tests/testthat/test-epiparameter.R

In epiparameter: Classes and Helper Functions for Working with Epidemiological Parameters

suppressMessages({
  ep <- epiparameter_db(single_epiparameter = TRUE)
})

test_that("epiparameter works with minimal viable input", {
  # message about missing citation suppressed
  ebola_dist <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1)
    )
  ))

  expect_s3_class(ebola_dist, class = "epiparameter")
  expect_length(ebola_dist, 10)
})

test_that("epiparameter works with all arguments set", {
  # suppress message about citation
  mers_dist <- suppressMessages(
    epiparameter(
      disease = "MERS",
      pathogen = "MERS_CoV",
      epi_name = "serial_interval",
      prob_distribution = create_prob_distribution(
        prob_distribution = "lnorm",
        prob_distribution_params = c(meanlog = 2, sdlog = 1)
      ),
      uncertainty = list(
        meanlog = create_uncertainty(
          ci_limits = c(1, 3),
          ci = 95,
          ci_type = "confidence interval"
        ),
        sdlog = create_uncertainty(
          ci_limits = c(0.1, 1.9),
          ci = 95,
          ci_type = "confidence interval"
        )
      ),
      summary_stats = create_summary_stats(
        mean = 1,
        mean_ci_limits = c(0.8, 1.2),
        mean_ci = 95,
        sd = 0.5,
        sd_ci_limits = c(0.4, 0.6),
        sd_ci = 95,
        median = 1,
        median_ci_limits = c(0.9, 1.1),
        median_ci = 95,
        lower_range = 0.1,
        upper_range = 1.9,
        quantiles = c(
          "2.5" = 0.2, "5" = 0.3, "25" = 0.5, "75" = 0.7, "87.5" = 1.1,
          "95" = 1.2, "97.5" = 1.5
        )
      ), citation = create_citation(
        author = person(given = "John", family = "Smith"),
        year = 2002,
        title = "A title",
        journal = "A journal",
        doi = "10.23271/176237.x",
        pmid = 28372882
      ),
      metadata = create_metadata(
        units = "days",
        sample_size = 100,
        region = "UK",
        transmission_mode = "vector_borne",
        vector = NA,
        extrinsic = FALSE,
        inference_method = "MLE"
      ),
      method_assess = create_method_assess(
        censored = TRUE,
        right_truncated = FALSE,
        phase_bias_adjusted = FALSE
      ),
      discretise = FALSE,
      truncation = NA_real_,
      notes = "No notes"
    )
  )
  expect_s3_class(mers_dist, class = "epiparameter")
  expect_length(mers_dist, 10)
})

test_that("epiparameter works with default helper functions", {
  # message about missing citation suppressed
  sars_dist <- suppressMessages(epiparameter(
    disease = "SARS",
    pathogen = "SARS_CoV",
    epi_name = "onset_to_death",
    prob_distribution = create_prob_distribution(
      prob_distribution = "lnorm",
      prob_distribution_params = c(meanlog = 2, sdlog = 1),
      discretise = FALSE,
      truncation = NA
    ),
    uncertainty = list(
      meanlog = create_uncertainty(),
      sdlog = create_uncertainty()
    ),
    summary_stats = create_summary_stats(),
    citation = create_citation(),
    metadata = create_metadata(),
    method_assess = create_method_assess(),
    notes = "No notes"
  ))

  expect_s3_class(sars_dist, class = "epiparameter")
  expect_length(sars_dist, 10)
})

test_that("epiparameter fails as expected", {
  expect_error(
    epiparameter(
      disease = 1,
      epi_name = "incubation",
      prob_distribution = create_prob_distribution(
        prob_distribution = "gamma",
        prob_distribution_params = c(shape = 1, scale = 1)
      )
    ),
    regexp = paste0(
      "Assertion on 'disease' failed: Must be of type ",
      "'string', not 'double'."
    )
  )

