wormsbynames: GET AphiaRecordsByNames

In janhoo/worms: Retriving Aphia Information from World Register of Marine Species

Description

takes character vector with taxon names and retrives AphiaRecords from WoRMS

Usage

wormsbynames(taxon_names, ids = FALSE, verbose = TRUE, chunksize = 50,
  like = TRUE, marine_only = FALSE, match = FALSE,
  sleep_btw_chunks_in_sec = 0.1)

Arguments

taxon_names	character vector with names of taxa to look up.
ids	add column "id" and "name" with running id and search names
verbose	be verbose
chunksize	there is a limit to the number of taxa that can be looked up at once, so request are split up into chunks. This limit seems to be variable. 50 is very safe.
like	Returns also entries of match_type 'like'. Default=TRUE
marine_only	Limit to marine taxa. Default=TRUE
match	TRUE for fuzzy name matching (AphiaRecordsByMatchNames). FALSE for default matching (AphiaRecordsByNames). Default=FALSE
sleep_btw_chunks_in_sec	pause between requests

Details

This function will take a character vector with taxon names, retrive AphiaRecords (CC-BY) from www.marinespecies.org using the GET /AphiaRecordsByName/ScientificName Method described at http://www.marinespecies.org/rest/. Results will be output to a data.frame with each row being a record. For each name given, only the one AphiaRecord will be retrived. AphiaRecord with "accepted" status are preferred. If not present last entry will be taken which seems to result in best results.

Value

a data frame.

Examples

taxon_names <- c( "Westwodilla caecula" ,  "Abra alba", "Chaetozone cf. setosa",  "Algae" )
w <- wormsbynames(taxon_names)
## print unrecognized returns
failed_species <- rownames(w[is.na(w[,1]),])

## try again with fuzzy matching turned on
w <- wormsbynames(taxon_names, match=TRUE)

## this is how to load taxon_names from file
write.csv(taxon_names , file = "tax.csv", 
        row.names = FALSE,
        na = "")
## check it out, then load it
read.csv(file = "tax.csv",
        na = "", 
        stringsAsFactors = FALSE,
        col.names = FALSE)
## save results to file to inspect with, e.g. spreadsheet software
write.csv(w,file = "aphiainfo.csv", 
        na = "", 
        col.names = TRUE,
        row.names = TRUE)

        

janhoo/worms documentation built on May 20, 2019, 2:45 p.m.