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Look up taxonomic information by common name

Source: R/filter_common.R
filter_common.Rd

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 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.

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

# \donttest{
  # \dontshow{
   ## All examples use a temporary directory
   options("taxadb_default_provider"="itis_test")
   Sys.setenv(TAXADB_HOME=file.path(tempdir(), "taxadb"))
  # }

filter_common("Pied Tamarin")
#> # A tibble: 2 × 16
#>   vernacularName language update_date acceptedNameUsageID taxonID scientificName
#>   <chr>          <chr>    <date>      <chr>               <chr>   <chr>         
#> 1 Pied Tamarin   English  2014-06-26  ITIS:572923         ITIS:1… Midas bicolor 
#> 2 Pied Tamarin   English  2014-06-26  ITIS:572923         ITIS:5… Saguinus bico…
#> # ℹ 10 more variables: taxonRank <chr>, taxonomicStatus <chr>, kingdom <chr>,
#> #   phylum <chr>, class <chr>, order <chr>, family <chr>, genus <chr>,
#> #   specificEpithet <chr>, infraspecificEpithet <lgl>

# }

  # \dontshow{
   ## All examples use a temporary directory
   Sys.unsetenv("TAXADB_HOME")
   options("taxadb_default_provider" = NULL)
  # }