  expect_error(
    epiparameter(
      disease = "ebola",
      epi_name = 1,
      prob_distribution = create_prob_distribution(
        prob_distribution = "gamma",
        prob_distribution_params = c(shape = 1, scale = 1)
      )
    ),
    regexp = paste0(
      "Assertion on 'epi_name' failed: Must be of type ",
      "'string', not 'double'."
    )
  )

  expect_error(
    suppressMessages(
      epiparameter(
        disease = "ebola",
        epi_name = "incubation",
        prob_distribution = 1
      )
    ),
    regexp = "(<epiparameter> $prob_distribution must contain)*(<distribution>)"
  )

  expect_error(
    # message about missing citation suppressed
    suppressMessages(
      epiparameter(
        disease = "ebola",
        epi_name = "incubation",
        prob_distribution = "gamma",
        prob_distribution_params = c(shape = "NA", scale = 1)
      ),
      regexp = paste0(
        "(Assertion on 'prob_distribution_params' failed)*(Must be of type)*",
        "(numeric)*(NULL)*(character)."
      )
    )
  )
})

test_that("epiparameter.plot does not produce an error", {
  # plotting changes global state of graphics pars so they are restored
  op <- par(no.readonly = TRUE)
  ebola_dist <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1)
    )
  ))
  expect_silent(plot(ebola_dist))
  f <- function() plot(ebola_dist)
  vdiffr::expect_doppelganger(
    title = "epiparameter.plot",
    fig = f
  )
  # restore graphics pars
  par(op)
})

test_that("epiparameter.plot prints units in x-axis", {
  # plotting changes global state of graphics pars so they are restored
  op <- par(no.readonly = TRUE)
  ebola_dist <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1)
    ),
    metadata = create_metadata(units = "days")
  ))
  expect_silent(plot(ebola_dist))
  f <- function() plot(ebola_dist)
  vdiffr::expect_doppelganger(
    title = "epiparameter.plot units",
    fig = f
  )
  # restore graphics pars
  par(op)
})

test_that("epiparameter.plot works with non-default x-axis", {
  # plotting changes global state of graphics pars so they are restored
  op <- par(no.readonly = TRUE)
  ebola_dist <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1)
    )
  ))
  expect_silent(
    plot(
      ebola_dist,
      xlim = c(0, 20)
    )
  )
  f <- function() {
    plot(
      ebola_dist,
      xlim = c(0, 20)
    )
  }
  vdiffr::expect_doppelganger(
    title = "epiparameter.plot non-default range",
    fig = f
  )
  # restore graphics pars
  par(op)
})

test_that("new_epiparameter works with minimal viable input", {
  epiparameter_obj <- suppressMessages(
    new_epiparameter(
      disease = "ebola",
      pathogen = "ebola virus",
      epi_name = "incubation",
      prob_distribution = create_prob_distribution(
        prob_distribution = "gamma",
        prob_distribution_params = c(shape = 1, scale = 1)
      ),
      uncertainty = list(
        shape = create_uncertainty(
          ci_limits = c(0, 2),
          ci = 95,
          ci_type = "confidence interval"
        ),
        scale = create_uncertainty(
          ci_limits = c(0, 2),
          ci = 95,
          ci_type = "confidence interval"
        )
      ),
      citation = create_citation(
        author = person(given = "John", family = "Smith"),
        year = 2002,
        title = "Ebola incubation",
        journal = "Journal of Epi"
      ),
      notes = "No notes"
    )
  )

  expect_s3_class(epiparameter_obj, class = "epiparameter")
  expect_length(epiparameter_obj, 10)
  expect_s3_class(assert_epiparameter(epiparameter_obj), class = "epiparameter")
})

test_that("assert_epiparameter & test_epiparameter passes when expected", {
  expect_silent(assert_epiparameter(ep))
  expect_invisible(assert_epiparameter(ep))
  expect_silent(test_epiparameter(ep))
  expect_true(test_epiparameter(ep))
})

