tests/testthat/test_aba_n2k_inla.R

In inbo/n2kanalysis: Generic Functions to Analyse Data from the 'Natura 2000' Monitoring

this_result_datasource_id <- sha1(sample(letters))
this_scheme_id <- sha1(sample(letters))
this_species_group_id <- sha1(sample(letters))
this_location_group_id <- sha1(sample(letters))
this_analysis_date <- Sys.time()
this_model_type <- "inla poisson: A * (B + C) + C:D"
this_formula <-
  "Count ~ A * (B + C) + C:D +
    f(E, model = \"rw1\", replicate = as.integer(A)) +
    f(G, model = \"iid\")"
this_first_imported_year <- 1990L
this_last_imported_year <- 2015L
this_last_analysed_year <- 2014L
this_duration <- 1L
dataset <- test_data()
this_lc <- dataset %>%
  select("A", "B", "C", "D") %>%
  filter(.data$C == max(.data$C), .data$D == max(.data$D)) %>%
  distinct() %>%
  model.matrix(object = ~A * (B + C) + C:D)
object <- n2k_inla(
  result_datasource_id = this_result_datasource_id,
  scheme_id = this_scheme_id,
  species_group_id = this_species_group_id,
  location_group_id = this_location_group_id,
  model_type = this_model_type,
  formula = this_formula,
  first_imported_year = this_first_imported_year,
  last_imported_year = this_last_imported_year,
  analysis_date = this_analysis_date,
  data = dataset
)
model_object <- INLA::inla(
  Count ~ A * (B + C) + C:D +
    f(E, model = "rw1", replicate = as.integer(A)) +
    f(G, model = "iid"),
  data = object@Data,
  family = "poisson"
)
model_truth <- INLA::inla(
  Count ~ A * (B + C) + C:D +
    f(E, model = "rw1", replicate = as.integer(A)) +
    f(G, model = "iid"),
  data = dataset,
  family = "poisson"
)
test_that("n2k_inla() adds the data as a data.frame", {
  expect_that(
    object@Data,
    is_identical_to(dataset)
  )
  expect_equal(
    model_object$summary.fixed,
    model_truth$summary.fixed,
    tolerance = 1e-3
  )
  expect_equal(
    model_object$summary.random,
    model_truth$summary.random,
    tolerance = 1e-2
  )
})
test_that("n2k_inla(), uses 'new' as default status", {
  expect_that(
    object@AnalysisMetadata$status,
    is_identical_to("new")
  )
})
test_that("n2k_inla() requires a correct status", {
  expect_that(
    n2k_inla(
      data = dataset,
      result_datasource_id = this_result_datasource_id,
      scheme_id = this_scheme_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date,
      status = "junk"
    ),
    throws_error("status must be one of the following")
  )
  expect_that(
    n2k_inla(
      data = dataset, result_datasource_id = this_result_datasource_id,
      scheme_id = this_scheme_id, species_group_id = this_species_group_id,
      location_group_id = this_location_group_id, model_type = this_model_type,
      formula = this_formula, first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date, status = NA_character_
    ),
    throws_error("status must be one of the following")
  )
})
test_that("n2k_inla() checks the model type", {
  expect_that(
    n2k_inla(
      data = dataset, result_datasource_id = this_result_datasource_id,
      scheme_id = this_scheme_id, species_group_id = this_species_group_id,
      location_group_id = this_location_group_id, model_type = "junk",
      formula = this_formula, first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date
    ),
    throws_error("model_type should be 'inla poisson'")
  )
})
test_that("n2k_inla() sets the correct seed", {
  this_seed <- 12345L
  expect_that(
    n2k_inla(
      data = dataset, result_datasource_id = this_result_datasource_id,
      scheme_id = this_scheme_id, species_group_id = this_species_group_id,
      location_group_id = this_location_group_id, model_type = this_model_type,
      formula = this_formula, first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date, seed = this_seed
    )@AnalysisMetadata$seed,
    is_identical_to(this_seed)
  )
})
test_that("n2k_inla() converts numeric seed, when possible", {
  this_seed <- 12345
  expect_that(
    n2k_inla(
      data = dataset, result_datasource_id = this_result_datasource_id,
      scheme_id = this_scheme_id, species_group_id = this_species_group_id,
      location_group_id = this_location_group_id, model_type = this_model_type,
      formula = this_formula, first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date, seed = this_seed
    )@AnalysisMetadata$seed,
    is_identical_to(as.integer(this_seed))
  )
  expect_that(
    n2k_inla(
      data = dataset, result_datasource_id = this_result_datasource_id,
      scheme_id = this_scheme_id, species_group_id = this_species_group_id,
      location_group_id = this_location_group_id, model_type = this_model_type,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date, seed = this_seed + 0.1
    ),
    throws_error("seed is not a count")
  )
})
test_that("n2k_inla() sets a random seed when not provided", {
  expect_is(object@AnalysisMetadata$seed, "integer")
})

