tests/testthat/test-data_extraction.R

In 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", avg = 9)

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

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

# 2) for H2O:
wiso_ref <- neonUtilities::stackEddy(fin, level = "dp01", avg = 3)

high <- subset(wiso_ref[["ONAQ"]],
               wiso_ref[["ONAQ"]]$verticalPosition == "h2oHigh")
med  <- subset(wiso_ref[["ONAQ"]],
               wiso_ref[["ONAQ"]]$verticalPosition == "h2oMed")
low  <- subset(wiso_ref[["ONAQ"]],
               wiso_ref[["ONAQ"]]$verticalPosition == "h2oLow")

test_that("extract_water_calibration_data returns 16 columns for by_site method", {
  expect_equal(ncol(extract_water_calibration_data(high,
                                                   standard = "high",
                                                   method = "by_site")), 16)
  expect_equal(ncol(extract_water_calibration_data(med,
                                                   standard = "med",
                                                   method = "by_site")), 16)
  expect_equal(ncol(extract_water_calibration_data(low,
                                                   standard = "low",
                                                   method = "by_site")), 16)
})

test_that("extract_water_calibration_data returns error if invalid standard provided", {
  expect_error(extract_water_calibration_data(low,
                                              standard = "cheese",
                                              method = "by_site"))
  expect_error(extract_water_calibration_data(low,
                                              standard = "cheese",
                                              method = "by_month"))
})