test_that("assert_epiparameter & test_epiparameter fails when expected", {
  ep_ <- ep
  ep_$disease <- NULL
  expect_error(
    assert_epiparameter(ep_),
    regexp = "(<epiparameter> must contain one disease)"
  )
  expect_false(suppressMessages(test_epiparameter(ep_)))

  ep_$disease <- factor("disease")
  expect_error(
    assert_epiparameter(ep_),
    regexp = "(<epiparameter> must contain one disease)"
  )
  expect_false(suppressMessages(test_epiparameter(ep_)))

  ep_ <- ep
  ep_$epi_name <- c("incubation", "period")
  expect_error(
    assert_epiparameter(ep_),
    regexp = "(<epiparameter> must contain one epidemiological parameter)"
  )
  expect_false(suppressMessages(test_epiparameter(ep_)))

  ep_ <- ep
  ep_$citation <- "reference"
  expect_error(
    assert_epiparameter(ep_),
    regexp = "(<epiparameter> \\$citation must be a <bibentry>)"
  )
  expect_false(suppressMessages(test_epiparameter(ep_)))

  expect_error(
    assert_epiparameter(1),
    regexp = "(Object should be of class <epiparameter>)"
  )
  expect_false(suppressMessages(test_epiparameter(1)))
})

test_that("density works as expected on continuous epiparameter object", {
  ebola_dist <- suppressMessages(
    epiparameter(
      disease = "ebola",
      epi_name = "incubation_period",
      prob_distribution = create_prob_distribution(
        prob_distribution =  "gamma",
        prob_distribution_params = c(shape = 1, scale = 1)
      )
    )
  )

  res <- stats::density(ebola_dist, at = 0.5)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)

  res <- stats::density(ebola_dist, at = 0)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)

  res <- stats::density(ebola_dist, at = 1.5)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)

  res <- stats::density(ebola_dist, at = 10)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)
})

test_that("density works as expected on discrete epiparameter object", {
  ebola_dist <- suppressMessages(
    epiparameter(
      disease = "ebola",
      epi_name = "incubation_period",
      prob_distribution = create_prob_distribution(
        prob_distribution = "gamma",
        prob_distribution_params = c(shape = 1, scale = 1),
        discretise = TRUE
      )
    )
  )

  res <- stats::density(ebola_dist, at = 0.5)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)

  res <- stats::density(ebola_dist, at = 0)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)

  res <- stats::density(ebola_dist, at = 1.5)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)

  res <- stats::density(ebola_dist, at = 10)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)
})

test_that("density works as expected on continuous epiparameter object with vector
          input", {
  ebola_dist <- suppressMessages(
    epiparameter(
      disease = "ebola",
      epi_name = "incubation_period",
      prob_distribution = create_prob_distribution(
        prob_distribution = "gamma",
        prob_distribution_params = c(shape = 1, scale = 1)
      )
    )
  )

  res <- stats::density(ebola_dist, at = seq(0.1, 0.9, by = 0.1))
  expect_length(res, 9)
  expect_type(res, "double")
  expect_true(all(res >= 0))
})

test_that("density works as expected on discrete epiparameter object with vector
          input", {
  ebola_dist <- suppressMessages(
    epiparameter(
      disease = "ebola",
      epi_name = "incubation_period",
      prob_distribution = create_prob_distribution(
        prob_distribution = "gamma",
        prob_distribution_params = c(shape = 1, scale = 1),
        discretise = TRUE
      )
    )
  )

  res <- stats::density(ebola_dist, at = seq(0.1, 0.9, by = 0.1))
  expect_length(res, 9)
  expect_type(res, "double")
  expect_true(all(res >= 0))
})

test_that("cdf works as expected on continuous epiparameter object", {
  ebola_dist <- suppressMessages(
    epiparameter(
      disease = "ebola",
      epi_name = "incubation_period",
      prob_distribution = create_prob_distribution(
        prob_distribution = "gamma",
        prob_distribution_params = c(shape = 1, scale = 1)
      )
    )
  )

  res <- distributional::cdf(ebola_dist, q = 0.5)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)
  expect_lte(res, 1)

