algaebase_search_df: Search algaebase for information about a list of...

In algaeClassify: Determine Phytoplankton Functional Groups Based on Functional Traits

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)

algaeClassify documentation built on Nov. 22, 2023, 1:08 a.m.