tests/testthat/test-identify-outliers.R

In bcgov/wqbc: Tidy Water Quality Data and Calculate Thresholds for British Columbia

# Copyright 2016 Province of British Columbia
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and limitations under the License.

context("identify-outliers")

test_that("adequate_unique_outliers", {
  x <- data.frame(Value = 1:10, Outlier = TRUE)

  expect_false(adequate_unique_outliers(x))
  x$Outlier <- FALSE
  expect_true(adequate_unique_outliers(x))
  expect_false(adequate_unique_outliers(x[1:2, ]))
  expect_true(adequate_unique_outliers(x[1:3, ]))
  expect_false(adequate_unique_outliers(x[c(1:2, 1:2), ]))
})

test_that("identify_outliers", {
  data <- data.frame(Value2 = c(1, NA), Variable = "pH")
  expect_error(identify_outliers(data), class = "chk_error")

  data$Value <- data$Value2
  expect_identical(identify_outliers(data, messages = FALSE)$Outlier, c(FALSE, FALSE))
  expect_message(identify_outliers(data, messages = TRUE), "Identified 0 outliers in water quality data.")
  expect_message(identify_outliers(wqbc::dummy, sds = 2, messages = TRUE), "Identified 5 outliers in water quality data.")
  expect_identical(identify_outliers(data.frame(Value = c(NA_real_, NA_real_), Variable = "pH"), messages = FALSE)$Outlier, c(FALSE, FALSE))
  data <- data.frame(Value = c(rep(100, 2), rep(0, 1000)), Variable = "pH")
  expect_message(identify_outliers(data, messages = TRUE), "Identified 0 outliers in water quality data.")
  expect_message(identify_outliers(data, ignore_undetected = FALSE, messages = TRUE), "Identified 0 outliers in water quality data.")
  data <- data.frame(Value = c(101, rep(100, 2), rep(0, 1000)), Variable = "pH")
  expect_message(identify_outliers(data, sds = 10, ignore_undetected = FALSE, messages = TRUE), "Identified 3 outliers in water quality data.")
  data <- data.frame(Value = c(-101, rep(100, 2), rep(0, 1000)), Variable = "pH")
  expect_message(identify_outliers(data, sds = 10, ignore_undetected = FALSE, messages = TRUE), "Identified 2 outliers in water quality data.")
  expect_message(identify_outliers(data, sds = 10, ignore_undetected = FALSE, large_only = FALSE, messages = TRUE), "Identified 3 outliers in water quality data.")

  data <- expand.grid(
    Value = c(-101, rep(100, 2), rep(0, 1000)), Other = c("x", "y"),
    Variable = "pH"
  )
  expect_message(identify_outliers(data, by = "Other", sds = 10, ignore_undetected = FALSE, large_only = FALSE, messages = TRUE), "Identified 6 outliers in water quality data.")
})

test_that("identify_outliers by Variable!", {
  data <- wqbc::dummy
  outliers <- identify_outliers(wqbc::dummy, sds = 2, messages = FALSE)
  expect_equivalent(outliers[names(wqbc::dummy)], wqbc::dummy[order(wqbc::dummy$Variable), ])
  expect_identical(outliers$Outlier, c(
    TRUE, FALSE, FALSE, TRUE, FALSE, FALSE, TRUE, FALSE, TRUE,
    TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE,
    FALSE
  ))
})