  res <- distributional::cdf(ebola_dist, q = 0)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)
  expect_lte(res, 1)

  res <- distributional::cdf(ebola_dist, q = 1.5)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)
  expect_lte(res, 1)

  res <- distributional::cdf(ebola_dist, q = 10)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)
  expect_lte(res, 1)
})

test_that("cdf works as expected on discrete epiparameter object", {
  ebola_dist <- suppressMessages(
    epiparameter(
      disease = "ebola",
      epi_name = "incubation_period",
      prob_distribution = create_prob_distribution(
        prob_distribution = "gamma",
        prob_distribution_params = c(shape = 1, scale = 1),
        discretise = TRUE
      )
    )
  )

  res <- distributional::cdf(ebola_dist, q = 0.5)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)
  expect_lte(res, 1)

  res <- distributional::cdf(ebola_dist, q = 0)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)
  expect_lte(res, 1)

  res <- distributional::cdf(ebola_dist, q = 1.5)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)
  expect_lte(res, 1)

  res <- distributional::cdf(ebola_dist, q = 10)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)
  expect_lte(res, 1)
})

test_that("cdf works as expected on continuous epiparameter object with vector
          input", {
  ebola_dist <- suppressMessages(
    epiparameter(
      disease = "ebola",
      epi_name = "incubation_period",
      prob_distribution = create_prob_distribution(
        prob_distribution = "gamma",
        prob_distribution_params = c(shape = 1, scale = 1)
      )
    )
  )

  res <- distributional::cdf(ebola_dist, q = seq(0.1, 0.9, by = 0.1))
  expect_length(res, 9)
  expect_type(res, "double")
  expect_true(all(res >= 0))
  expect_true(all(res <= 1))
})

test_that("cdf works as expected on discrete epiparameter object with vector
          input", {
  ebola_dist <- suppressMessages(
    epiparameter(
      disease = "ebola",
      epi_name = "incubation_period",
      prob_distribution = create_prob_distribution(
        prob_distribution = "gamma",
        prob_distribution_params = c(shape = 1, scale = 1),
        discretise = TRUE
      )
    )
  )

  res <- distributional::cdf(ebola_dist, q = seq(0.1, 0.9, by = 0.1))
  expect_length(res, 9)
  expect_type(res, "double")
  expect_true(all(res >= 0))
  expect_true(all(res <= 1))
})

test_that("quantile works as expected on continuous epiparameter object", {
  ebola_dist <- suppressMessages(
    epiparameter(
      disease = "ebola",
      epi_name = "incubation_period",
      prob_distribution = create_prob_distribution(
        prob_distribution = "gamma",
        prob_distribution_params = c(shape = 1, scale = 1)
      )
    )
  )

  res <- quantile(ebola_dist, p = 0.5)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)

  res <- quantile(ebola_dist, p = 0)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)

  res <- quantile(ebola_dist, p = 1)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)
})

test_that("quantile works as expected on discrete epiparameter object", {
  ebola_dist <- suppressMessages(
    epiparameter(
      disease = "ebola",
      epi_name = "incubation_period",
      prob_distribution = create_prob_distribution(
        prob_distribution = "gamma",
        prob_distribution_params = c(shape = 1, scale = 1),
        discretise = TRUE
      )
    )
  )

  res <- quantile(ebola_dist, p = 0.5)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)

  res <- quantile(ebola_dist, p = 0)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)

  res <- quantile(ebola_dist, p = 1)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)
})

test_that("quantile works as expected on continuous epiparameter object with vector
          input", {
  ebola_dist <- suppressMessages(
    epiparameter(
      disease = "ebola",
      epi_name = "incubation_period",
      prob_distribution = create_prob_distribution(
        prob_distribution = "gamma",
        prob_distribution_params = c(shape = 1, scale = 1)
      )
    )
  )

  res <- quantile(ebola_dist, p = seq(0.1, 0.9, by = 0.1))
  expect_length(res, 9)
  expect_type(res, "double")
  expect_true(all(res >= 0))
})

