tests/testthat/test_utils.R

In steffilazerte/rems2aquachem: BC Groundwater Chemistry Analysis Tool

save_plot <- function(code, width = 400, height = 400) {
  path <- tempfile(fileext = ".png")
  png(path, width = width, height = height)
  capture.output(print(code))
  dev.off()

  path
}

# meq and charge balance --------------------------------------------

test_that("internal data correct", {
  expect_snapshot(meq_conversion)
})


test_that("meq() and charge_balance()", {
  skip_on_ci()

  # See local_test_context() for dealing with weird sorting problems
  local({
    local_test_context()
    expect_message(p <- rems_to_aquachem("E298873", save = FALSE, interactive = FALSE,
                                         date_range = c("2014-01-01", "2014-12-31")) %>%
                     units_remove(), "For consistency") %>%
      suppressMessages()

    expect_equal(
      dplyr::select(p, dplyr::contains("_meq")),
      dplyr::tibble(
        Al_diss_meq = 7.6721053e-05,
        CO3_meq = 0.016664195,
        Ca_meq = 0.48355706,
        Cl_meq = 0.16077624,
        Cu_diss_meq = 6.2317062e-06,
        F_meq = 0.00126326427,
        Fe_diss_meq = 3.5813412e-05,
        HCO3_meq = 0.62770524,
        K_meq = 0.035295652,
        Meas_Alk_meq = 0.62745474,
        Mg_meq = 0.136597408,
        Mn_diss_meq = 0.00029123718,
        NH4_meq = 0.00035697202,
        NO2_meq = 0.000142788808,
        NO3_meq = 0.038196006,
        Na_meq = 0.224447657,
        SO4_meq = 0.0599609,
        Zn_diss_meq = 3.12022025e-05))

    expect_message(cb <- charge_balance(p), "For consistency")
    expect_equal(cb$charge_balance, -0.4, tolerance = 0.000001)
    expect_equal(cb$anion_sum, 0.89, tolerance = 0.000001)
    expect_equal(cb$cation_sum, 0.88, tolerance = 0.000001)
  })

  expect_message(p <- rems_to_aquachem("E314330", save = FALSE,
                                       interactive = FALSE,
                                       date_range = c("2019-01-01", "2019-12-31")) %>%
                   units_remove(), "For consistency") %>%
    suppressMessages() %>%
    suppressWarnings()

  expect_message(cb <- charge_balance(p), "For consistency")
  expect_equal(dplyr::select(cb, "anion_sum", "cation_sum", "charge_balance"),
               dplyr::select(p, "anion_sum", "cation_sum", "charge_balance"))

  expect_equal(cb$charge_balance, c(23.2, 21.0))
  expect_equal(cb$anion_sum, c(1.08, 1.09))
  expect_equal(cb$cation_sum, c(1.73, 1.67))

  expect_message(p <- rems_to_aquachem("E307047", save = FALSE, interactive = FALSE,
                                       date_range = c("2018-01-01", "2022-02-01")) %>%
                   units_remove(), "For consistency") %>%
    suppressMessages() %>%
    suppressWarnings()

  expect_message(cb <- charge_balance(p), "For consistency")
  expect_equal(dplyr::select(cb, "anion_sum", "cation_sum", "charge_balance"),
               dplyr::select(p, "anion_sum", "cation_sum", "charge_balance"))

  expect_equal(cb$charge_balance[1:2], c(-1.4, -3.8))
  expect_equal(cb$anion_sum[1:2], c(6.25, 6.61))
  expect_equal(cb$cation_sum[1:2], c(6.08, 6.13))
})

test_that("is_valid", {
  expect_true(all(is_valid(c(-10:10))))
  expect_true(all(!is_valid(c(-10.1, 10.1, 20, 50, -20, -100))))
})



