Working with different partners/institutes/researchers results in a diversity of taxonomic names to define species. This hardens comparison amongst datasets, as in many occasions, aggregation is aimed for or filtering on specific species. By translating all species names to a common taxonomic backbone (ensuring unique ID’s for each species name), this can be done. The gbif_species_name_match
function supports matching with the GBIF taxonomic backbone.
This function provides the functionality to add the species information from the GBIF backbone to any data table (data.frame
) by requesting this information via the GBIF API. For each match, the corresponding accepted name is looked for. Nevertheless there will always be errors and control is still required!
The gbif_species_name_match
function extends the matching function provided by Rgbif to be compatible with a data.frame
data structure.
Loading the functionality can be done by loading the inborutils
package:
library(inborutils)
Consider the example data set species_example
:
knitr::kable(species_example)
scientificName | kingdom | euConcernStatus |
---|---|---|
Alopochen aegyptiaca | Animalia | under consideration |
Cotoneaster ganghobaensis | Plantae | |
Cotoneaster hylmoei | Plantae |
To add the species information, using the scientificName
column, and the default fields:
my_data_update <- gbif_species_name_match(species_example,
name_col = "scientificName")
## [1] "All column names present"
knitr::kable(my_data_update)
usageKey | scientificName | rank | order | matchType | phylum | kingdom | genus | class | confidence | synonym | status | family | scientificName1 | kingdom1 | euConcernStatus |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2498252 | Alopochen aegyptiaca (Linnaeus, 1766) | SPECIES | Anseriformes | EXACT | Chordata | Animalia | Alopochen | Aves | 98 | FALSE | ACCEPTED | Anatidae | Alopochen aegyptiaca | Animalia | under consideration |
3025989 | Cotoneaster ganghobaensis J. Fryer & B. Hylmö | SPECIES | Rosales | EXACT | Tracheophyta | Plantae | Cotoneaster | Magnoliopsida | 98 | TRUE | SYNONYM | Rosaceae | Cotoneaster ganghobaensis | Plantae | |
3025758 | Cotoneaster hylmoei K.E. Flinck & J. Fryer | SPECIES | Rosales | EXACT | Tracheophyta | Plantae | Cotoneaster | Magnoliopsida | 98 | TRUE | SYNONYM | Rosaceae | Cotoneaster hylmoei | Plantae |
When not satisfied by the default fields provided ´(‘usageKey’,‘scientificName’,‘rank’,‘order’,‘matchType’,‘phylum’, ‘kingdom’,‘genus’, ‘class’,‘confidence’, ‘synonym’, ‘status’,‘family’)´, you can alter these by the gbif_terms
argument, for example:
gbif_terms_to_use <- c('scientificName', 'order')
my_data_update <- gbif_species_name_match(species_example,
name_col = "scientificName" ,
gbif_terms = gbif_terms_to_use)
## [1] "All column names present"
knitr::kable(my_data_update)
scientificName | order | scientificName1 | kingdom | euConcernStatus |
---|---|---|---|---|
Alopochen aegyptiaca (Linnaeus, 1766) | Anseriformes | Alopochen aegyptiaca | Animalia | under consideration |
Cotoneaster ganghobaensis J. Fryer & B. Hylmö | Rosales | Cotoneaster ganghobaensis | Plantae | |
Cotoneaster hylmoei K.E. Flinck & J. Fryer | Rosales | Cotoneaster hylmoei | Plantae |