test_that("quantile works as expected on discrete epiparameter object with vector
          input", {
  ebola_dist <- suppressMessages(
    epiparameter(
      disease = "ebola",
      epi_name = "incubation_period",
      prob_distribution = create_prob_distribution(
        prob_distribution = "gamma",
        prob_distribution_params = c(shape = 1, scale = 1),
        discretise = TRUE
      )
    )
  )

  res <- quantile(ebola_dist, p = seq(0.1, 0.9, by = 0.1))
  expect_length(res, 9)
  expect_type(res, "double")
  expect_true(all(res >= 0))
})

test_that("generate works as expected on continuous epiparameter object", {
  ebola_dist <- suppressMessages(
    epiparameter(
      disease = "ebola",
      epi_name = "incubation_period",
      prob_distribution = create_prob_distribution(
        prob_distribution = "gamma",
        prob_distribution_params = c(shape = 1, scale = 1)
      )
    )
  )

  res <- distributional::generate(ebola_dist, times = 1)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)

  res <- distributional::generate(ebola_dist, times = 10)
  expect_length(res, 10)
  expect_type(res, "double")
  expect_true(all(res >= 0))
})

test_that("generate works as expected on discrete epiparameter object", {
  ebola_dist <- suppressMessages(
    epiparameter(
      disease = "ebola",
      epi_name = "incubation_period",
      prob_distribution = create_prob_distribution(
        prob_distribution = "gamma",
        prob_distribution_params = c(shape = 1, scale = 1),
        discretise = TRUE
      )
    )
  )

  res <- distributional::generate(ebola_dist, times = 1)
  expect_length(res, 1)
  expect_type(res, "double")
  expect_gte(res, 0)

  res <- distributional::generate(ebola_dist, times = 10)
  expect_length(res, 10)
  expect_type(res, "double")
  expect_true(all(res >= 0))
})

test_that("generate fails as expected on continuous epiparameter object with vector
          input", {
  ebola_dist <- suppressMessages(
    epiparameter(
      disease = "ebola",
      epi_name = "incubation_period",
      prob_distribution = create_prob_distribution(
        prob_distribution = "gamma",
        prob_distribution_params = c(shape = 1, scale = 1)
      )
    )
  )

  expect_error(distributional::generate(ebola_dist, times = c(10, 15)))
})

test_that("generate fails as expected on discrete epiparameter object with vector
          input", {
  ebola_dist <- suppressMessages(
    epiparameter(
      disease = "ebola",
      epi_name = "incubation_period",
      prob_distribution = create_prob_distribution(
        prob_distribution = "gamma",
        prob_distribution_params = c(shape = 1, scale = 1),
        discretise = TRUE
      )
    )
  )

  expect_error(distributional::generate(ebola_dist, times = c(10, 15)))
})

test_that("is_epiparameter returns TRUE when expected", {
  # suppress message about citation
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "serial_interval",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1)
    )
  ))

  expect_true(is_epiparameter(ep))
})

test_that("is_epiparameter returns FALSE when expected", {
  false_ep <- list(
    disease = "ebola",
    epi_name = "serial_interval",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1)
    )
  )

  expect_false(is_epiparameter(false_ep))
})

test_that("discretise works as expected on continuous gamma", {
  # suppress message about citation
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1)
    )
  ))
  ep <- discretise(ep)

  expect_s3_class(ep$prob_distribution, "distcrete")
  expect_identical(ep$prob_distribution$parameters, list(shape = 1, scale = 1))
  expect_identical(ep$prob_distribution$name, "gamma")
})

test_that("discretise works as expected on continuous lognormal", {
  # suppress message about citation
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation",
    prob_distribution = create_prob_distribution(
      prob_distribution = "lnorm",
      prob_distribution_params = c(meanlog = 1, sdlog = 1)
    )
  ))
  ep <- discretise(ep)

  expect_s3_class(ep$prob_distribution, "distcrete")
  expect_identical(ep$prob_distribution$parameters, list(meanlog = 1, sdlog = 1))
  expect_identical(ep$prob_distribution$name, "lnorm")
})

