tests/testthat/test-infection.R

In mrc-ide/malariasimulation: An individual based model for malaria

test_that('blood_immunity returns correct values', {
  ib <-  c(0., 1., 10.)

  parameters <- list(
    b0    = 0.590076,
    b1    = 0.5,
    ib0   = 43.8787,
    kb    = 2.15506
  )
  expect_equal(
    blood_immunity(
      ib,
      parameters
    ),
    c(.5900, .5898, .5771),
    tolerance=1e-3
  )
})

test_that('clinical immunity returns correct values', {
  acquired_immunity <-  c(0., 1., 10.)
  maternal_immunity <-  c(.97, .5, .3)
  parameters <- list(
    phi0  = .0749886,
    phi1  = .0001191,
    ic0     = 18.02366,
    kc      = 2.36949
  )
  expect_equal(
    clinical_immunity(acquired_immunity, maternal_immunity, parameters),
    c(.07491, .07458, .05781),
    tolerance=1e-5
  )
})

test_that('severe immunity returns correct values', {
  acquired_immunity <-  c(0., 1., 6.)
  maternal_immunity <-  c(.97, .5, .3)
  age <- c(0, 5, 30)
  parameters <- list(
    theta0  = .0749886,
    theta1  = .0001191,
    kv      = 2.00048,
    fv0     = 0.141195,
    av      = 2493.41,
    gammav  = 2.91282,
    iv0     = 1.09629
  )
  expect_equal(
    severe_immunity(age, acquired_immunity, maternal_immunity, parameters),
    c(0.06752, 0.05101, 0.01165),
    tolerance=1e-5
  )
})

test_that('asymptomatic_infectivity returns the correct values', {
  age <- c(0, 5, 30, 6)
  immunity <- c(2.4, 1.2, 0., 4.)
  days_per_timestep <- 1
  parameters <- list(
    cu    = 0.00062,
    cd    = 0.068,
    gamma1= 1.82425,
    fd0   = 0.007055,
    ad    = 21.9 * 365 / days_per_timestep,
    gammad= 4.8183,
    d1    = .2,
    id0   = 1.577533,
    kd    = .476614
  )
  expect_equal(
    asymptomatic_infectivity(age, immunity, parameters),
    c(0.06716227, 0.06732774, 0.06800000, 0.06664776),
    tolerance=1e-3
  )
})