algaebase_search_df {algaeClassify}

Search algaebase for information about a list of phytoplankton names

Description

Search algaebase for information about a list of phytoplankton names

Usage

algaebase_search_df(
  df,
  apikey = NULL,
  handle = NULL,
  genus.only = FALSE,
  genus.name = "genus",
  species.name = "species",
  higher = TRUE,
  print.full.json = FALSE,
  long = FALSE,
  exact.matches.only = TRUE,
  api_file = NULL,
  sleep.time = 1
)

Arguments

df

data frame containing columns with genus and species names

apikey

valid key for algaebase API as character string

handle

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

genus.only

boolean: should searches be based solely on the genus name?

genus.name

name of data.frame column that contains genus names

species.name

name of data.frame column that contains species names

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)

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

sleep.time

delay between algaebase queries (in seconds). Should be at least 1 second if querying more than 10 names at once.

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: 
data(lakegeneva)
#example dataset with 50 rows

new.lakegeneva <- genus_species_extract(lakegeneva,'phyto_name')
lakegeneva.algaebase<-algaebase_search_df(new.lakegeneva[1:10,],higher=TRUE,long=TRUE)
head(lakegeneva.algaebase)
## End(Not run)