Look up taxonomic information by scientific name
Usage
filter_name(
name,
provider = getOption("taxadb_default_provider", "itis"),
version = latest_version(),
collect = TRUE,
ignore_case = FALSE,
db = td_connect()
)Arguments
- name
a character vector of scientific names, e.g. "Homo sapiens"
- provider
from which provider should the hierarchy be returned? Default is 'itis', which can also be configured using
options(default_taxadb_provider=..."). See[td_create]for a list of recognized providers.- version
Which version of the taxadb provider database should we use? defaults to latest. See tl_import for details.
- collect
logical, default
TRUE. 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.)- ignore_case
should we ignore case (capitalization) in matching names? Can be significantly slower to run.
- db
a connection to the taxadb database. See details.
Details
Most but not all authorities can match against both species level and
higher-level (or lower, e.g. subspecies or variety) taxonomic names.
The rank level is indicated by taxonRank column.
Most authorities include both known synonyms and accepted names in the
scientificName column, (with the status indicated by taxonomicStatus).
This is convenient, as users will typically not know if the names they
have are synonyms or accepted names, but will want to get the match to the
accepted name and accepted ID in either case.
See also
Other filter_by:
filter_by(),
filter_common(),
filter_id(),
filter_rank()
Examples
# \donttest{
sp <- c("Trochalopteron henrici gucenense",
"Trochalopteron elliotii")
filter_name(sp)
#> # A tibble: 0 × 15
#> # ℹ 15 variables: taxonID <chr>, scientificName <chr>, taxonRank <chr>,
#> # acceptedNameUsageID <chr>, taxonomicStatus <chr>, update_date <lgl>,
#> # kingdom <chr>, phylum <chr>, class <chr>, order <chr>, family <chr>,
#> # genus <chr>, specificEpithet <chr>, vernacularName <chr>,
#> # infraspecificEpithet <lgl>
# }