tests/testthat/fixtures/make-test-fixtures.R

In rWCVP: Generating Summaries, Reports and Plots from the World Checklist of Vascular Plants

library(rWCVPdata)
library(dplyr)

fixture_dir <- "tests/testthat/fixtures"

# wcvp extracts ----
## names ----
names <- rWCVPdata::wcvp_names

wcvp_names_extract <- names |>
  filter(genus == "Poa" | genus == "Myrcia")

saveRDS(wcvp_names_extract, file = file.path(fixture_dir, "wcvp_names_extract.rds"))

## distributions ----
distributions <- rWCVPdata::wcvp_distributions

wcvp_distributions_extract <- distributions |>
  filter(plant_name_id %in% wcvp_names_extract$plant_name_id)

saveRDS(wcvp_distributions_extract, file = file.path(fixture_dir, "wcvp_distributions_extract.rds"))

# match data ----

match_data <- tibble(
  taxonId = c("taxon1", "taxon2", "taxon3", "taxon4", "taxon5", "taxon6", "taxon7"),
  scientificName = c(
    "Poa annua", "Myrcia acuminatissima",
    "Abutilon angulatum var. angulatum", "Mercia almasensis",
    "Myrcia almosensis", "× Tromostapelia mutabilis var americana",
    "Astragalus canadense"
  ),
  genus = c(
    "Poa", "Myrcia", "Abutilon", "Mercia", "Myrcia", "Tromostapelia",
    "Astragalus"
  ),
  species = c(
    "annua", "acuminatissima", "angulatum", "almasensis", "almosensis",
    "mutabilis", "canadense"
  ),
  infra_rank = c(
    NA_character_, NA_character_, "var.", NA_character_, NA_character_,
    "var", NA_character_
  ),
  infra = c(
    NA_character_, NA_character_, "angulatum", NA_character_, NA_character_,
    "americana", NA_character_
  ),
  authority = c(
    "L.", "O.Berg", NA_character_, NA_character_, "NicLug", NA_character_,
    NA_character_
  ),
  assessmentId = 1:7
)

saveRDS(match_data, file = file.path(fixture_dir, "match_data.rds"))

lookup_data <- tibble(
  plant_name_id = c(
    "435194-wcs", "130999-wcs", "130998-wcs", "534944-wcs",
    "1261494-az", "610452-az", "131016-wcs", "512990-wcs",
    "658189-az", "662570-az"
  ),
  ipni_id = c(
    "320035-2", "598579-1", "598578-1", "77199392-1", "77227834-1",
    "1125427-2", "304073-2", "970028-1", "24595-2", "479631-1"
  ),
  taxon_name = c(
    "Poa annua", "Myrcia acuminatissima", "Myrcia acuminatissima",
    "Myrcia acutissima", "Abutilon angulatum var. angulatum",
    "Abutilon angulatum", "Myrcia almasensis",
    "× Tromostapelia mutabilis var. americana", "Astragalus canadensis",
    "Astragalus saguntinus"
  ),
  taxon_rank = c(
    "Species", "Species", "Species", "Species", "Variety", "Species",
    "Species", "Variety", "Species", "Species"
  ),
  taxon_status = c(
    "Accepted", "Unplaced", "Synonym", "Accepted", "Accepted",
    "Accepted", "Accepted", "Synonym", "Accepted", "Invalid"
  ),
  taxon_authors = c(
    "L.", "Hieron.", "O.Berg", "(Urb.) K.Campbell & K.Samra",
    "", "(Guill. & Perr.) Mast.", "NicLugh.", "P.V.Heath", "L.", "Pau"
  ),
  family = c(
    "Poaceae", "Myrtaceae", "Myrtaceae", "Myrtaceae", "Malvaceae",
    "Malvaceae", "Myrtaceae", "Apocynaceae", "Fabaceae", "Fabaceae"
  ),
  genus = c(
    "Poa", "Myrcia", "Myrcia", "Myrcia", "Abutilon", "Abutilon", "Myrcia",
    "Tromostapelia", "Astragalus", "Astragalus"
  ),
  accepted_plant_name_id = c(
    "435194-wcs", NA_character_, "131542-wcs", "534944-wcs",
    "1261494-az", "610452-az", "131016-wcs", "512989-wcs",
    "658189-az", "662772-az"
  ),
  homotypic_synonym = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA)
)
saveRDS(lookup_data, file = file.path(fixture_dir, "lookup_data.rds"))