tests/testthat/test_coef_by_group.R

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

suppressPackageStartupMessages(library(dplyr))
data("usz_13c")
data = usz_13c %>%
  dplyr::filter(
    patient_id %in%
      c(
        "norm_001",
        "norm_002",
        "norm_004",
        "norm_007",
        "pat_004",
        "pat_012",
        "pat_023"
      )
  ) %>%
  cleanup_data()
fit = nls_fit(data)
cm = comment(fit$data)

test_that("Result with default parameters is tbl_df with required columns", {
  cf = coef_by_group(fit)
  expect_s3_class(cf, "tbl_df")
  expect_s3_class(cf, "coef_by_group")
  expect_identical(ncol(cf), 7L)
  expect_equal(
    names(cf),
    c(
      "parameter",
      "method",
      "group",
      "estimate",
      "conf.low",
      "conf.high",
      "diff_group"
    )
  )
  expect_identical(nrow(cf), 36L)
  # The following test fails for multcomp 1.4-22
  #expect_identical(unique(cf$diff_group), c("a", "c", "b", "bc", "ab"))
  expect_equal(
    unique(cf$group),
    c("liquid_normal", "liquid_patient", "solid_normal", "solid_patient")
  )
  expect_equal(comment(cf), cm)
})

digs = function(x) {
  nchar(stringr::str_replace_all(paste(abs(x)), "[0\\.]", ""))
}

test_that("Options digits is served", {
  options(digits = 4)
  cf = coef_by_group(fit)
  expect_s3_class(cf, "tbl_df")
  expect_lte(digs(cf[[1, "estimate"]]), 4L)
})


test_that("Fit must be of class breathtestfit", {
  expect_error(coef_by_group(NULL))
})

test_that("nlme_fit can be used to compute coefficients for multiple records in one group", {
  data = cleanup_data(simulate_breathtest_data(4))
  fit = nlme_fit(data)
  cf = coef_by_group(fit)
  expect_s3_class(cf, "tbl_df")
  expect_identical(ncol(cf), 7L)
  expect_equal(unique(cf$group), "A")
  expect_equal(unique(cf$diff_group), "a")
  expect_equal(
    names(cf),
    c(
      "parameter",
      "method",
      "group",
      "estimate",
      "conf.low",
      "conf.high",
      "diff_group"
    )
  )
})

test_that("nlme_fit can be used to compute coefficients for multiple groups", {
  skip_on_cran() # Does no converge on some CRAN settings
  fit = nlme_fit(data)
  cf = coef_by_group(fit)
  expect_s3_class(cf, "tbl_df")
  expect_identical(ncol(cf), 7L)
  expect_equal(
    names(cf),
    c(
      "parameter",
      "method",
      "group",
      "estimate",
      "conf.low",
      "conf.high",
      "diff_group"
    )
  )
})

test_that("Fit of a single curve returns valid data", {
  data = usz_13c %>%
    dplyr::filter(patient_id == "pat_001") %>%
    cleanup_data()
  comment(data) = "comment"
  options(digits = 4)
  fit = nls_fit(data)
  cf = coef_by_group(fit)
  expect_identical(ncol(cf), 7L)
  expect_identical(nrow(cf), 9L)
  expect_equal(cf$conf.low, rep(NA, 9L))
  expect_equal(cf$conf.high, rep(NA, 9L))
  expect_equal(comment(cf), "comment")
  expect_lte(digs(cf[[1, "estimate"]]), 4L)
})