test_that("n2k_inla() sets the correct scheme_id", {
  expect_identical(
    n2k_inla(
      data = dataset, result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id, model_type = this_model_type,
      formula = this_formula, first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date, scheme_id = this_scheme_id
    )@AnalysisMetadata$scheme_id,
    this_scheme_id
  )
})

test_that("n2k_inla() sets the correct species_group_id", {
  expect_identical(
    n2k_inla(
      data = dataset, result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id, model_type = this_model_type,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date, formula = this_formula,
      scheme_id = this_scheme_id
    )@AnalysisMetadata$species_group_id,
    this_species_group_id
  )
})

test_that("n2k_inla() sets the correct location_group_id", {
  expect_identical(
    n2k_inla(
      data = dataset, result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id, model_type = this_model_type,
      formula = this_formula, first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date, scheme_id = this_scheme_id
    )@AnalysisMetadata$location_group_id,
    this_location_group_id
  )
})

test_that("n2k_inla() sets the correct first_imported_year", {
  expect_identical(
    n2k_inla(
      data = dataset, result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id, model_type = this_model_type,
      formula = this_formula, first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date, scheme_id = this_scheme_id
    )@AnalysisMetadata$first_imported_year,
    this_first_imported_year
  )
})
test_that("n2k_inla() checks that first_imported_year is from the past", {
  expect_error(
    n2k_inla(
      data = dataset, result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id, model_type = this_model_type,
      formula = this_formula,
      first_imported_year = as.integer(format(Sys.time(), "%Y")) + 1,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date, scheme_id = this_scheme_id
    ),
    "first_imported_year cannot exceed last_imported_year"
  )
  expect_is(
    n2k_inla(
      data = dataset, result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id, model_type = this_model_type,
      formula = this_formula,
      first_imported_year = as.integer(format(Sys.time(), "%Y")),
      last_imported_year = as.integer(format(Sys.time(), "%Y")),
      analysis_date = this_analysis_date, scheme_id = this_scheme_id
    ),
    "n2kInla"
  )
})

test_that("n2k_inla() sets the correct last_imported_year", {
  expect_that(
    n2k_inla(
      data = dataset,
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date,
      scheme_id = this_scheme_id
    )@AnalysisMetadata$last_imported_year,
    is_identical_to(this_last_imported_year)
  )
})
test_that("n2k_inla() converts numeric last_imported_year, when possible", {
  expect_that(
    n2k_inla(
      data = dataset,
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = as.numeric(this_last_imported_year),
      analysis_date = this_analysis_date,
      scheme_id = this_scheme_id
    )@AnalysisMetadata$last_imported_year,
    is_identical_to(this_last_imported_year)
  )
  expect_that(
    n2k_inla(
      data = dataset,
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year + 0.1,
      analysis_date = this_analysis_date,
      scheme_id = this_scheme_id
    ),
    throws_error(
      "last_imported_year is not a count \\(a single positive integer\\)"
    )
  )
})
test_that("n2k_inla() checks that last_imported_year is from the past", {
  expect_that(
    n2k_inla(
      data = dataset,
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = as.integer(format(Sys.time(), "%Y")) + 1,
      analysis_date = this_analysis_date,
      scheme_id = this_scheme_id
    ),
    throws_error("last_imported_year from the future")
  )
})
test_that(
  "n2k_inla() checks that last_imported_year is not earlier than
  first_imported_year ", {
  expect_that(
    n2k_inla(
      data = dataset,
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = 2000,
      last_imported_year = 1999,
      analysis_date = this_analysis_date,
      scheme_id = this_scheme_id
    ),
    throws_error("first_imported_year cannot exceed last_imported_year")
  )
})