test_that("discretise works as expected on discretised dist", {
  # suppress message about citation
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1),
      discretise = TRUE
    )
  ))
  expect_message(
    discretise(ep),
    regexp = "Distribution in `epiparameter` is already discretised"
  )

  expect_s3_class(ep$prob_distribution, "distcrete")
  expect_identical(ep$prob_distribution$parameters, list(shape = 1, scale = 1))
  expect_identical(ep$prob_distribution$name, "gamma")
})

test_that("discretise works as expected on truncated dist", {
  # suppress message about citation
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1),
      truncation = 10
    )
  ))

  expect_warning(
    discretise(ep),
    regexp = paste(
      "Discretising a truncated continuous distribution,",
      "returning non-truncated discretised distribution"
    )
  )

  ep <- suppressWarnings(discretise(ep))

  expect_s3_class(ep$prob_distribution, "distcrete")
  expect_identical(ep$prob_distribution$parameters, list(shape = 1, scale = 1))
  expect_identical(ep$prob_distribution$name, "gamma")
})

test_that("discretise fails as expected on non-epiparameter object", {
  expect_error(
    discretise("epiparameter"),
    regexp = "No discretise method defined for class character"
  )

  expect_error(
    discretise(c(1, 2, 3)),
    regexp = "No discretise method defined for class numeric"
  )
})

test_that("parameters works as expected on continuous gamma", {
  # suppress message about citation
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1)
    )
  ))
  params <- get_parameters(ep)

  expect_vector(params, ptype = numeric(), size = 2)
  expect_named(params, expected = c("shape", "scale"))
})

test_that("parameters works as expected on continuous lognormal", {
  # suppress message about citation
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation",
    prob_distribution = create_prob_distribution(
      prob_distribution = "lnorm",
      prob_distribution_params = c(meanlog = 1, sdlog = 1)
    )
  ))
  params <- get_parameters(ep)

  expect_vector(params, ptype = numeric(), size = 2)
  expect_named(params, expected = c("meanlog", "sdlog"))
})

test_that("parameters works as expected on discretised dist", {
  # suppress message about citation
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1),
      discretise = TRUE
    )
  ))
  params <- get_parameters(ep)

  expect_vector(params, ptype = numeric(), size = 2)
  expect_named(params, expected = c("shape", "scale"))
})

test_that("parameters works as expected on truncated dist", {
  # suppress message about citation
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1),
      truncation = 10
    )
  ))
  params <- get_parameters(ep)

  expect_vector(params, ptype = numeric(), size = 4)
  expect_named(params, expected = c("shape", "scale", "lower", "upper"))
})

test_that("parameters fails as expected on non-epiparameter object", {
  expect_error(
    get_parameters("epiparameter"),
    regexp = paste0(
      "(no applicable method for)*(parameters)*",
      "(applied to an object of class)*(character)"
    )
  )

  expect_error(
    get_parameters(c(1, 2, 3)),
    regexp = paste0(
      "(no applicable method for)*(parameters)*",
      "(applied to an object of class)*(numeric)"
    )
  )
})

test_that("family works as expected for distributional", {
  # message about missing citation suppressed
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation_period",
    prob_distribution = create_prob_distribution(
      prob_distribution = "lnorm",
      prob_distribution_params = c(meanlog = 1, sdlog = 1)
    )
  ))
  expect_identical(family(ep), "lnorm")
})

test_that("family works as expected for distcrete", {
  # message about missing citation suppressed
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation_period",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1),
      discretise = TRUE
    )
  ))
  expect_identical(family(ep), "gamma")
})

test_that("family works as expected for distributional truncated", {
  # message about missing citation suppressed
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation_period",
    prob_distribution = create_prob_distribution(
      prob_distribution = "weibull",
      prob_distribution_params = c(shape = 1, scale = 1),
      truncation = 10
    )
  ))
  expect_identical(family(ep), "truncated")
})

