tests/testthat/test-data_extraction.R

In SPATIAL-Lab/NEONiso: Tools to Calibrate and Work with NEON Atmospheric Isotope Data

# test-data_extraction

# co2 test first - testing extract_carbon_calibration_data function

fin <- system.file("extdata",
                   "NEON.D15.ONAQ.DP4.00200.001.nsae.2019-05.basic.packed.h5",
                   package = "NEONiso", mustWork = TRUE)
# 1) for CO2:
co2test <- ingest_data(fin, analyte = "Co2", amb_avg = 9, ref_avg = 9)

test_that("extract_carbon_calibration_data fails if incorrect list provided to function", {
  expect_error(extract_carbon_cal_data(co2test$reference))
  expect_error(extract_carbon_cal_data(fin))
  expect_silent(extract_carbon_cal_data(co2test$refe_stacked))
})

test_that("extract_carbon_calibration_data output has correct structure", {
  tmp <- extract_carbon_cal_data(co2test$refe_stacked)
  expect_equal(ncol(tmp), 23)
  expect_s3_class(tmp$timeBgn, "POSIXct")
  expect_s3_class(tmp$timeEnd, "POSIXct")
})

test_that("extract_carbon_calibration_data removes standards correctly", {

  expect_lt(nrow(extract_carbon_cal_data(co2test$refe_stacked,
                                         standards = c("co2Low", "co2Med"))),
            nrow(extract_carbon_cal_data(co2test$refe_stacked)))

  expect_lt(nrow(extract_carbon_cal_data(co2test$refe_stacked,
                                         standards = c("co2Low", "co2High"))),
            nrow(extract_carbon_cal_data(co2test$refe_stacked)))

  expect_lt(nrow(extract_carbon_cal_data(co2test$refe_stacked,
                                         standards = "co2Low")),
            nrow(extract_carbon_cal_data(co2test$refe_stacked,
                                         standards = c("co2High", "co2Med"))))
})

# 2) for H2O:
h2otest <- ingest_data(fin, analyte = "H2o", amb_avg = 9, ref_avg = 3)

test_that("extract_carbon_calibration_data fails if incorrect list provided to function", {
  expect_error(extract_water_calibration_data(h2otest$reference))
  expect_error(extract_water_calibration_data(fin))
  expect_silent(extract_water_calibration_data(h2otest$refe_stacked))
})

h2otest2 <- extract_water_calibration_data(h2otest$refe_stacked)


test_that("extract_water_calibration_data output has correct structure", {
  tmp <- extract_water_calibration_data(h2otest$refe_stacked)
  expect_equal(ncol(tmp), 23)
  expect_s3_class(tmp$timeBgn, "POSIXct")
  expect_s3_class(tmp$timeEnd, "POSIXct")
})