tests/testthat/test-read_diving_pam_data.R

In pam: Fast and Efficient Processing of PAM Data

test_that("read_diving_pam_II_data 2026_07_06_diving_pam_II.csv - default", {
  test_data_file <- testthat::test_path("data", "diving_pam_II_data", "2026_07_06_diving_pam_II.csv")
  data <- read_diving_pam_II_data(test_data_file)

  par <- data$par
  expect_equal(par[1], 0)
  expect_equal(par[2], 34)
  expect_equal(par[3], 63)
  expect_equal(par[4], 91)
  expect_equal(par[5], 126)
  expect_equal(par[6], 176)
  expect_equal(par[7], 269)
  expect_equal(par[8], 403)
  expect_equal(par[9], 592)
  expect_equal(par[10], 878)
  expect_equal(par[11], 1152)
  expect_equal(par[12], 1620)
  expect_equal(par[13], 2111)

  yield_1 <- data$yield_1
  expect_equal(yield_1[1], NA_real_)
  expect_equal(yield_1[2], NA_real_)
  expect_equal(yield_1[3], NA_real_)
  expect_equal(yield_1[4], NA_real_)
  expect_equal(yield_1[5], NA_real_)
  expect_equal(yield_1[6], NA_real_)
  expect_equal(yield_1[7], NA_real_)
  expect_equal(yield_1[8], NA_real_)
  expect_equal(yield_1[9], NA_real_)
  expect_equal(yield_1[10], NA_real_)
  expect_equal(yield_1[11], NA_real_)
  expect_equal(yield_1[12], NA_real_)
  expect_equal(yield_1[13], NA_real_)

  yield_2 <- data$yield_2
  expect_equal(yield_2[1], 0.72)
  expect_equal(yield_2[2], 0.399)
  expect_equal(yield_2[3], 0.361)
  expect_equal(yield_2[4], 0.351)
  expect_equal(yield_2[5], 0.332)
  expect_equal(yield_2[6], 0.298)
  expect_equal(yield_2[7], 0.229)
  expect_equal(yield_2[8], 0.162)
  expect_equal(yield_2[9], 0.125)
  expect_equal(yield_2[10], 0.085)
  expect_equal(yield_2[11], 0.08)
  expect_equal(yield_2[12], 0.057)
  expect_equal(yield_2[13], 0.038)

  etr_1 <- data$etr_1
  expect_equal(etr_1[1], NA_real_)
  expect_equal(etr_1[2], NA_real_)
  expect_equal(etr_1[3], NA_real_)
  expect_equal(etr_1[4], NA_real_)
  expect_equal(etr_1[5], NA_real_)
  expect_equal(etr_1[6], NA_real_)
  expect_equal(etr_1[7], NA_real_)
  expect_equal(etr_1[8], NA_real_)
  expect_equal(etr_1[9], NA_real_)
  expect_equal(etr_1[10], NA_real_)
  expect_equal(etr_1[11], NA_real_)
  expect_equal(etr_1[12], NA_real_)
  expect_equal(etr_1[13], NA_real_)

  etr_2 <- data$etr_2
  expect_equal(etr_2[1], 0)
  expect_equal(etr_2[2], 5.697720)
  expect_equal(etr_2[3], 9.552060)
  expect_equal(etr_2[4], 13.41522)
  expect_equal(etr_2[5], 17.56944)
  expect_equal(etr_2[6], 22.02816)
  expect_equal(etr_2[7], 25.87242)
  expect_equal(etr_2[8], 27.42012)
  expect_equal(etr_2[9], 31.08)
  expect_equal(etr_2[10], 31.34460)
  expect_equal(etr_2[11], 38.7072)
  expect_equal(etr_2[12], 38.78280)
  expect_equal(etr_2[13], 33.691560)
})

