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()
.
Usage
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 bytaxadb::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 bytaxadb::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'.
- ...
Arguments passed to
taxadb::td_create()
.
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,
...
)
} # }