tests/testthat/test-additional_coverage.R

In AntonioJBT/episcout: Quickly Clean, Explore and Visualise Large Epidemiological Datasets

context("additional coverage tests")

library(episcout)
library(testthat)
library(dplyr)
library(stringi)

######################
print("Function being tested: epi_clean_count_classes with POSIXct")

test_that("epi_clean_count_classes counts multi-class columns", {
  df <- data.frame(
    time = as.POSIXct("2020-01-01") + 0:1,
    value = 1:2
  )
  cc <- epi_clean_count_classes(df)
  expect_true(all(c("POSIXct", "POSIXt", "integer") %in% names(cc)))
  expect_equal(unname(cc["POSIXct"]), 1)
  expect_equal(unname(cc["POSIXt"]), 1)
})

######################
print("Function being tested: epi_stats_tidy")

test_that("epi_stats_tidy computes row sums and percent", {
  sum_df <- data.frame(
    id = c("g1", "g1", "g2", "g2"),
    x = c("A", "B", "A", "B"),
    n = c(2, 3, 4, 1),
    stringsAsFactors = FALSE
  )
  tidy_df <- epi_stats_tidy(sum_df, perc_n = 10)
  expect_equal(tidy_df$row_sums, c(5, 5))
  expect_equal(tidy_df$percent, c(50, 50))
  expect_equal(names(tidy_df)[1], "id")
})

######################
print("Function being tested: epi_plot_hist additional args")

test_that("epi_plot_hist passes extra parameters", {
  df <- data.frame(x = rnorm(100))
  skip_if_not_installed("ggthemes")
  p <- epi_plot_hist(df, "x", binwidth = 0.5)
  expect_s3_class(p, "ggplot")
  bw <- p$layers[[1]]$stat_params$binwidth
  expect_equal(bw, 0.5)
})

######################
print("Function being tested: epi_clean_compare_str with options")

test_that("epi_clean_compare_str uses additional parameters", {
  df <- data.frame(a = c("abc", "ABC"), b = c("ABC", "abc"), stringsAsFactors = FALSE)
  expect_false(epi_clean_compare_str(df, 2, "a", "b"))
  expect_true(epi_clean_compare_str(df, 2, "a", "b", opts_fixed = list(case_insensitive = TRUE)))
})

######################
print("Function being tested: epi_stats_corr")

test_that("epi_stats_corr returns correct correlations", {
  df <- data.frame(x = 1:5, y = seq(2, 10, 2))
  skip_if_not_installed("Hmisc")
  res <- epi_stats_corr(df, method = "pearson")
  expect_equal(res$cormat$r[1, 2], 1)
  expect_equal(res$cormat$r[2, 1], 1)
})

######################
print("Function being tested: epi_plot_bar custom palette")

test_that("epi_plot_bar applies custom palette", {
  df <- data.frame(cat = c("a", "b", "a", "b"))
  p <- epi_plot_bar(df, "cat", custom_palette = c("red", "blue"))
  expect_s3_class(p, "ggplot")
  cols <- p$scales$scales[[1]]$palette(2)
  expect_equal(cols, c("red", "blue"))
})

######################
print("Function being tested: epi_read with custom NA strings")

test_that("epi_read handles additional NA strings", {
  tmp <- tempfile(fileext = ".csv")
  writeLines(c("a,b", "1,NA", "2,N/A"), tmp)
  df <- epi_read(tmp, na.strings = c("NA", "N/A"))
  expect_true(all(is.na(df$b[1:2])))
  unlink(tmp)
})

######################
print("Function being tested: epi_stats_dates")

test_that("epi_stats_dates returns key statistics", {
  dates <- as.Date(c("2020-01-01", "2020-06-01", NA, "2020-12-31"))
  res <- epi_stats_dates(dates)
  expect_equal(res$Value[res$Statistic == "N"], "4")
  expect_equal(res$Value[res$Statistic == "N Missing"], "1")
  expect_equal(res$Value[res$Statistic == "Min"], "2020-01-01")
  expect_equal(res$Value[res$Statistic == "Max"], "2020-12-31")
})

######################
print("Function being tested: epi_stats_dates_multi")

test_that("epi_stats_dates_multi summarises multiple columns", {
  df <- data.frame(
    a = as.Date("2020-01-01") + 0:2,
    b = as.Date("2021-01-01") + 0:2
  )
  skip_if_not_installed("lubridate")
  res <- epi_stats_dates_multi(df)
  expect_true(all(c("Column", "N", "Min") %in% names(res)))
  expect_equal(nrow(res), 2)
})

######################
print("Function being tested: epi_stats_summary error handling")

test_that("epi_stats_summary errors with bad parameters", {
  df <- data.frame(a = 1:3)
  expect_error(epi_stats_summary(df, class_type = "wrong"))
  expect_error(epi_stats_summary(df, action = "oops"))
})

######################
print("Function being tested: epi_clean_make_names options")

test_that("epi_clean_make_names handles duplicates and replacement", {
  strings <- c("a", "a", "b c")
  out <- epi_clean_make_names(strings, str_replacement = "-")
  expect_true(length(unique(out)) == length(out))
  expect_true(!any(grepl("-", out)))
  expect_true(all(make.names(out) == out))
})

######################
print("Function being tested: epi_clean_replace_value no match")

test_that("epi_clean_replace_value leaves values when no match", {
  df <- data.frame(col = c("cat", "dog"), stringsAsFactors = FALSE)
  res <- epi_clean_replace_value(df, "col", "bird", "new")
  expect_equal(res, df$col)
})

######################
print("Function being tested: epi_clean_transpose roundtrip")

test_that("epi_clean_transpose roundtrip works", {
  df <- data.frame(id = 1:3, a = 4:6)
  df$id_col <- df$id
  tdf <- epi_clean_transpose(df, 3)
  # Recreate original by transposing back
  back <- epi_clean_transpose(tdf, 1)
  expect_equal(dim(back), dim(df))
})