tests/testthat/test-data_regression.R

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

# test-data_regression

#----------------------
# CARBON FUNCTIONS
#----------------------

# test to make sure that the I/O structures
# across regression functions are correct.
fin <- system.file("extdata",
                   "NEON.D15.ONAQ.DP4.00200.001.nsae.2019-05.basic.packed.h5",
                   package = "NEONiso", mustWork = TRUE)
co2test <- ingest_data(fin, analyte = "Co2", amb_avg = 9, ref_avg = 9)
co2data <- NEONiso:::extract_carbon_cal_data(co2test$refe_stacked,
                                             standards = c("co2Low",
                                                           "co2Med",
                                                           "co2High"))
caldf_b03 <- NEONiso:::fit_carbon_regression(co2data,
                                             method = "Bowling_2003",
                                             calibration_half_width = 2)
caldf_lr <- NEONiso:::fit_carbon_regression(co2data,
                                            method = "linreg",
                                            calibration_half_width = 2)

test_that("fit_carbon_regression returns data.frame", {
  skip_on_cran()
  expect_s3_class(fit_carbon_regression(co2data,
                                        method = "Bowling_2003",
                                        calibration_half_width = 2),
                  "data.frame")
  expect_s3_class(fit_carbon_regression(co2data,
                                        method = "linreg",
                                        calibration_half_width = 2),
                  "data.frame")
})

test_that("calibration data frames have 14 columns", {
  skip_on_cran()
  expect_equal(ncol(caldf_b03), 14)
  expect_equal(ncol(caldf_lr), 14)
})

test_that("carbon calibration data frames correct even when no input data", {
  skip_on_cran()
  # empty ref data frame:
  empty_df <- data.frame(matrix(nrow = 0, ncol = ncol(co2data)))
  names(empty_df) <- names(co2data)
  expect_no_error(fit_carbon_regression(empty_df,
                                        method = "Bowling_2003"))
  expect_no_error(fit_carbon_regression(empty_df,
                                        method = "linreg"))
  expect_equal(ncol(fit_carbon_regression(empty_df,
                                          method = "Bowling_2003")), 14)
  expect_equal(ncol(fit_carbon_regression(empty_df,
                                          method = "linreg",
                                          calibration_half_width = 2)), 14)
})


# work through ambient calibrations

# test carbon - bowling ambient calibration
temp <- calibrate_ambient_carbon_Bowling2003(co2test$ambient$`000_010_09m`,
                                             caldf_b03,
                                             site = "ONAQ")
temp_gf <- calibrate_ambient_carbon_Bowling2003(co2test$ambient$`000_010_09m`,
                                                caldf_b03,
                                                site = "ONAQ",
                                                gap_fill_parameters = TRUE)

test_that("calibrate_ambient_carbon_Bowling2003 returns a list",{
  skip_on_cran()
  expect_equal(class(temp), "list")
  expect_equal(class(temp_gf), "list")
})

test_that("calibrate_ambient_carbon_Bowling2003 returns correct variables", {
  skip_on_cran()
  vars <- c("dlta13CCo2", "pres", "presEnvHut", "rhEnvHut",
            "rtioMoleDry12CCo2", "rtioMoleDry13CCo2", "rtioMoleDryCo2",
            "rtioMoleDryH2o", "rtioMoleWet12CCo2", "rtioMoleWet13CCo2",
            "rtioMoleWetCo2", "rtioMoleWetH2o",
            "rtioMoleWetH2oEnvHut", "temp", "tempEnvHut")
  expect_equal(names(temp), vars)
  expect_equal(names(temp_gf), vars)
})

test_that("calibrated d13C values have been added to calibrate_ambient_cabron_Bowling2003 output", {
  skip_on_cran()
  expect_gt(ncol(temp$dlta13CCo2),
            ncol(co2test$ambient$`000_010_09m`$dlta13CCo2))
  expect_gt(ncol(temp_gf$dlta13CCo2),
            ncol(co2test$ambient$`000_010_09m`$dlta13CCo2))
})