test_that("n2k_inla() sets the correct duration", {
  expect_that(
    n2k_inla(
      data = dataset,
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      duration = this_duration,
      analysis_date = this_analysis_date,
      scheme_id = this_scheme_id
    )@AnalysisMetadata$duration,
    is_identical_to(this_duration)
  )
  expect_that(
    n2k_inla(
      data = dataset,
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date,
      scheme_id = this_scheme_id
    )@AnalysisMetadata$duration,
    is_identical_to(this_last_imported_year - this_first_imported_year + 1L)
  )
})
test_that("n2k_inla() converts numeric duration, when possible", {
  expect_that(
    n2k_inla(
      data = dataset,
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      last_analysed_year = this_last_analysed_year,
      duration = as.numeric(this_duration),
      analysis_date = this_analysis_date,
      scheme_id = this_scheme_id
    )@AnalysisMetadata$duration,
    is_identical_to(this_duration)
  )
  expect_that(
    n2k_inla(
      data = dataset,
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      duration = this_duration + 0.1,
      analysis_date = this_analysis_date,
      scheme_id = this_scheme_id
    ),
    throws_error("duration is not a count \\(a single positive integer\\)")
  )
})
test_that(
"n2k_inla() checks that duration is not outside the FirstImportYear -
last_imported_year ranges", {
  expect_that(
    n2k_inla(
      data = dataset,
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = 1999,
      last_imported_year = 1999,
      duration = 2,
      analysis_date = this_analysis_date,
      scheme_id = this_scheme_id
    ),
    throws_error(
      "duration longer than the interval from first_imported_year to"
    )
  )
  expect_that(
    n2k_inla(
      data = dataset,
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = 1999,
      last_imported_year = 1999,
      duration = 0,
      analysis_date = this_analysis_date,
      scheme_id = this_scheme_id
    ),
    throws_error(
      "duration is not a count \\(a single positive integer\\)"
    )
  )
})

test_that("sets the correct last_analysed_year", {
  expect_that(
    n2k_inla(
      data = dataset,
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      last_analysed_year = this_last_analysed_year,
      duration = 1L,
      analysis_date = this_analysis_date,
      scheme_id = this_scheme_id
    )@AnalysisMetadata$last_analysed_year,
    is_identical_to(this_last_analysed_year)
  )
  expect_that(
    n2k_inla(
      data = dataset,
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date,
      scheme_id = this_scheme_id
    )@AnalysisMetadata$last_analysed_year,
    is_identical_to(this_last_imported_year)
  )
})
test_that("n2k_inla() converts numeric last_analysed_year, when possible", {
  expect_that(
    n2k_inla(
      data = dataset,
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      last_analysed_year = as.numeric(this_last_analysed_year),
      duration = 1,
      analysis_date = this_analysis_date,
      scheme_id = this_scheme_id
    )@AnalysisMetadata$last_analysed_year,
    is_identical_to(this_last_analysed_year)
  )
  expect_that(
    n2k_inla(
      data = dataset,
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      duration = 1,
      last_analysed_year = this_last_analysed_year + 0.1,
      analysis_date = this_analysis_date,
      scheme_id = this_scheme_id
    ),
    throws_error(
      "last_analysed_year is not a count \\(a single positive integer\\)"
    )
  )
})
test_that("n2k_inla() checks that last_analysed_year is within the range", {
  expect_that(
    n2k_inla(
      data = dataset,
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      duration = 1,
      last_analysed_year = this_last_imported_year + 1,
      analysis_date = this_analysis_date,
      scheme_id = this_scheme_id
    ),
    throws_error("last_analysed_year cannot exceed last_imported_year")
  )
  expect_that(
    n2k_inla(
      data = dataset,
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      last_analysed_year = this_first_imported_year + this_duration - 2,
      duration = this_duration,
      analysis_date = this_analysis_date,
      scheme_id = this_scheme_id
    ),
    throws_error("last_analysed_year smaller than first_imported_year")
  )
})

