tests/testthat/test-qaqc.R

In SWMPr: Retrieving, Organizing, and Analyzing Estuary Monitoring Data

# Test cases for qaqc function
test_that("qaqc correctly removes flagged values", {

  # Call qaqc with default parameters
  qaqc_dat <- qaqc(apacpwq, trace = T)
  
  # Check if qaqc columns are removed
  expect_false("f_do_mgl" %in% colnames(qaqc_dat))
  expect_false("f_ph" %in% colnames(qaqc_dat))
  
  # Call qaqc with qaqc_keep as NULL
  qaqc_dat <- qaqc(apacpwq, qaqc_keep = NULL)
  
  # Check if qaqc columns are removed
  expect_false("f_do_mgl" %in% colnames(qaqc_dat))
  expect_false("f_ph" %in% colnames(qaqc_dat))
  
})

test_that("qaqc correctly keeps specified flags", {
  
  # Call qaqc with specified flags to keep
  qaqc_dat <- qaqc(apacpwq, qaqc_keep = "1")
  result <- sum(!is.na(qaqc_dat$sal))
  expect_equal(result, 18)
  
  # Call qaqc with specified flags to keep
  qaqc_dat <- qaqc(apacpwq, qaqc_keep = c("1", "CND"))
  result <- sum(!is.na(qaqc_dat$sal))
  expect_equal(result, 57)
                   
})

test_that("qaqc returns warning if no qaqc flags", {
  
  expect_warning(qaqc(wq), 'No qaqc columns in input data')

})

test_that("qaqc adds censored columns", {
  
  swmpr_in <- subset(apacpnut, select = 'nh4f')
  attr(swmpr_in, 'cens_cols') <- T
  swmpr_in$c_nh4f <- sample(c(T, F), nrow(swmpr_in), replace = T)
  qaqc_dat <- qaqc(swmpr_in, cens_id = T)
  
  # Check if censored columns present
  expect_true("c_nh4f" %in% colnames(qaqc_dat))
  
})