inst/vign/taxonomic_names.md

Taxonomic Names

You have probably, or will, run into problems with taxonomic names. For example, you may think you know how a taxonomic name is spelled, but then GBIF will not agree with you. Or, perhaps GBIF will have multiple versions of the taxon, spelled in slightly different ways. Or, the version of the name that they think is the right one does not match what yo think is the right one.

This isn't really anyone's fault. It's a result of there not being one accepted taxonomic source of truth across the globe. There are many different taxonomic databases. GBIF makes their own backbone taxonomy that they use as a source of internal truth for taxonomic names. The accepted names in the backbone taxonomy match those in the database of occurrences - so do try to figure out what backbone taxonomy version of the name you want.

Another source of problems stems from the fact that names are constantly changing. Sometimes epithets change, sometimes generic names, and sometimes higher names like family or tribe. These changes can take a while to work their way in to GBIF's data.

The following are some examples of confusing name bits. We'll update these if GBIF's name's change. The difference between each pair of names is highlighted in bold.

Load rgbif

library("rgbif")

Helper function

To reduce code duplication, we'll use a little helper function to make a call to name_backbone() for each input name, then rbind them together:

name_rbind <- function(..., rank = "species") {
 df <- data.frame(do.call(rbind, lapply(list(...), name_backbone, rank = rank)))
 df[, c('usageKey', 'scientificName', 'canonicalName', 'rank',
       'status', 'confidence', 'matchType', 'synonym')]
}

And another function to get the taxonomic data provider

taxon_provider <- function(x) {
  tt <- name_usage(key = x)$data
  datasets(uuid = tt$constituentKey)$data$title
}

We use taxon_provider() below to get the taxonomy provider in the bulleted list of details for each taxon (even though you don't see it called, we use it, but the code isn't shown :)).

Pinus sylvestris vs. P. silvestris

(c1 <- name_rbind("Pinus sylvestris", "Pinus silvestris"))
#>   usageKey      scientificName    canonicalName    rank   status
#> 1  5285637 Pinus sylvestris L. Pinus sylvestris SPECIES ACCEPTED
#> 2  5285637 Pinus sylvestris L. Pinus sylvestris SPECIES ACCEPTED
#>   confidence matchType synonym
#> 1         97     EXACT   FALSE
#> 2         94     FUZZY   FALSE

Macrozamia platyrachis vs. M. platyrhachis

(c2 <- name_rbind("Macrozamia platyrachis", "Macrozamia platyrhachis"))
#>   usageKey                     scientificName           canonicalName
#> 1  2683551 Macrozamia platyrhachis F.M.Bailey Macrozamia platyrhachis
#> 2  2683551 Macrozamia platyrhachis F.M.Bailey Macrozamia platyrhachis
#>      rank   status confidence matchType synonym
#> 1 SPECIES ACCEPTED         96     FUZZY   FALSE
#> 2 SPECIES ACCEPTED         98     EXACT   FALSE

Cycas circinalis vs. C. circinnalis

(c3 <- name_rbind("Cycas circinalis", "Cycas circinnalis"))
#>   usageKey      scientificName    canonicalName    rank   status
#> 1  2683264 Cycas circinalis L. Cycas circinalis SPECIES ACCEPTED
#> 2  2683264 Cycas circinalis L. Cycas circinalis SPECIES ACCEPTED
#>   confidence matchType synonym
#> 1         98     EXACT   FALSE
#> 2         95     FUZZY   FALSE

Isolona perrieri vs. I. perrierii

(c4 <- name_rbind("Isolona perrieri", "Isolona perrierii"))
#>   usageKey          scientificName     canonicalName    rank   status
#> 1  6308376 Isolona perrierii Diels Isolona perrierii SPECIES ACCEPTED
#> 2  6308376 Isolona perrierii Diels Isolona perrierii SPECIES ACCEPTED
#>   confidence matchType synonym
#> 1         96     FUZZY   FALSE
#> 2         98     EXACT   FALSE

Wiesneria vs. Wisneria

(c5 <- name_rbind("Wiesneria", "Wisneria", rank = "genus"))
#>   usageKey                                                 scientificName
#> 1  2864604                                              Wiesneria Micheli
#> 2  7327444 Wisneria Micheli in Alph. de Candolle & A.C. de Candolle, 1881
#>   canonicalName  rank   status confidence matchType synonym
#> 1     Wiesneria GENUS ACCEPTED         96     EXACT   FALSE
#> 2      Wisneria GENUS ACCEPTED         96     EXACT   FALSE

The take away messages from this vignette



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rgbif documentation built on Nov. 17, 2017, 8:14 a.m.