wormsaccepted: Constructs "accepted_id" column which contains the "AphiaID"...

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

Description

takes data.frame as output by wormsbynames , wormsbymatchnames, or wormsbyid and add field "accepted_id" wich contains the "AphiaID" of the respective "accepted" taxon

Usage

wormsaccepted(x, verbose = TRUE, n_iter = 10)

Arguments

x	data.frame
verbose	be verbose
n_iter	maximum search depth. Usually 3 is sufficient. Safety feature for breaking the while loop

Details

This function helps updating you taxon information and eliminates ambiguity because the valid AphiaID is nor neccessary the AphiaID of an accepted taxon. You should run wormsconsolidate bevorhand to enshure all "accepted" taxons are present.

Value

a data frame.

Examples

## start with IDs that are no longer up to date 
# get the Aphia information
u<-wormsbyid(c(424548,340537))

#recursively retrive information on the taxa they refer to
v<-wormsconsolidate(u)

# what are the currently correct "accepted" taxa? Answer: "accepted_id".
w<-wormsaccepted(v)
w[,c("scientificname","AphiaID","status","valid_AphiaID","valid_name","accepted_id")]

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