test_that("read_diving_pam_II_data 2026_07_06_diving_pam_II.csv - etr_factor 0.5", {
  test_data_file <- testthat::test_path("data", "diving_pam_II_data", "2026_07_06_diving_pam_II.csv")
  data <- read_diving_pam_II_data(test_data_file, etr_factor = 0.5)

  par <- data$par
  expect_equal(par[1], 0)
  expect_equal(par[2], 34)
  expect_equal(par[3], 63)
  expect_equal(par[4], 91)
  expect_equal(par[5], 126)
  expect_equal(par[6], 176)
  expect_equal(par[7], 269)
  expect_equal(par[8], 403)
  expect_equal(par[9], 592)
  expect_equal(par[10], 878)
  expect_equal(par[11], 1152)
  expect_equal(par[12], 1620)
  expect_equal(par[13], 2111)

  yield_1 <- data$yield_1
  expect_equal(yield_1[1], NA_real_)
  expect_equal(yield_1[2], NA_real_)
  expect_equal(yield_1[3], NA_real_)
  expect_equal(yield_1[4], NA_real_)
  expect_equal(yield_1[5], NA_real_)
  expect_equal(yield_1[6], NA_real_)
  expect_equal(yield_1[7], NA_real_)
  expect_equal(yield_1[8], NA_real_)
  expect_equal(yield_1[9], NA_real_)
  expect_equal(yield_1[10], NA_real_)
  expect_equal(yield_1[11], NA_real_)
  expect_equal(yield_1[12], NA_real_)
  expect_equal(yield_1[13], NA_real_)

  yield_2 <- data$yield_2
  expect_equal(yield_2[1], 0.72)
  expect_equal(yield_2[2], 0.399)
  expect_equal(yield_2[3], 0.361)
  expect_equal(yield_2[4], 0.351)
  expect_equal(yield_2[5], 0.332)
  expect_equal(yield_2[6], 0.298)
  expect_equal(yield_2[7], 0.229)
  expect_equal(yield_2[8], 0.162)
  expect_equal(yield_2[9], 0.125)
  expect_equal(yield_2[10], 0.085)
  expect_equal(yield_2[11], 0.08)
  expect_equal(yield_2[12], 0.057)
  expect_equal(yield_2[13], 0.038)

  etr_1 <- data$etr_1
  expect_equal(etr_1[1], NA_real_)
  expect_equal(etr_1[2], NA_real_)
  expect_equal(etr_1[3], NA_real_)
  expect_equal(etr_1[4], NA_real_)
  expect_equal(etr_1[5], NA_real_)
  expect_equal(etr_1[6], NA_real_)
  expect_equal(etr_1[7], NA_real_)
  expect_equal(etr_1[8], NA_real_)
  expect_equal(etr_1[9], NA_real_)
  expect_equal(etr_1[10], NA_real_)
  expect_equal(etr_1[11], NA_real_)
  expect_equal(etr_1[12], NA_real_)
  expect_equal(etr_1[13], NA_real_)

  etr_2 <- data$etr_2
  expect_equal(etr_2[1], 0)
  expect_equal(etr_2[2], 3.3915)
  expect_equal(etr_2[3], 5.68575)
  expect_equal(etr_2[4], 7.98525)
  expect_equal(etr_2[5], 10.458)
  expect_equal(etr_2[6], 13.112)
  expect_equal(etr_2[7], 15.40025)
  expect_equal(etr_2[8], 16.32150)
  expect_equal(etr_2[9], 18.50)
  expect_equal(etr_2[10], 18.65750)
  expect_equal(etr_2[11], 23.040)
  expect_equal(etr_2[12], 23.085)
  expect_equal(etr_2[13], 20.05450)
})

test_that("read_diving_pam_II_data 2026_07_06_diving_pam_II.csv - fraction_photosystem > 1", {
  test_data_file <- testthat::test_path("data", "diving_pam_II_data", "2026_07_06_diving_pam_II.csv")
  expect_error(read_diving_pam_II_data(test_data_file, fraction_photosystem_I = 0.9, fraction_photosystem_II = 0.2))
})

