tests/testthat/test_na_util.R

In exploratory-io/exploratory_func: R package for Exploratory

context("test na_util")
test_that("test impute_na with factor", {
  input <- factor(c(letters[1:5], NA_character_, letters[1:5], NA_character_))

  ret1 <- impute_na(input, type = "value", val = "new")
  expect_equal(ret1, as.factor(c(letters[1:5], "new", letters[1:5], "new")))

  ret2 <- impute_na(input, type = "value", val = letters[seq(length(input))])
  expect_equal(ret2, as.factor(c(letters[1:5], letters[6], letters[1:5], letters[12])))

})

test_that("test impute_na with factor with values already included in original factor", {
  input <- factor(c(letters[1:5], NA_character_, letters[1:5], NA_character_))

  ret <- impute_na(input, type = "value", val = "a")
  expect_equal(ret, as.factor(c(letters[1:5], "a", letters[1:5], "a")))
})

test_that("test impute_na with predict type", {
  test_data <- data.frame(
    rep(c(NA, NA, seq(7), NA), 10),
    rep(c(10, seq(8), NA), 10),
    rep(c(NA, seq(8), NA), 10),
    letters[rep(c(NA, seq(3), NA), 20)],
    letters[rep(seq(2), each = 50)],
    letters[rep(seq(4), each = 25)]
  )
  colnames(test_data) <- c("col 1", "col-2", "col_3", "chars", "group1", "group2")

  ret1 <- test_data %>%
    dplyr::group_by(group1) %>%
    dplyr::mutate(filled_na = impute_na(`col 1`, `col-2`, col_3, chars, type = "predict"))

  expect_true(any(is.na(test_data[["col 1"]]) & !is.na(ret1[["filled_na"]])))

  ret2 <- test_data %>%
    dplyr::group_by(group2) %>%
    dplyr::mutate(filled_na = impute_na(`col 1`, `col-2`, col_3, chars, type = "predict"))

  # result should be changed by group_by
  expect_true(any(ret1[["filled_na"]][!is.na(ret1[["filled_na"]])] != ret2[["filled_na"]][!is.na(ret2[["filled_na"]])]))

  # Test the case where no predictor is specified.
  expect_error({
    ret3 <- test_data %>%
      dplyr::mutate(filled_na = impute_na(`col 1`, type = "predict"))
  }, "Please choose predictor columns")
})

test_that("test impute_na", {
  test_data <- data.frame(
    rep(c(NA, NA, seq(7), NA), 10),
    rep(c(10, seq(8), NA), 10),
    rep(c(NA, seq(8), NA), 10),
    letters[rep(c(NA, seq(3), NA), 20)],
    letters[rep(seq(2), each = 50)],
    letters[rep(seq(4), each = 25)]
  )
  colnames(test_data) <- c("col 1", "col-2", "col_3", "chars", "group1", "group2")
  expect_error({
    test_data %>%
      dplyr::group_by(group1) %>%
      dplyr::mutate(filled_na = impute_na(`col 1`, type = "predict"))
  }, "Please choose predictor columns")
})

test_that("test impute_na with mean", {
  test_data <- data.frame(
    rep(c(NA, NA, seq(7), NA), 10),
    rep(c(10, seq(8), NA), 10),
    rep(c(NA, seq(8), NA), 10),
    letters[rep(c(NA, seq(3), NA), 20)]
  )
  colnames(test_data) <- c("col 1", "col-2", "col_3", "chars")
  ret <- test_data %>%
    dplyr::mutate(filled_na = impute_na(`col 1`, type = "mean"))

  val <- mean(test_data[["col 1"]], na.rm = TRUE)
  expect_equal(ret[["filled_na"]], rep(c(val, val, seq(7), val), 10))
})