test_that("n2k_inla() checks if analysis date is from the past", {
  expect_that(
    n2k_inla(
      data = dataset,
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = Sys.time() + 24 * 60 * 60,
      scheme_id = this_scheme_id
    ),
    throws_error("analysis_date must be in the past")
  )
})
test_that(
  "n2k_inla() checks if all variable in formula are available in the data", {
  expect_that(
    n2k_inla(
      data = dataset[, c("A", "B", "C", "D", "E", "G")],
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date,
      scheme_id = this_scheme_id
    ),
    throws_error("Missing variable `Count` in Data slot")
  )
  expect_that(
    n2k_inla(
      data = dataset[, c("Count", "B", "C", "D", "E", "G")],
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date,
      scheme_id = this_scheme_id
    ),
    throws_error("Missing variable `A` in Data slot")
  )
  expect_that(
    n2k_inla(
      data = dataset[, c("Count", "A", "B", "C", "D", "E")],
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date,
      scheme_id = this_scheme_id
    ),
    throws_error("Missing variable `G` in Data slot")
  )
  expect_that(
    n2k_inla(
      data = dataset[, c("A", "B", "C", "Count", "E", "G")],
      result_datasource_id = this_result_datasource_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date,
      scheme_id = this_scheme_id
    ),
    throws_error("Missing variable `D` in Data slot")
  )
})

