algaebase_species_search {algaeClassify}

Retrieve taxonomic information from the algaebase online database (www.algaebase.org) based on a user-specified genus and species name . This function requires a valid API key for algaebase.

Description

Retrieve taxonomic information from the algaebase online database (www.algaebase.org) based on a user-specified genus and species name . This function requires a valid API key for algaebase.

Usage

algaebase_species_search(
  genus,
  species,
  apikey = NULL,
  handle = NULL,
  higher = TRUE,
  print.full.json = FALSE,
  newest.only = TRUE,
  long = FALSE,
  exact.matches.only = TRUE,
  api_file = NULL
)

Arguments

genus

genus name as character string

species

species name as character string

apikey

valid key for algaebase API as character string

handle

curl handle with API key. Will be created if not present.

higher

boolean should higher taxonomy be included in output?

print.full.json

boolean returns raw json output if TRUE. Default is FALSE (return R data frame)

newest.only

boolean should results be limited to the most recent matching entry in algaebase?

long

boolean return long output including full species name and authorship, and entry date from algaebase.

exact.matches.only

boolean should results be limited to exact matches?

api_file

path to text file containing a valid API key

Value

data frame that may include: accepted.name (currently accepted synonym if different from input name), input.name (name supplied by user), input.match (1 if exact match, else 0), currently.accepted (1=TRUE/0=FALSE), genus.only (1=genus search/0=genus+species search),higher taxonomy (kingdom,phylum,class,order,family), genus, species (always NA for genus search), infraspecies name (always NA for genus search), long.name (includes author and date if given), taxonomic.status (currently accepted, synonym, or unverified), taxon.rank (taxonomic rank of accepted name (genus, species, infraspecies), mod.date (date when entry was last modified in algaebase).

Examples

## Not run: algaebase_species_search("Anabaena flos-aquae") #not run