Import and convert taxadb taxonomies to BeeBDC format

Source: R/taxadbToBeeBDC.R

Uses the taxadb R package to download a requested taxonomy and then transforms it into the input BeeBDC format. This means that any taxonomy in their databases can be used with BeeBDC. You can also save the output to your computer and to the R environment for immediate use. See details below for a list of providers or see taxadb::td_create().

taxadbToBeeBDC(
  name = NULL,
  rank = NULL,
  provider = "gbif",
  version = "22.12",
  collect = TRUE,
  ignore_case = TRUE,
  db = NULL,
  removeEmptyNames = TRUE,
  outPath = getwd(),
  fileName = NULL
)

Arguments

name

Character. Taxonomic scientific name (e.g. "Aves"). As defined by taxadb::filter_rank().

rank

Character. Taxonomic rank name. (e.g. "class"). As defined by taxadb::filter_rank().

provider

Character. From which provider should the hierarchy be returned? Default is 'gbif', which can also be configured using options(default_taxadb_provide = ..."). See taxadb::td_create() for a list of recognized providers. NOTE: gbif seems to have the most-complete columns, especially in terms of scientificNameAuthorship, which is important for matching ambiguous names. As defined by taxadb::filter_rank().

version

Character. Which version of the taxadb provider database should we use? defaults to latest. See tl_import for details. Default = 22.12. As defined by taxadb::filter_rank().

collect

Logical. Should we return an in-memory data.frame (default, usually the most convenient), or a reference to lazy-eval table on disk (useful for very large tables on which we may first perform subsequent filtering operations.). Default = TRUE. As defined by taxadb::filter_rank().

ignore_case

Logical. should we ignore case (capitalization) in matching names? Can be significantly slower to run. Default = TRUE. As defined by taxadb::filter_rank().

db

a connection to the taxadb database. See details of taxadb::filter_rank(). Default = Null which should work. As defined by taxadb::filter_rank().

removeEmptyNames

Logical. If True (default), it will remove entries without an entry for specificEpithet.

outPath

Character. The path to a directory (folder) in which the output should be saved.

fileName

Character. The name of the output file, ending in '.csv'.

Value

Returns a taxonomy file (to the R environment and to the disk, if a fileName is provided) as a tibble that can be used with BeeBDC::harmoniseR().

See also

beesTaxonomy() for the bee taxonomy and harmoniseR() for the taxon-cleaning function where these taxonomies are implemented.

Examples

if (FALSE) { # \dontrun{
  # Run the function using the bee genus Apis as an example...
ApisTaxonomy <- BeeBDC::taxadbToBeeBDC(
  name = "Apis",
  rank = "Genus",
  provider = "gbif",
  version = "22.12",
  removeEmptyNames = TRUE,
  outPath = getwd(),
  fileName = NULL
  )
  } # }