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"
)
})
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