taxadb (version 0.1.0)

filter_common: Look up taxonomic information by common name

Description

Look up taxonomic information by common name

Usage

filter_common(
  name,
  provider = getOption("taxadb_default_provider", "itis"),
  version = latest_version(),
  collect = TRUE,
  ignore_case = TRUE,
  db = td_connect()
)

Arguments

name

a character vector of common (vernacular English) names, e.g. "Humans"

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 available_versions 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? default is TRUE.

db

a connection to the taxadb database. See details.

Value

a data.frame in the Darwin Core tabular format containing the matching taxonomic entities.

See Also

Other filter_by: filter_by(), filter_id(), filter_name(), filter_rank()

Examples

# NOT RUN {
     ## All examples use a temporary directory
   Sys.setenv(TAXADB_HOME=tempdir())
  

filter_common("Angolan Giraffe")

# }
# NOT RUN {
# }