# test carbon - linreg ambient calibration
temp <- calibrate_ambient_carbon_linreg(co2test$ambient$`000_010_09m`,
                                        caldf_lr,
                                        site = "ONAQ")
temp_gf <- calibrate_ambient_carbon_linreg(co2test$ambient$`000_010_09m`,
                                           caldf_lr,
                                           site = "ONAQ",
                                           gap_fill_parameters = TRUE)

test_that("calibrate_ambient_carbon_linreg returns a list", {
  skip_on_cran()
  expect_equal(class(temp), "list")
  expect_equal(class(temp_gf), "list")
})

test_that("calibrate_ambient_carbon_linreg returns correct variables", {
  skip_on_cran()
  vars <- c("dlta13CCo2", "pres", "presEnvHut", "rhEnvHut",
            "rtioMoleDry12CCo2", "rtioMoleDry13CCo2", "rtioMoleDryCo2",
            "rtioMoleDryH2o", "rtioMoleWet12CCo2", "rtioMoleWet13CCo2",
            "rtioMoleWetCo2", "rtioMoleWetH2o",
            "rtioMoleWetH2oEnvHut", "temp", "tempEnvHut")
  expect_equal(names(temp), vars)
  expect_equal(names(temp_gf), vars)
})

test_that("calibrated d13C values have been added to calibrate_ambient_cabron_linreg output", {
  skip_on_cran()
  expect_gt(ncol(temp$dlta13CCo2),
            ncol(co2test$ambient$`000_010_09m`$dlta13CCo2))
  expect_gt(ncol(temp_gf$dlta13CCo2),
            ncol(co2test$ambient$`000_010_09m`$dlta13CCo2))
})


#----------------------
# WATER FUNCTIONS
#----------------------

# test to make sure that the I/O structures across regression functions are correct.
fin <- system.file("extdata",
                   "NEON.D15.ONAQ.DP4.00200.001.nsae.2019-05.basic.packed.h5",
                   package = "NEONiso", mustWork = TRUE)
h2otest <- ingest_data(fin, analyte = "H2o", amb_avg = 9, ref_avg = 3)
h2odata <- NEONiso:::extract_water_calibration_data(h2otest$refe_stacked)

caldf <- NEONiso:::fit_water_regression(h2odata,
                                        calibration_half_width = 2)

test_that("fit_water_regression returns data.frame", {
  skip_on_cran()
  expect_s3_class(fit_water_regression(h2odata,
                                       calibration_half_width = 2),
                  "data.frame")
})

test_that("calibration data frames have 14 columns", {
  skip_on_cran()
  expect_equal(ncol(caldf), 14)
})


# work through ambient calibrations

# test carbon - bowling ambient calibration
temp <- calibrate_ambient_water_linreg(h2otest$ambient$`000_010_09m`,
                                       caldf,
                                       site = "ONAQ")
# no gapfilling in the water functions yet!
#temp_gf <- calibrate_ambient_water_linreg(h2otest$ambient$`000_010_09m`,
#                                               calDf,
#                                               site = "ONAQ",
#                                               gap_fill_parameters = TRUE)

test_that("calibrate_ambient_water_linreg returns a list", {
  skip_on_cran()
  str(temp)
  expect_equal(class(temp), "list")
  #expect_equal(class(temp_gf), "list")
})

test_that("calibrate_ambient_water_linreg returns correct variables", {
  skip_on_cran()
  vars <- c("dlta18OH2o", "dlta2HH2o", "pres", "presEnvHut", "rhEnvHut",
            "rtioMoleDryH2o", "rtioMoleWetH2o",
            "rtioMoleWetH2oEnvHut", "temp", "tempEnvHut")
  expect_equal(names(temp), vars)
 #expect_equal(names(temp_gf), vars)
})

test_that("calibrated water isotope values have been added to calibrate_ambient_water_linreg output", {
  skip_on_cran()
  expect_gt(ncol(temp$dlta18OH2o),
            ncol(h2otest$ambient$`000_010_09m`$dlta18OH2o))
  expect_gt(ncol(temp$dlta2HH2o),
            ncol(h2otest$ambient$`000_010_09m`$dlta2HH2o))
})