# water type ---------------------------------------------------------
test_that("water_type", {

  d <- data.frame(Sample_Date = "2022-01-01", SampleID = "999990-01", StationID = 000,
                  Cl_meq = 0.0226, SO4_meq = 0.0208, HCO3_meq = 1.54,
                  Ca_meq = 0.187, Mg_meq = 0.490, Na_meq = 0.465, K_meq = 0.0665,
                  charge_balance = 0.5)

  expect_silent(d <- water_type(d))
  expect_equal(d$water_type, "Mg-Na-HCO3")

  d <- data.frame(SampleID = "999990-01", StationID = 000,
                  Cl_meq = 0.0226, SO4_meq = 0.0208, HCO3_meq = 1.54,
                  Ca_meq = 0.187, Mg_meq = 0.490, Na_meq = 0.465, K_meq = 0.0665,
                  charge_balance = 0.5)

  expect_error(d <- water_type(d), "Missing required columns")


  d <- data.frame(Sample_Date = "2022-01-01", SampleID = "999990-01", StationID = 000,
                  Cl_meq = NA, SO4_meq = 0.0208, HCO3_meq = NA,
                  Ca_meq = 0.187, Mg_meq = 0.490, Na_meq = 0.465, K_meq = 0.0665,
                  charge_balance = 0.5)

  expect_silent(d <- water_type(d))
  expect_equal(d$water_type, "Mg-Na-Ca")

  skip_on_ci()
  expect_message(p <- rems_to_aquachem(c("E298873", "E292373"),
                                      save = FALSE, interactive = FALSE,
                                      date_range = c("2015-01-01", "2016-12-31")) %>%
                  units_remove(), "For consistency") %>%
    suppressMessages()

  expect_equal(p$water_type,
               c("Ca-Mg-Na", "Ca-Na-HCO3-Cl", "Ca-Na-HCO3-Cl", "Ca-Na-HCO3"))
})

# plots -------------------------------------
test_that("plots", {
  skip_on_ci()
  set.seed(1111)
  expect_message(p <- rems_to_aquachem("E298873", save = FALSE, interactive = FALSE,
                                       date_range = c("2014-01-01", "2014-12-31")),
                 "For consistency") %>%
    suppressMessages()

  path <- save_plot(stiff_plot(p))
  expect_snapshot_file(path, name = "stiff1.png")

  path <- save_plot(piper_plot(p))
  expect_snapshot_file(path, name = "piper1.png")

})

test_that("plots customized", {
  skip_on_ci()
  suppressMessages({
    r <- rems_to_aquachem(ems_ids = c("1401030", "1401377", "E292373"),
                          save = FALSE) %>%
      units_remove() %>%
      dplyr::mutate(Year = lubridate::year(Sample_Date)) %>%
      dplyr::mutate(Year_cat = dplyr::case_when(Year < 2010 ~ "Pre 2010s",
                                                Year >= 2010 & Year <= 2015 ~ "2010-2015",
                                                Year > 2015 ~ ">2015"),
                    Year_cat = factor(Year_cat,
                                      levels = c("Pre 2010s", "2010-2015", ">2015")))
  })

  path <- piper_plot(d = r, group = "Year_cat",
                     point_colour = c("#21908C90", "#44015490", "#9AD93C90"),
                     point_shape = c("square", "triangle", "circle"),
                     point_size = 0.2,
                     legend_position = c(-1.5, 1),
                     legend_title = "Year") %>%
  save_plot()
  expect_snapshot_file(path, name = "piper2.png")

})

test_that("plot messages", {
  skip_on_ci()
  set.seed(1111)
  expect_message(p <- rems_to_aquachem(c("1401030", "1401377"),
                                       save = FALSE,
                                       date_range = c("1991-01-01", "1992-01-01")),
                 "For consistency") %>%
    suppressMessages()

  expect_message(piper_plot(p), "Not enough good quality data")
  expect_message(stiff_plot(p), "Not enough good quality data")
  expect_message(stiff_plot(p, valid = FALSE), "Not enough data")
  expect_silent(piper_plot(p, valid = FALSE, plot_data = TRUE))
})