- A0 <- S0 <- T0 <- array(0, c(2, n_vax))

  #half of population in A0 and half in S0
  #everyone begins vaccinated
  N0 <- pars$N0 * outer(pars$q, c(0, 1, 0))
  A0 <- pars$N0 * outer(pars$q, c(0, 0.5, 0))
  S0 <- pars$N0 * outer(pars$q, c(0, 0.5, 0))

  init_params <- list(U0 = U0, I0 = I0, A0 = A0, S0 = S0, T0 = T0)
  init_params_list <- list(init_params, init_params)

  y2 <- run_onevax_xvwv(tt, gono_params = gp, init_params = init_params_list,
                        ved = 1, dur = 1e99)

  for (i in 1:2){
    expect_equal(y2[[i]]$A[, , 2], y2[[i]]$S[, , 2]) # 2 = V stratum
  }

})