spp_list_algaebase {algaeClassify}R Documentation

Wrapper for applying algae_search function to a data.frame that contains phytoplankton species

Description

Wrapper for applying algae_search function to a data.frame that contains phytoplankton species

Usage

spp_list_algaebase(phyto.df, phyto.name = 1, lakename = "",
  long = FALSE, write = FALSE)

Arguments

phyto.df

data.frame containing a character column with binomial names

phyto.name

Name or number of column that contains binomial names

lakename

Character string for naming output files

long

TRUE/FALSE: should higher taxonomy (Kingdom:Family) be included in output?

write

TRUE/FALSE: should output be written as .csv file?

Value

A data.frame with the following fields: orig.name (submitted name), match.name (best match), genus and species (from the match.name), exact.match (1 indicates whether there was a perfect match for orig.name. 0 otherwise), accepted (1 if the orig.name currently accepted, 0 otherwise), synonyms (currently accepted synonyms, if any. For genus-only search, returns genera associated with species formerly classified with the orig.name genus) Empire,Kingdom,Phylum,Class,Order,Family: character strings with current higher taxonomy associated with match.name

See Also

http://www.algaebase.org for up-to-date phytoplankton taxonomy, https://powellcenter.usgs.gov/geisha for project information. Algaebase should be cited separately in any publications using this function: <doi:10.7872/crya.v35.iss2.2014.105>

Examples

data(lakegeneva)
lakegeneva=lakegeneva[1,] ##use 1 row for testing
lakegeneva.algaebase<-
spp_list_algaebase(lakegeneva,phyto.name='phyto_name',long=FALSE,write=FALSE)


[Package algaeClassify version 1.2.0 Index]