test_that("family works for distributional truncated with base_dist = TRUE", {
  # message about missing citation suppressed
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation_period",
    prob_distribution = create_prob_distribution(
      prob_distribution = "weibull",
      prob_distribution_params = c(shape = 1, scale = 1),
      truncation = 10
    )
  ))
  expect_identical(family(ep, base_dist = TRUE), "weibull")
})

test_that("is_truncated works as expected for continuous distributions", {
  # message about missing citation suppressed
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation_period",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1)
    )
  ))
  expect_false(is_truncated(ep))
})

test_that("is_truncated works as expected for discretised distributions", {
  # message about missing citation suppressed
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation_period",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1),
      discretise = TRUE
    )
  ))
  expect_false(is_truncated(ep))
})

test_that("is_truncated works as expected for truncated distributions", {
  # message about missing citation suppressed
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation_period",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1),
      truncation = 10
    )
  ))
  expect_true(is_truncated(ep))
})

test_that("is_continuous works as expected for continuous distributions", {
  # message about missing citation suppressed
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation period",
    prob_distribution = create_prob_distribution(
      prob_distribution = "lnorm",
      prob_distribution_params = c(meanlog = 1, sdlog = 1)
    )
  ))
  expect_true(is_continuous(ep))

  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation period",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1)
    )
  ))
  expect_true(is_continuous(ep))
})

test_that("is_continuous works as expected for discrete distributions", {
  # message about missing citation suppressed
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "offspring distribution",
    prob_distribution = create_prob_distribution(
      prob_distribution = "nbinom",
      prob_distribution_params = c(mean = 2, dispersion = 0.5)
    )
  ))
  expect_false(is_continuous(ep))

  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation period",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1),
      discretise = TRUE
    )
  ))
  expect_false(is_continuous(ep))
})

test_that("mean works as expected when mean is supplied", {
  ep <- suppressMessages(
    epiparameter(
      disease = "Ebola",
      epi_name = "incubation_period",
      prob_distribution = "gamma",
      summary_stats = create_summary_stats(mean = 5)
    )
  )
  expect_identical(mean(ep), 5)
})

test_that("mean works as expected with params and no mean", {
  ep <- suppressMessages(
    epiparameter(
      disease = "Ebola",
      epi_name = "incubation_period",
      prob_distribution = create_prob_distribution(
        prob_distribution = "gamma",
        prob_distribution_params = c(shape = 1, scale = 1)
      )
    )
  )
  expect_identical(mean(ep), 1)
})

test_that("mean works as expected with no params and no mean", {
  ep <- suppressMessages(
    epiparameter(
      disease = "Ebola",
      epi_name = "incubation_period",
      prob_distribution = "gamma"
    )
  )
  expect_true(is.na(mean(ep)))
})

test_that("mean works for corrupted epiparameter", {
  ep <- suppressMessages(
    epiparameter(
      disease = "Ebola",
      epi_name = "incubation_period",
      prob_distribution = "gamma"
    )
  )
  ep$summary_stats <- list()
  expect_true(is.na(mean(ep)))
})

test_that("as.function works as expected for density", {
  # message about missing citation suppressed
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1)
    )
  ))
  ep_func <- as.function(ep, func_type = "density")
  expect_type(ep_func, type = "closure")
  expect_length(formals(ep_func), 1)
})

test_that("as.function works as expected for cdf", {
  # message about missing citation suppressed
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1)
    )
  ))
  ep_func <- as.function(ep, func_type = "cdf")
  expect_type(ep_func, type = "closure")
  expect_length(formals(ep_func), 1)
})

test_that("as.function works as expected for generate", {
  # message about missing citation suppressed
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1)
    )
  ))
  ep_func <- as.function(ep, func_type = "generate")
  expect_type(ep_func, type = "closure")
  expect_length(formals(ep_func), 1)
})

test_that("as.function works as expected for quantile", {
  # message about missing citation suppressed
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1)
    )
  ))
  ep_func <- as.function(ep, func_type = "quantile")
  expect_type(ep_func, type = "closure")
  expect_length(formals(ep_func), 1)
})

test_that("as.function fails as expected", {
  # message about missing citation suppressed
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1)
    )
  ))
  expect_error(
    as.function(ep, func_type = "random"),
    regexp = "(arg)*(should be one of)*(density)*(cdf)*(generate)*(quantile)"
  )