test_that("test impute_na with median", {
  test_data <- data.frame(
    rep(c(NA, NA, seq(7), NA), 10),
    rep(c(10, seq(8), NA), 10),
    rep(c(NA, seq(8), NA), 10),
    letters[rep(c(NA, seq(3), NA), 20)]
  )
  colnames(test_data) <- c("col 1", "col-2", "col_3", "chars")
  ret <- test_data %>%
    dplyr::mutate(filled_na = impute_na(`col 1`, type = "median"))

  val <- median(test_data[["col 1"]], na.rm = TRUE)
  expect_equal(ret[["filled_na"]], rep(c(val, val, seq(7), val), 10))
})

test_that("test impute_na with mode", {
  test_data <- data.frame(
    rep(c(NA, NA, seq(7), NA), 10),
    rep(c(10, seq(8), NA), 10),
    rep(c(NA, seq(8), NA), 10),
    letters[rep(c(NA, seq(3), NA), 20)]
  )
  colnames(test_data) <- c("col 1", "col-2", "col_3", "chars")
  ret <- test_data %>%
    dplyr::mutate(filled_na = impute_na(`col 1`, type = "mode"))

  val <- get_mode(test_data[["col 1"]], na.rm = TRUE)
  expect_equal(ret[["filled_na"]], rep(c(val, val, seq(7), val), 10))
})

test_that("test impute_na with sd", {
  test_data <- data.frame(
    rep(c(NA, NA, seq(7), NA), 10),
    rep(c(10, seq(8), NA), 10),
    rep(c(NA, seq(8), NA), 10),
    letters[rep(c(NA, seq(3), NA), 20)]
  )
  colnames(test_data) <- c("col 1", "col-2", "col_3", "chars")
  ret <- test_data %>%
    dplyr::mutate(filled_na = impute_na(`col 1`, type = sd))

  val <- sd(test_data[["col 1"]], na.rm = TRUE)
  expect_equal(ret[["filled_na"]], rep(c(val, val, seq(7), val), 10))
})

test_that("test impute_na with val", {
  test_data <- data.frame(
    rep(c(NA, NA, seq(7), NA), 10),
    rep(c(10, seq(8), NA), 10),
    rep(c(NA, seq(8), NA), 10),
    letters[rep(c(NA, seq(3), NA), 20)]
  )
  colnames(test_data) <- c("col 1", "col-2", "col_3", "chars")
  ret <- test_data %>%
    dplyr::mutate(filled_na = impute_na(`col 1`, type = "value", val = 0))

  val <- 0
  expect_equal(ret[["filled_na"]], rep(c(val, val, seq(7), val), 10))
})

test_that("test impute_na with POSIXct", {
  test_data <- data.frame(
    rep(as.POSIXct(as.Date(c("2013-01-01", "2014-01-01", "2015-01-01", NA, "2016-01-01"))), 20)
  )
  colnames(test_data) <- "col 1"
  ret <- test_data %>%
    dplyr::mutate(filled_na = impute_na(`col 1`, type = "value", val = as.POSIXct(as.Date("2013-01-01"))))

  expect_equal(ret[["filled_na"]], rep(as.POSIXct(as.Date(c("2013-01-01", "2014-01-01", "2015-01-01", "2013-01-01", "2016-01-01"))), 20))
})

test_that("fill_ts_na", {
  test_data <- tibble::tibble(
    time=as.Date(c("2021-01-01", "2021-01-02", "2021-01-03", "2021-01-04", "2021-01-05")),
    value=c(NA, 2, NA, 3, NA))
  ret <- test_data %>%
    dplyr::mutate(filled_na = exploratory:::fill_ts_na(value, time))

  expect_equal(ret$filled_na, c(0, 2, 2, 3, 3))

})

test_that("test impute_na with a column", {
  test_data <- data.frame(
    rep(c("2013-01-01", "2014-01-01", "2015-01-01", NA, "2016-01-01")),
    rep(c("2013-01-01", "2014-01-01", NA, "2015-01-01", "2016-01-01"))
  )
  colnames(test_data) <- c("col 1", "col-2")
  ret <- test_data %>%
    dplyr::mutate(filled_na = impute_na(`col 1`, type = "value", val = `col-2`))

