taxadb (version 0.1.0)

taxa_tbl: Return a reference to a given table in the taxadb database

Description

Return a reference to a given table in the taxadb database

Usage

taxa_tbl(
  provider = getOption("taxadb_default_provider", "itis"),
  schema = c("dwc", "common"),
  version = latest_version(),
  db = td_connect()
)

Arguments

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.

schema

One of "dwc" (for Darwin Core data) or "common" (for the Common names table.)

version

Which version of the taxadb provider database should we use? defaults to latest. See available_versions for details.

db

a connection to the taxadb database. See details.

Examples

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

  #Clean a list of messy common names
  names <- clean_names(c("Steller's jay", "coopers Hawk"),
                binomial_only = FALSE, remove_sp = FALSE, remove_punc = TRUE)

  #Get cleaned common names from a provider and
  # search for cleaned names in that table
  taxa_tbl("itis", "common") %>%
  mutate_db(clean_names, "vernacularName", "vernacularNameClean",
            binomial_only = FALSE, remove_sp = FALSE, remove_punc = TRUE) %>%
  filter(vernacularNameClean %in% names)



# }