tests/testthat/test-successful_infections.R

In IhsanKhaliq/ascotraceR: Simulate the Spread of Ascochyta Blight in Chickpea

# for manual automatic check() testing
load(test_path("test-data_successful_infections.rda"))
seeding_rate <- 40

# makePaddock equivalent
paddock <- CJ(x = 1:100,
              y = 1:100)

primary_infection_foci <- c(50, 50)

# define paddock variables at time 1
paddock[, c("new_gp",
            # Change in the number of growing points since last iteration
            "susceptible_gp",
            "exposed_gp",
            "infectious_gp",
            # replacing InfectiveElementList
            "cdd_at_infection") :=
          list(
            seeding_rate,
            fifelse(
              x == primary_infection_foci[1] &
                y == primary_infection_foci[2],
              seeding_rate - 1,
              seeding_rate
            ),
            0,
            fifelse(x == primary_infection_foci[1] &
                      y == primary_infection_foci[2], 1,
                    0),
            0
          )]



spore_interception_parameter <-
  0.00006 * (15000 / 350)

set.seed(666)



test1 <- successful_infections(
  spore_targets = data.frame(
    x = 50,
    y = 50,
    spores_per_packet = 1
  ),
  paddock = paddock,
  spore_interception_parameter = spore_interception_parameter,
  max_interception_probability = 1
)

test_that("test1 provides correct output", {
  expect_is(test1, "integer")
  expect_true(is.vector(test1))
  expect_length(test1, 1)
  expect_equal(sum(test1), 0)
  expect_equal(max(test1), 0)
  expect_equal(min(test1), 0)
  expect_false(any(is.na(test1)))
})


test2 <- successful_infections(
  spore_targets = spore_dat,
  paddock = paddock,
  spore_interception_parameter = spore_interception_parameter,
  max_interception_probability = 1
)

test_that("test2 provides correct output", {
  expect_is(test2, "integer")
  expect_true(is.vector(test2))
  expect_length(test2, nrow(spore_dat))
  expect_equal(sum(test2), 12)
  expect_equal(max(test2), 1)
  expect_equal(min(test2), 0)
  expect_false(any(is.na(test2)))
})

test_that("successful_infections returns an error with incorrect input", {
  expect_error(
    test3 <- successful_infections(
      spore_targets = as.list(spore_dat),
      paddock = paddock,
      spore_interception_parameter = spore_interception_parameter,
      max_interception_probability = 1
    )
  )

})