tests/testthat/test_auk-unique.r

In ebird/auk: eBird Data Processing with AWK

context("auk_unique")

test_that("auk_unique removes duplicates", {
  ebd <- system.file("extdata/zerofill-ex_ebd.txt", package = "auk") %>%
    read_ebd(unique = FALSE)
  ebd_unique <- auk_unique(ebd)

  ebd_g <- ebd[!is.na(ebd$group_identifier), ]
  ebd_unique_g <- ebd_unique[!is.na(ebd_unique$group_identifier), ]

  unique_cols <- c("scientific_name", "group_identifier")

  expect_lt(nrow(ebd_unique), nrow(ebd))
  expect_equal(ncol(ebd_unique), ncol(ebd) + 1)
  expect_true(!"checklist_id" %in% names(ebd))
  expect_true("checklist_id" %in% names(ebd_unique))
  expect_gt(anyDuplicated(ebd_g[, unique_cols]), 0)
  expect_equal(anyDuplicated(ebd_unique_g[, unique_cols]), 0)
  expect_equal(class(ebd), class(ebd_unique))
})

test_that("auk_unique removes duplicates in sampling file", {
  ebd <- system.file("extdata/zerofill-ex_sampling.txt", package = "auk") %>%
    read_sampling(unique = FALSE)
  ebd_unique <- auk_unique(ebd, checklists_only = TRUE)

  ebd_g <- ebd[!is.na(ebd$group_identifier), ]
  ebd_unique_g <- ebd_unique[!is.na(ebd_unique$group_identifier), ]

  unique_cols <- "group_identifier"

  expect_lt(nrow(ebd_unique), nrow(ebd))
  expect_equal(ncol(ebd_unique), ncol(ebd) + 1)
  expect_true(!"checklist_id" %in% names(ebd))
  expect_true("checklist_id" %in% names(ebd_unique))
  expect_gt(anyDuplicated(ebd_g[, unique_cols]), 0)
  expect_equal(anyDuplicated(ebd_unique_g[, unique_cols]), 0)
  expect_equal(class(ebd), class(ebd_unique))
})

test_that("auk_unique throws error for invalid input", {
  ebd <- system.file("extdata/zerofill-ex_ebd.txt", package = "auk") %>%
    read_ebd(unique = FALSE)
  sed <- system.file("extdata/zerofill-ex_sampling.txt", package = "auk") %>%
    read_sampling(unique = FALSE)

  expect_error(auk_unique(sed))
  expect_error(auk_unique(ebd, group_id = "abc"))
  expect_error(auk_unique(ebd, checklist_id = "abc"))
  expect_error(auk_unique(ebd, species_id = "abc"))
})