tests/testthat/test-ref_values.R

In bodycompref: Reference Values for CT-Assessed Body Composition

# Unit tests for calculating reference values


# Testing if data packages are available
if (requireNamespace("adiposerefdata", quietly = TRUE)) {

  testthat::test_that(".Get_reference_percentile works", {
    metric <- "CSFA"
    sex <- "Female"
    level <- "T5"
    age <- 40
    measurement <- 208.18
    testthat::expect_equal(.Get_reference_percentile(metric, sex, level, age, measurement), 50)
    testthat::expect_output(.Get_reference_percentile(metric, sex, level, age, measurement, verbose = TRUE), "For a 40-yo Female, a CSFA of 208.18 corresponds to percentile 50")
  })


  testthat::test_that(".Get_reference_z_score works", {
    metric <- "CSFA"
    sex <- "Female"
    level <- "T5"
    age <- 40
    measurement <- 208.18
    testthat::expect_equal(.Get_reference_z_score(metric, sex, level, age, measurement, digits = 10), 0.0000387444)
    testthat::expect_output(.Get_reference_z_score(metric, sex, level, age, measurement, verbose = TRUE), "For a 40-yo Female, a CSFA of 208.18 corresponds to a z-score of 0")
  })


  testthat::test_that(".Get_reference_value works", {
    metric <- "CSFA"
    sex <- "Female"
    level <- "T5"
    age <- 40
    percentile <- 50
    z_score <- 0
    testthat::expect_equal(.Get_reference_value(metric, sex, level, age, percentile = percentile, digits = 2), 208.18)
    testthat::expect_equal(.Get_reference_value(metric, sex, level, age, z_score = z_score), 208)
    testthat::expect_output(.Get_reference_value(metric, sex, level, age, z_score = 0.1, verbose = TRUE), "For a 40-yo Female, a z-score of 0.1 corresponds to a CSFA of 220")
  })


  testthat::test_that(".Get_percent_predicted works", {
    metric <- "CSFA"
    sex <- "Female"
    level <- "T5"
    age <- 40
    measurement <- 104
    testthat::expect_equal(.Get_percent_predicted(metric, sex, level, age, measurement), 50)
    testthat::expect_output(.Get_percent_predicted(metric, sex, level, age, measurement, verbose = TRUE), "For a 40-yo Female, a CSFA of 104 corresponds to 50% of the expected 208")
  })


  testthat::test_that("reference_percentiles works", {
    metric <- c("CSFA", "CSFA")
    sex <- c("Female", "Male")
    level <- c("T5", "T8")
    age <- c(40, 60)
    measurement <- c(109, 220)
    testthat::expect_equal(reference_percentiles(metric, sex, level, age, measurement), c(17, 80))
  })


  testthat::test_that("reference_z_scores works", {
    metric <- c("CSFA", "CSFA")
    sex <- c("Female", "Male")
    level <- c("T5", "T8")
    age <- c(40, 60)
    measurement <- c(109, 220)
    testthat::expect_equal(reference_z_scores(metric, sex, level, age, measurement), c(-0.95, 0.84))
  })


  testthat::test_that("reference_values works", {
    metric <- c("CSFA", "CSFA")
    sex <- c("Female", "Male")
    level <- c("T5", "T8")
    age <- c(40, 60)
    percentile <- c(50, 50)
    testthat::expect_equal(reference_values(metric, sex, level, age, percentile), c(208, 158))
  })


  testthat::test_that("percent_predicted works", {
    metric <- c("CSFA", "CSFA")
    sex <- c("Female", "Male")
    level <- c("T5", "T8")
    age <- c(40, 60)
    measurement <- c(109, 220)
    testthat::expect_equal(percent_predicted(metric, sex, level, age, measurement), c(52, 139))
  })


  testthat::test_that(".Get_lambda works", {
    testthat::expect_equal(.Get_lambda("CSFA", "Female", "T5"), 0.6)
    testthat::expect_equal(.Get_lambda("CSVFA", "Female", "L3"), 0.3)
    testthat::expect_equal(.Get_lambda("SMG", "Female", "T5"), NA)
  })


  testthat::test_that("L3 models work", {
    metric <- c("TAT", "TATI", "VAT_SAT_ratio")
    sex <- c("Female", "Male", "Female")
    level <- c("L3", "L3", "L3")
    age <- c(40, 60, 70)
    measurement <- c(200, 200, 2)
    testthat::expect_equal(percent_predicted(metric, sex, level, age, measurement), c(87, 128, 384))
    level <- c("T5", "T8", "L3")
    testthat::expect_error(percent_predicted(metric, sex, level, age, measurement), regexp = 'level not equal to "L3"')
  })

}

# Testing if data packages are not available (CRAN)

if (!requireNamespace("adiposerefdata", quietly = TRUE)) {
  testthat::test_that("Missing adiposerefdata warnings work", {
    metric <- "CSFA"
    sex <- "Male"
    level <- "L3"
    age <- 50
    measurement <- 200
    level <- "L3"
    testthat::expect_snapshot(cat(percent_predicted(metric, sex, level, age, measurement)))
    testthat::expect_warning(suppressMessages(percent_predicted(metric, sex, level, age, measurement)))
    testthat::expect_message(suppressWarnings(percent_predicted(metric, sex, level, age, measurement)), regexp = '"https://p-mq.github.io/drat")')
    testthat::expect_snapshot(cat(percent_predicted(metric, sex, level, age, measurement)))
  })
}

if (!requireNamespace("musclerefdata", quietly = TRUE)) {
  testthat::test_that("Missing musclerefdata warnings work", {
    metric <- "CSMA"
    sex <- "Male"
    level <- "L3"
    age <- 50
    measurement <- 200
    level <- "L3"
    testthat::expect_snapshot(cat(percent_predicted(metric, sex, level, age, measurement)))
    testthat::expect_warning(suppressMessages(percent_predicted(metric, sex, level, age, measurement)))
    testthat::expect_message(suppressWarnings(percent_predicted(metric, sex, level, age, measurement)), regexp = '"https://p-mq.github.io/drat")')
    testthat::expect_snapshot(cat(percent_predicted(metric, sex, level, age, measurement)))
  })
}