Nothing
# Data to be reused by multiple testing blocks
db <- suppressMessages(epiparameter_db())
test_that("parameter_tbl works as expected supplied with db", {
dist_tbl <- parameter_tbl(multi_epiparameter = db)
expect_s3_class(dist_tbl, "data.frame")
expect_identical(dim(dist_tbl), c(125L, 7L))
expect_named(
dist_tbl,
c("disease", "pathogen", "epi_name", "prob_distribution",
"author", "year", "sample_size")
)
expect_snapshot(dist_tbl)
})
test_that("parameter_tbl works for incubation period with db", {
incub_tbl <- parameter_tbl(
multi_epiparameter = db,
epi_name = "incubation period"
)
expect_s3_class(incub_tbl, "data.frame")
expect_identical(dim(incub_tbl), c(73L, 7L))
expect_named(
incub_tbl,
c("disease", "pathogen", "epi_name", "prob_distribution",
"author", "year", "sample_size")
)
expect_snapshot(incub_tbl)
})
test_that("parameter_tbl works for different distribution with db", {
serial_tbl <- parameter_tbl(
multi_epiparameter = db,
epi_name = "serial interval"
)
expect_s3_class(serial_tbl, "data.frame")
expect_identical(dim(serial_tbl), c(18L, 7L))
expect_named(
serial_tbl,
c("disease", "pathogen", "epi_name", "prob_distribution",
"author", "year", "sample_size")
)
expect_snapshot(serial_tbl)
})
test_that("parameter_tbl works for COVID-19 db", {
incub_tbl <- parameter_tbl(
multi_epiparameter = db,
disease = "COVID-19"
)
expect_s3_class(incub_tbl, "data.frame")
expect_identical(dim(incub_tbl), c(27L, 7L))
expect_named(
incub_tbl,
c("disease", "pathogen", "epi_name", "prob_distribution",
"author", "year", "sample_size")
)
expect_snapshot(incub_tbl)
})
test_that("parameter_tbl works for SARS-CoV-2 db", {
incub_tbl <- parameter_tbl(
multi_epiparameter = db,
pathogen = "SARS-CoV-2"
)
expect_s3_class(incub_tbl, "data.frame")
expect_identical(dim(incub_tbl), c(27L, 7L))
expect_named(
incub_tbl,
c("disease", "pathogen", "epi_name", "prob_distribution",
"author", "year", "sample_size")
)
expect_snapshot(incub_tbl)
})
test_that("parameter_tbl works for disease & epi_name subset with db", {
incub_tbl <- parameter_tbl(
multi_epiparameter = db,
disease = "COVID-19",
epi_name = "incubation period"
)
expect_s3_class(incub_tbl, "data.frame")
expect_identical(dim(incub_tbl), c(15L, 7L))
expect_named(
incub_tbl,
c("disease", "pathogen", "epi_name", "prob_distribution",
"author", "year", "sample_size")
)
expect_snapshot(incub_tbl)
})
test_that("parameter_tbl works when supplied a subset db", {
db <- suppressMessages(epiparameter_db(disease = "COVID-19"))
covid_tbl <- parameter_tbl(multi_epiparameter = db, disease = "COVID-19")
expect_s3_class(covid_tbl, "data.frame")
expect_identical(dim(covid_tbl), c(27L, 7L))
expect_named(
covid_tbl,
c("disease", "pathogen", "epi_name", "prob_distribution",
"author", "year", "sample_size")
)
expect_snapshot(covid_tbl)
})
test_that("parameter_tbl works as expected supplied with <epiparameter>", {
db <- suppressMessages(epiparameter_db(single_epiparameter = TRUE))
dist_tbl <- parameter_tbl(multi_epiparameter = db)
expect_s3_class(dist_tbl, "data.frame")
expect_identical(dim(dist_tbl), c(1L, 7L))
expect_named(
dist_tbl,
c("disease", "pathogen", "epi_name", "prob_distribution",
"author", "year", "sample_size")
)
expect_snapshot(dist_tbl)
})
test_that("parameter_tbl works as expected with discretised <epiparameter>", {
ep <- suppressMessages(
epiparameter(
disease = "Ebola",
epi_name = "serial interval",
prob_distribution = "gamma",
prob_distribution_params = c(shape = 1, scale = 1),
citation = create_citation(
author = person(given = "John", family = "Smith"),
year = 2022,
title = "A title",
journal = "A journal",
doi = "10.32561.x"
),
discretise = TRUE
)
)
dist_tbl <- parameter_tbl(multi_epiparameter = ep)
expect_s3_class(dist_tbl, "data.frame")
expect_identical(dim(dist_tbl), c(1L, 7L))
expect_named(
dist_tbl,
c("disease", "pathogen", "epi_name", "prob_distribution",
"author", "year", "sample_size")
)
expect_snapshot(dist_tbl)
})
test_that("parameter_tbl fails correctly when subsetting a subset db", {
ep <- suppressMessages(epiparameter_db(disease = "Ebola"))
expect_error(
parameter_tbl(multi_epiparameter = ep, disease = "COVID-19"),
regexp = "(distribution not available for COVID-19)"
)
})
test_that("parameter_tbl fails correctly", {
# check for incorrect input
expect_error(
parameter_tbl(
multi_epiparameter = list(),
epi_name = "incubation_period"
),
regexp = "List of <epiparameter> objects should be supplied to multi_epiparameter"
)
expect_error(
parameter_tbl(multi_epiparameter = db, epi_name = "random"),
regexp = "random distribution not available"
)
# check for multiple match input
expect_error(
parameter_tbl(multi_epiparameter = db, epi_name = "onset"),
regexp = "onset distribution not available"
)
})
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