  # message about missing citation suppressed
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation",
    prob_distribution = "gamma"
  ))
  expect_error(
    as.function(ep),
    regexp = "Cannot convert unparameterised <epiparameter> to distribution function"
  )
})

test_that("as.data.frame works for <epiparameter>", {
  # message about missing citation suppressed
  ep <- suppressMessages(epiparameter(
    disease = "ebola",
    epi_name = "incubation",
    prob_distribution = create_prob_distribution(
      prob_distribution = "gamma",
      prob_distribution_params = c(shape = 1, scale = 1)
    )
  ))
  df <- as.data.frame(ep)
  expect_s3_class(df, class = "data.frame")
  expect_identical(dim(df), c(1L, 10L))
  expect_identical(
    colnames(df),
    c("disease", "pathogen", "epi_name", "prob_distribution",
      "uncertainty", "summary_stats", "citation", "metadata", "method_assess",
      "notes")
  )
})

test_that("as.data.frame works for <epiparameter> from db", {
  # message about missing citation suppressed
  ep <- suppressMessages(epiparameter_db(single_epiparameter = TRUE))
  df <- as.data.frame(ep)
  expect_s3_class(df, class = "data.frame")
  expect_identical(dim(df), c(1L, 10L))
  expect_identical(
    colnames(df),
    c("disease", "pathogen", "epi_name", "prob_distribution",
      "uncertainty", "summary_stats", "citation", "metadata", "method_assess",
      "notes")
  )
})

{
  suppressMessages(
    db <- epiparameter_db()
  )
  ep <- db[[1]]
}

test_that("c.epiparameter works as expected with two <epiparameter>s", {
  res <- c(ep, ep)
  expect_s3_class(res, class = "multi_epiparameter")
  expect_length(res, 2)
  expect_s3_class(res[[1]], class = "epiparameter")
})

test_that("c.epiparameter works as expected with one <epiparameter>", {
  res <- c(ep)
  expect_s3_class(res, class = "epiparameter")
  expect_true(test_epiparameter(res))
})

test_that("c.epiparameter works with <epiparameter> & <multi_epiparameter>", {
  res <- c(ep, db)
  expect_s3_class(res, class = "multi_epiparameter")
  expect_length(res, length(db) + 1)
  expect_s3_class(res[[1]], class = "epiparameter")
})

test_that("c.multi_epiparameter works with two <multi_epiparameter>s", {
  res <- c(db, db)
  expect_s3_class(res, class = "multi_epiparameter")
  expect_length(res, 250)
  expect_s3_class(res[[1]], class = "epiparameter")
})

test_that("c.multi_epiparameter works with one <multi_epiparameter>", {
  res <- c(db)
  expect_s3_class(res, class = "multi_epiparameter")
  expect_length(res, length(db))
})

test_that("c.multi_epiparameter works <multi_epiparameter> & <epiparameter>", {
  res <- c(db, ep)
  expect_s3_class(res, class = "multi_epiparameter")
  expect_length(res, length(db) + 1)
  expect_s3_class(res[[1]], class = "epiparameter")
})

test_that("c.epiparameter preserves input order", {
  res <- c(ep, db, ep)
  expect_s3_class(res, class = "multi_epiparameter")
  expect_length(res, length(db) + 2)
  expect_true(identical(res[[1]], res[[2]]))
  expect_true(identical(res[[1]], res[[length(res)]]))
})

test_that("c.epiparameter fails as expected", {
  expect_error(
    c(ep, 1),
    regexp = "Can only combine <epiparameter> or <multi_epiparameter> objects"
  )
})