test_that("read_diving_pam_II_data 2026_07_06_diving_pam_II.csv - fraction_photosystem_I = 0.2, fraction_photosystem_II = 0.8", {
  test_data_file <- testthat::test_path("data", "diving_pam_II_data", "2026_07_06_diving_pam_II.csv")
  data <- read_diving_pam_II_data(test_data_file, fraction_photosystem_I = 0.2, fraction_photosystem_II = 0.8)

  par <- data$par
  expect_equal(par[1], 0)
  expect_equal(par[2], 34)
  expect_equal(par[3], 63)
  expect_equal(par[4], 91)
  expect_equal(par[5], 126)
  expect_equal(par[6], 176)
  expect_equal(par[7], 269)
  expect_equal(par[8], 403)
  expect_equal(par[9], 592)
  expect_equal(par[10], 878)
  expect_equal(par[11], 1152)
  expect_equal(par[12], 1620)
  expect_equal(par[13], 2111)

  yield_1 <- data$yield_1
  expect_equal(yield_1[1], NA_real_)
  expect_equal(yield_1[2], NA_real_)
  expect_equal(yield_1[3], NA_real_)
  expect_equal(yield_1[4], NA_real_)
  expect_equal(yield_1[5], NA_real_)
  expect_equal(yield_1[6], NA_real_)
  expect_equal(yield_1[7], NA_real_)
  expect_equal(yield_1[8], NA_real_)
  expect_equal(yield_1[9], NA_real_)
  expect_equal(yield_1[10], NA_real_)
  expect_equal(yield_1[11], NA_real_)
  expect_equal(yield_1[12], NA_real_)
  expect_equal(yield_1[13], NA_real_)

  yield_2 <- data$yield_2
  expect_equal(yield_2[1], 0.72)
  expect_equal(yield_2[2], 0.399)
  expect_equal(yield_2[3], 0.361)
  expect_equal(yield_2[4], 0.351)
  expect_equal(yield_2[5], 0.332)
  expect_equal(yield_2[6], 0.298)
  expect_equal(yield_2[7], 0.229)
  expect_equal(yield_2[8], 0.162)
  expect_equal(yield_2[9], 0.125)
  expect_equal(yield_2[10], 0.085)
  expect_equal(yield_2[11], 0.08)
  expect_equal(yield_2[12], 0.057)
  expect_equal(yield_2[13], 0.038)

  etr_1 <- data$etr_1
  expect_equal(etr_1[1], NA_real_)
  expect_equal(etr_1[2], NA_real_)
  expect_equal(etr_1[3], NA_real_)
  expect_equal(etr_1[4], NA_real_)
  expect_equal(etr_1[5], NA_real_)
  expect_equal(etr_1[6], NA_real_)
  expect_equal(etr_1[7], NA_real_)
  expect_equal(etr_1[8], NA_real_)
  expect_equal(etr_1[9], NA_real_)
  expect_equal(etr_1[10], NA_real_)
  expect_equal(etr_1[11], NA_real_)
  expect_equal(etr_1[12], NA_real_)
  expect_equal(etr_1[13], NA_real_)

  etr_2 <- data$etr_2
  expect_equal(etr_2[1], 0)
  expect_equal(etr_2[2], 9.1163520)
  expect_equal(etr_2[3], 15.2832960)
  expect_equal(etr_2[4], 21.4643520)
  expect_equal(etr_2[5], 28.1111040)
  expect_equal(etr_2[6], 35.245056)
  expect_equal(etr_2[7], 41.395872)
  expect_equal(etr_2[8], 43.8721920)
  expect_equal(etr_2[9], 49.728)
  expect_equal(etr_2[10], 50.15136)
  expect_equal(etr_2[11], 61.93152)
  expect_equal(etr_2[12], 62.05248)
  expect_equal(etr_2[13], 53.9064960)
})