tests/testthat/test-treatment.R

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

test_that('You can set time varying clinical treatment', {
  parameters <- get_parameters()
  parameters <- set_drugs(parameters, list(DHA_PQP_params, AL_params))
  parameters <- set_clinical_treatment(
    parameters,
    drug = 1,
    timesteps = c(50, 100),
    coverages = c(.2, .5)
  )
  parameters <- set_clinical_treatment(
    parameters,
    drug = 2,
    timesteps = c(25, 75),
    coverages = c(.3, .4)
  )
  
  expect_error(
    parameters <- set_clinical_treatment(
      parameters,
      drug = 2,
      timesteps = c(25, 75),
      coverages = c(-0.5, 0.5)
    ), "all(coverages >= 0) && all(coverages <= 1) is not TRUE",
    fixed = TRUE
  )
  expect_error(
    parameters <- set_clinical_treatment(
      parameters,
      drug = 2,
      timesteps = c(25, 75),
      coverages = c(0.5, 1.5)
    ), "all(coverages >= 0) && all(coverages <= 1) is not TRUE",
    fixed = TRUE
  )

  expect_equal(
    get_treatment_coverages(parameters, 10),
    c(0, 0)
  )

  expect_equal(
    get_treatment_coverages(parameters, 25),
    c(0, .3)
  )

  expect_equal(
    get_treatment_coverages(parameters, 30),
    c(0, .3)
  )

  expect_equal(
    get_treatment_coverages(parameters, 50),
    c(.2, .3)
  )

  expect_equal(
    get_treatment_coverages(parameters, 80),
    c(.2, .4)
  )
})

test_that('You cannot set invalid coverages', {
  parameters <- get_parameters()
  parameters <- set_drugs(parameters, list(DHA_PQP_params, AL_params))
  parameters <- set_clinical_treatment(
    parameters,
    drug = 1,
    timesteps = c(50, 100),
    coverages = c(.2, .5)
  )
  expect_error(
    set_clinical_treatment(
      parameters,
      drug = 2,
      timesteps = c(25, 75),
      coverages = c(.3, .6)
    )
  )
})

test_that('set_drugs errors if a list is not provided', {
  parameters <- get_parameters()
  expect_error(
    set_drugs(parameters, AL_params),
    "is.list(drugs) is not TRUE",
    fixed = TRUE
  )
})