Get all members (descendants) of a given rank level
Usage
filter_rank(
name,
rank,
provider = getOption("taxadb_default_provider", "itis"),
version = latest_version(),
collect = TRUE,
ignore_case = TRUE,
db = td_connect()
)Arguments
- name
taxonomic scientific name (e.g. "Aves")
- rank
taxonomic rank name. (e.g. "class")
- 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.
See also
Other filter_by:
filter_by(),
filter_common(),
filter_id(),
filter_name()
Examples
# \donttest{
# \dontshow{
## All examples use a temporary directory
Sys.setenv(TAXADB_HOME=file.path(tempdir(), "taxadb"))
options("taxadb_default_provider"="itis_test")
# }
filter_rank("Aves", "class")
#> # 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>
# }