object_model <- n2k_inla(
  data = object, model_fit = model_object, status = "converged"
)
test_that("n2k_inla() keeps the objects", {
  expect_that(
    object_model@Data,
    is_identical_to(dataset)
  )
  expect_equal(
    object_model@Model$summary.fixed,
    model_truth$summary.fixed,
    tolerance = 1e-3
  )
  expect_equal(
    object_model@Model$summary.random,
    model_truth$summary.random,
    tolerance = 1e-2
  )
  expect_that(
    object_model@Model,
    is_identical_to(model_object)
  )
  expect_that(
    object_model@AnalysisMetadata$seed,
    is_identical_to(object@AnalysisMetadata$seed)
  )
  expect_that(
    n2k_inla(
      data = object, model_fit = model_object, status = "converged", seed = 1
    )@AnalysisMetadata$seed,
    is_identical_to(object@AnalysisMetadata$seed)
  )
  expect_that(
    object_model@AnalysisMetadata$scheme_id,
    is_identical_to(object@AnalysisMetadata$scheme_id)
  )
  expect_that(
    n2k_inla(
      data = object,
      model_fit = model_object,
      status = "converged",
      scheme_id = 999
    )@AnalysisMetadata$scheme_id,
    is_identical_to(object@AnalysisMetadata$scheme_id)
  )
  expect_that(
    object_model@AnalysisMetadata$species_group_id,
    is_identical_to(object@AnalysisMetadata$species_group_id)
  )
  expect_that(
    n2k_inla(
      data = object,
      model_fit = model_object,
      status = "converged",
      species_group_id = sha1(LETTERS)
    )@AnalysisMetadata$species_group_id,
    is_identical_to(object@AnalysisMetadata$species_group_id)
  )
  expect_that(
    object_model@AnalysisMetadata$location_group_id,
    is_identical_to(object@AnalysisMetadata$location_group_id)
  )
  expect_that(
    n2k_inla(
      data = object,
      model_fit = model_object,
      status = "converged",
      location_group_id = sha1(LETTERS)
    )@AnalysisMetadata$location_group_id,
    is_identical_to(object@AnalysisMetadata$location_group_id)
  )
  expect_that(
    object_model@AnalysisMetadata$model_type,
    is_identical_to(object@AnalysisMetadata$model_type)
  )
  expect_that(
    n2k_inla(
      data = object,
      model_fit = model_object,
      status = "converged",
      model_type = 999
    )@AnalysisMetadata$model_type,
    is_identical_to(object@AnalysisMetadata$model_type)
  )
  expect_that(
    object_model@AnalysisMetadata$Covariate,
    is_identical_to(object@AnalysisMetadata$Covariate)
  )
  expect_that(
    n2k_inla(
      data = object,
      model_fit = model_object,
      status = "converged",
      covariate = 999
    )@AnalysisMetadata$Covariate,
    is_identical_to(object@AnalysisMetadata$Covariate)
  )
  expect_that(
    object_model@AnalysisMetadata$first_imported_year,
    is_identical_to(object@AnalysisMetadata$first_imported_year)
  )
  expect_that(
    object_model@AnalysisMetadata$duration,
    is_identical_to(object@AnalysisMetadata$duration)
  )
  expect_that(
    n2k_inla(
      data = object,
      model_fit = model_object,
      status = "converged",
      duration = 999
    )@AnalysisMetadata$duration,
    is_identical_to(object@AnalysisMetadata$duration)
  )
  expect_that(
    n2k_inla(
      data = object,
      model_fit = model_object,
      status = "converged",
      first_imported_year = 999
    )@AnalysisMetadata$first_imported_year,
    is_identical_to(object@AnalysisMetadata$first_imported_year)
  )
  expect_that(
    object_model@AnalysisMetadata$last_imported_year,
    is_identical_to(object@AnalysisMetadata$last_imported_year)
  )
  expect_that(
    n2k_inla(
      data = object,
      model_fit = model_object,
      status = "converged",
      last_imported_year = 999
    )@AnalysisMetadata$last_imported_year,
    is_identical_to(object@AnalysisMetadata$last_imported_year)
  )
  expect_that(
    object_model@AnalysisMetadata$last_analysed_year,
    is_identical_to(object@AnalysisMetadata$last_analysed_year)
  )
  expect_that(
    n2k_inla(
      data = object,
      model_fit = model_object,
      status = "converged",
      last_analysed_year = 3000
    )@AnalysisMetadata$last_analysed_year,
    is_identical_to(object@AnalysisMetadata$last_analysed_year)
  )
  expect_that(
    object_model@AnalysisMetadata$analysis_date,
    is_identical_to(object@AnalysisMetadata$analysis_date)
  )
  expect_that(
    n2k_inla(
      data = object,
      model_fit = model_object,
      status = "converged",
      analysis.data = 999
    )@AnalysisMetadata$analysis_date,
    is_identical_to(object@AnalysisMetadata$analysis_date)
  )
})
test_that("n2k_inla() stores the new status", {
  expect_that(
    object_model@AnalysisMetadata$status,
    is_identical_to("converged")
  )
  expect_that(
    n2k_inla(
      data = object, model_fit = model_object, status = "junk"
    ),
    throws_error("status must be one of the following")
  )
})
model_other <- INLA::inla(
  Count ~ A * (B + C) + C:D +
    f(E, model = "rw1", replicate = as.integer(A)) +
    f(G, model = "iid"),
  data = object@Data, family = "nbinomial"
)
test_that("n2k_inla() checks if the family matches", {
  expect_that(
    n2k_inla(
      data = object, model_fit = model_other, status = "converged"
    ),
    throws_error("Model of the wrong family")
  )
})
test_that("n2kInla handles linear combinations", {
  expect_error(
    n2k_inla(
      result_datasource_id = this_result_datasource_id,
      scheme_id = this_scheme_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date,
      data = dataset,
      lin_comb = "junk"
    ),
    "lin_comb must be either a list or a matrix"
  )
  expect_is(
    object <- n2k_inla(
      result_datasource_id = this_result_datasource_id,
      scheme_id = this_scheme_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date,
      data = dataset,
      lin_comb = this_lc
    ),
    "n2kInla"
  )
  expect_identical(
    object@LinearCombination,
    this_lc
  )

  expect_error(
    n2k_inla(
      result_datasource_id = this_result_datasource_id,
      scheme_id = this_scheme_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date,
      data = dataset,
      lin_comb = this_lc,
      replicate_name = "junk"
    ),
    "replicate\\_name is not a list"
  )
  expect_error(
    n2k_inla(
      result_datasource_id = this_result_datasource_id,
      scheme_id = this_scheme_id,
      species_group_id = this_species_group_id,
      location_group_id = this_location_group_id,
      model_type = this_model_type,
      formula = this_formula,
      first_imported_year = this_first_imported_year,
      last_imported_year = this_last_imported_year,
      analysis_date = this_analysis_date,
      data = dataset,
      lin_comb = this_lc,
      replicate_name = list("junk")
    ),
    "replicate\\_name must have names"
  )
})