tests/testthat/test_usz_13c.R

In breathtestcore: Core Functions to Read and Fit 13c Time Series from Breath Tests

test_that("USZ data have the correct columns", {
  data("usz_13c")
  expect_equal(names(usz_13c), c("patient_id", "group", "minute", "pdr"))
  expect_identical(nrow(usz_13c), 10881L)
  expect_match(comment(usz_13c), "Zurich")
  # Check that there are no duplicates
  expect_identical(nrow(usz_13c[duplicated(usz_13c[, -4]), ]), 0L)
  nls_bad = attr(usz_13c, "nls_bad")
  # check for one known case
  expect_match(nls_bad, "pat_014")
})


test_that("USZ 13c a data have the correct columns", {
  data("usz_13c_a")
  expect_equal(names(usz_13c_a), c("patient_id", "group", "minute", "pdr"))
  # Check that there are no duplicates
  expect_identical(nrow(usz_13c_a[duplicated(usz_13c_a[, -4]), ]), 0L)
  library(dplyr)
  d = usz_13c_a %>%
    cleanup_data() %>%
    nlme_fit()
  expect_match(comment(d$data), "no successful fit with nlme")
})

test_that("USZ 13c d data have the correct columns", {
  data("usz_13c_d")
  expect_equal(names(usz_13c_d), c("patient_id", "group", "minute", "pdr"))
  # Check that there are no duplicates
  expect_identical(nrow(usz_13c_d[duplicated(usz_13c_d[, -4]), ]), 0L)
})