tests/testthat/test-validateTax.R

In LimaRAF/plantR: Managing Species Records from Biological Collections

# Creating a data frame with taxonomic information
df <- data.frame(
  family.new = c("Bignoniaceae", "Bignoniaceae","Bignoniaceae",
                 "Bignoniaceae","Bignoniaceae","Bignoniaceae"),
  identifiedBy.new = c("Gentry, A.H.", "Hatschbach, G.", NA, NA, NA, "Hatschbach, G."),
  recordedBy.new = c(NA, NA, NA, "Gentry, A.H.", NA, NA),
  typeStatus = c(NA, NA, "isotype", NA, NA, NA),
  numTombo = c("a_1","b_3","c_7","d_5","e_3","f_4"),
  basisOfRecord = c(rep("exsicata", 5),"obs"),
  stringsAsFactors = FALSE)

# Expected result
res0 <- c("high", "low", "high", "high", "unknown", "low")
res1 <- c("high", "medium", "high", "high", "unknown", "medium")
res2 <- c("high", "low", "high", "high", "unknown", "high")
res3 <- c("high", "medium", "high", "high", "unknown", "high")
res4 <- c("high", "high", "high", "high", "unknown", "high")
res5 <- c("high", "high", "high", "high", "unknown", "medium")
res6 <- c("high", "high", "high", "high", "unknown", "unknown")

# Tests
test_that("validateTax works", {
  expect_equal(validateTax(df, print = FALSE)$tax.check, res0)
  expect_equal(validateTax(df, print = FALSE, generalist = TRUE)$tax.check, res1)
  expect_equal(validateTax(df, print = FALSE, voucher.list = "f_4")$tax.check, res2)
  expect_equal(validateTax(df, print = FALSE, generalist = TRUE, voucher.list = "f_4")$tax.check, res3)
  expect_equal(validateTax(df, miss.taxonomist = "Bignoniaceae_Hatschbach, G.")$tax.check, res4)
  expect_equal(validateTax(df, print = FALSE,
                           miss.taxonomist = "Bignoniaceae_Hatschbach, G.",
                           other.records = 1)$tax.check, res5)
  expect_equal(validateTax(df, print = FALSE,
                           miss.taxonomist = "Bignoniaceae_Hatschbach, G.",
                           other.records = "unknown")$tax.check, res6)
  expect_equal(validateTax(df, print = TRUE)$tax.check, res0)
})