  # Before dplyr 1.0, dplyr::coallesce, which is called from impute_na, seems to have returned factor, but now it returns character.
  expect_equal(ret[["filled_na"]], c("2013-01-01", "2014-01-01", "2015-01-01", "2015-01-01", "2016-01-01"))
})

test_that("test impute_na with undefined type", {
  test_data <- data.frame(
    rep(c(NA, NA, seq(7), NA), 10),
    rep(c(10, seq(8), NA), 10),
    rep(c(NA, seq(8), NA), 10),
    letters[rep(c(NA, seq(3), NA), 20)]
  )
  colnames(test_data) <- c("col 1", "col-2", "col_3", "chars")
  expect_error({
    ret <- test_data %>%
      dplyr::mutate(filled_na = impute_na(`col 1`, type = "va"))
  }, "va is not supported as type")
})

test_that("test fill_between", {
  test_data <- data.frame(
    c(NA, 1, NA, 2, NA),
    c(NA, "a", NA, "b", NA),
    factor(c(NA, "a", NA, "b", NA)),
    stringsAsFactors=FALSE
  )
  colnames(test_data) <- c("col 1", "col-2", "col_3")
  ret <- test_data %>%
    fill_between(`col 1`,`col-2`, col_3)
  expect_equal(ret[["col 1"]], c(NA, 1, 1, 2, NA))
  expect_equal(ret[["col-2"]], c(NA, "a", "a", "b", NA))
  expect_equal(ret[["col_3"]], factor(c(NA, "a", "a", "b", NA)))
})

test_that("test fill_between with .direction=up", {
  test_data <- data.frame(
    c(NA, 1, NA, 2, NA),
    c(NA, "a", NA, "b", NA),
    factor(c(NA, "a", NA, "b", NA)),
    stringsAsFactors=FALSE
  )
  colnames(test_data) <- c("col 1", "col-2", "col_3")
  ret <- test_data %>%
    fill_between(`col 1`,`col-2`, col_3, .direction="up")
  expect_equal(ret[["col 1"]], c(NA, 1, 2, 2, NA))
  expect_equal(ret[["col-2"]], c(NA, "a", "b", "b", NA))
  expect_equal(ret[["col_3"]], factor(c(NA, "a", "b", "b", NA)))
})

test_that("test fill_between with value", {
  test_data <- data.frame(
    c(NA, 1, NA, 2, NA),
    c(NA, "a", NA, "b", NA),
    factor(c(NA, "a", NA, "b", NA)),
    stringsAsFactors=FALSE
  )
  colnames(test_data) <- c("col 1", "col-2", "col_3")
  ret <- test_data %>%
    fill_between(`col 1`, `col-2`, `col_3`, value=0)
  expect_equal(ret[["col 1"]], c(NA, 1, 0, 2, NA))
  expect_equal(ret[["col-2"]], c(NA, "a", "0", "b", NA))
  expect_equal(ret[["col_3"]], factor(c(NA, "a", NA, "b", NA))) # since 0 does not make sense as this factor.

  ret <- test_data %>%
    fill_between(`col 1`, `col-2`, `col_3`, value="a")
  expect_equal(ret[["col 1"]], c(NA, "1", "a", "2", NA))
  expect_equal(ret[["col-2"]], c(NA, "a", "a", "b", NA))
  expect_equal(ret[["col_3"]], factor(c(NA, "a", "a", "b", NA)))
})

test_that("test fill_between with group_by", {
  test_data <- data.frame(
    c(NA,1,NA,2,NA,1,NA,2,NA,NA),
    c("a","a","a","a","a","b","b","b","b","b"),
    stringsAsFactors=FALSE
  )
  colnames(test_data) <- c("col 1", "col-2")
  ret <- test_data %>%
    group_by(`col-2`) %>%
    fill_between(`col 1`)
  expect_equal(ret[["col 1"]],
               c(NA,1,1,2,NA,1,1,2,NA,NA))
})