tests/testthat/test_gbif_species_name_match.R

In inbo/inborutils: Collection of Useful R Utilities

context("gbif_species_name_match")

names <- c(
  "Lagenaceae", # family
  "Borzinemataceae", # family
  "Mastigamoebaceae", # family
  "Acipenseriformes" # order
)
kingdoms <- c(
  "Chromista",
  "Bacteria",
  "Protozoa",
  "Animalia"
)

df <- data.frame(
  name = names,
  kingdom_col = kingdoms,
  stringsAsFactors = FALSE
)

df2 <- read.csv(paste0(
  "https://raw.githubusercontent.com/inbo",
  "/inbo-pyutils/master/gbif/gbif_name_match",# nolint
  "/sample.csv"
),
strip.white = TRUE
)

# column with names is called as one of the returned cols from GBIF
df3 <- df[1:3, ]
names(df3) <- c("family", "kingdom_col")

testthat::test_that("check classes of input params", {
  expect_error(
    gbif_species_name_match(df = names),
    "Error: df. Expected a data.frame. Got an object of class character."
  )
  expect_error(
    gbif_species_name_match(df = df, name = 1),
    "name. Expected a character. Got an object of class numeric."
  )
  expect_error(
    gbif_species_name_match(df = df, gbif_terms = c(4, 3)),
    "gbif_terms. Expected a character. Got an object of class numeric."
  )
})

testthat::test_that("check validity of parameter values", {
  # wrong name parameter
  expect_error(
    gbif_species_name_match(df3, gbif_terms = c("family")),
    paste(
      "These columns exist in colnames but not",
      "in your dataframe: name and these exist in your",
      "dataframe but not in colnames: family kingdom_col"
    )
  )
  # wrong GBIF name_backbone parameter
  expect_error(gbif_species_name_match(df, kingdomsss = "kingdom_col"),
    paste(
      "Only optional parameters of GBIF name search",
      "allowed: rank, kingdom, phylum, class, order, family,",
      "genus, strict, verbose, start, limit, curlopts.",
      "Check ?name_backbone for more details."
    ),
    fixed = TRUE
  )
  # wrong GBIF name_backbone parameters
  expect_error(gbif_species_name_match(df,
    kingdomsss = "kingdom_col",
    strinctsss = TRUE
  ),
  paste(
    "Only optional parameters of GBIF name search",
    "allowed: rank, kingdom, phylum, class, order, family,",
    "genus, strict, verbose, start, limit, curlopts.",
    "Check ?name_backbone for more details."
  ),
  fixed = TRUE
  )
  # name column is equal to one of the returned GIBF terms
  expect_warning(
    gbif_species_name_match(df3,
      name = "family",
      gbif_terms = c(
        "familyKey",
        "family"
      )
    ),
    paste0(
      "Column with names \'family\' is also one of the",
      " returned gbif_terms. GBIF column name is",
      " authomatically recalled \'family1\'."
    )
  )
  # some GBIF terms not returned
  expect_warning(
    gbif_species_name_match(df, gbif_terms = c(
      "class",
      "classKey",
      "genus",
      "genusKey"
    )),
    paste(
      "The following terms are not returned by GBIF:",
      "genus, genusKey. It is possible they refer to ranks",
      "lower than rank of matched names."
    )
  )
})

testthat::test_that("Test output", {
  requested_gbif_terms <- c("class", "classKey")
  out <- gbif_species_name_match(df, gbif_terms = requested_gbif_terms)
  out2 <- gbif_species_name_match(df2, gbif_terms = c(
    "species",
    "kingdom"
  ))
  expect_true(all(names(df) %in% names(out)))
  expect_true(all(names(out) %in% c(names(df), names(out))))
  expect_true(all(requested_gbif_terms %in% names(out)))
  expect_true(nrow(out) == nrow(df))
  expect_true(all(is.na(out$genus)))
  expect_true(all(is.na(out$genusKey)))
  expect_true(all(out$name == df$name))
  expect_true(all(out$kingdom_col == df$kingdom_col))
})