taxon_id_worms: Enrich and certify a list of species names by comparing with...

In oggioniale/ReLTER: An Interface for the eLTER Community

Enrich and certify a list of species names by comparing with WoRMS.

Description

This function provide tibble object with all the columns of input table of taxa plus new columns such as valid_name, valid_authority, valid_AphiaID, status, synonyms, LSID, url, matchType, nOfWormsRecords, wormsRecords obtained from Word Register of Marine Species WoRMS rest API.

Usage

taxon_id_worms(input, taxaColumn = 1, verbose = TRUE, refine = FALSE)

Arguments

input	A tibble. The table that contain the species names list to be checked.
taxaColumn	A numeric. The cardinal number of the column where species list is. Default is 1.
verbose	A logical. Whit this selection, the function returns a message with number of record(s) that don't match with any Worms names and the number of record(s) that match with more that one Worms name. Default is TRUE.
refine	A logical. With this selection, the function allows to refine the result(s) that match with more Worms records. By a interactive use of the terminal, the user can chose the result. Default is FALSE.

Value

The output of the function is a tibble with the columns provided and new columns such as: valid_name, valid_authority, valid_AphiaID, status, synonyms, LSID, url, matchType, nOfWormsRecords, wormsRecords obtained by Worms rest API. The function also return, if verbose is TRUE, the list of records that don't match with Worms name species.

Most of the labels of the columns are the terms of Darwin Core terms. The columns labels are annotate with the link (URI) of the Darwin Core terms as attributes of the tibble.

Author(s)

Alessandro Oggioni, phD (2021) [e-mail]

Paolo Tagliolato, phD (2021) [e-mail]

References

\insertRef

worrmsRReLTER

\insertRef

dplyrRReLTER

Examples

phytoplankton <- tibble::tibble(
   ID = c(1, 2, 3, 4, 5, 6, 7),
   species = c(
   "Asterionella formosa", "Chrysococcus sp.",
   "Cryptomonas rostrata", "Dinobryon divergens",
   "Mallomonas akrokomos", "Melosira varians",
   "Cryptomonas rostrata"
 )
)
table <- taxon_id_worms(
  input = phytoplankton,
  taxaColumn = 2,
  verbose = TRUE,
  refine = TRUE
)
table

# The annotated URIs of columns label are achieved by:
attributes(table)$uri

oggioniale/ReLTER documentation built on Jan. 4, 2024, 3:48 p.m.