tests/testthat/test-taxon_relations.R

In kamapu/taxlist: Handling Taxonomic Lists

context("manipulating taxon concepts")

# Loading installed examples
pat <- system.file("taxlist_examples", "examples.Rda", package = "taxlist")

load(pat)

test_that("function taxon_relations is working", {
  expect_is(taxon_relations(Easplist), "data.frame")
  tmp <- Easplist
  tmp_rel <- Easplist@taxonRelations
  tmp_rel$ViewID <- NA
  expect_equal(
    all(is.na(({
      taxon_relations(tmp) <- tmp_rel
      tmp@taxonRelations$ViewID
    }))),
    TRUE
  )
})

test_that("function add_concept is working", {
  expect_equal(
    nrow(Easplist@taxonRelations) <
      nrow(add_concept(Easplist,
        TaxonName = "Euclea acutifolia",
        AuthorName = "E. Mey. ex A. DC.",
        Level = "species", Parent = 55707,
        ViewID = 1
      )@taxonRelations),
    TRUE
  )
  Euclea <- subset(Easplist, grepl("Euclea", TaxonName),
    slot = "names", keep_parents = TRUE
  )
  Diospyros <- subset(Easplist, grepl("Diospyros", TaxonName),
    slot = "names"
  )
  ## expect_is(add_concept(Diospyros, Euclea), "taxlist")
  # Same family in both taxlist objects retrieves error
  Diospyros <- subset(Easplist, grepl("Diospyros", TaxonName),
    slot = "names", keep_parents = TRUE
  )
  expect_error(add_concept(Diospyros, Euclea))
  # Working with lists without information on taxonomic levels
  ## expect_equal(nrow(add_concept(data2,
  ##   TaxonName = "Planta incognita"
  ## )@taxonRelations) >
  ##   nrow(data2@taxonRelations), TRUE)
  ## expect_warning(add_concept(data2,
  ##   TaxonName = "Planta incognita",
  ##   Level = "species"
  ## ))
  # Adding on a new object
  expect_equal(
    nrow(add_concept(new("taxlist"),
      TaxonName = "Planta incognita"
    )@taxonRelations),
    1
  )
  # Addition including taxon view
  tax_1 <- clean(subset(Easplist, TaxonName == "Cyperus papyrus",
    slot = "names"
  ))
  tax_1@taxonViews <- tax_1@taxonViews[tax_1@taxonViews$ViewID %in%
    tax_1@taxonRelations$ViewID, ]
  tax_2 <- clean(subset(Easplist, TaxonName == "Cyperaceae",
    slot = "names"
  ))
  tax_2@taxonViews <- tax_2@taxonViews[tax_2@taxonViews$ViewID %in%
    tax_2@taxonRelations$ViewID, ]
  ## expect_is(add_concept(tax_1, tax_2, insert_view = TRUE), "taxlist")
})

test_that("function update_concept is working", {
  expect_equal(with(
    update_concept(Easplist, 155,
      Level = "subspecies"
    )@taxonRelations,
    paste(Level[TaxonConceptID == 155])
  ), "subspecies")
})