rgnparser: Parse Scientific Names

Scott Chamberlain, Joel H. Nitta

2023-09-15

An R interface to gnparser (https://github.com/gnames/gnparser).

Installation

install.packages("rgnparser")
# OR
remotes::install_github("ropensci/rgnparser")

library(rgnparser)

Install gnparser

The command line tool written in Go, gnparser, is required to use this package.

Instructions for installation can be found at the gnparser repo (https://github.com/gnames/gnparser#installation).

gn_version()

Check the gnparser version:

gn_version()
#> $version
#> [1] "v1.7.1"
#> 
#> $build
#> [1] ""

gn_parse_tidy

Output a data.frame with more minimal information

x <- c("Quadrella steyermarkii (Standl.) Iltis &amp; Cornejo",
  "Parus major Linnaeus, 1788", "Helianthus annuus var. texanus")
gn_parse_tidy(x)
#> Rows: 3 Columns: 9
#> ── Column specification ────────────────────────────────────────
#> Delimiter: ","
#> chr (6): Id, Verbatim, CanonicalStem, CanonicalSimple, CanonicalFull, Authorship
#> dbl (3): Cardinality, Year, Quality
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> # A tibble: 3 × 9
#>   id                                   verbatim             cardinality canonicalstem canonicalsimple canonicalfull authorship  year quality
#>   <chr>                                <chr>                      <dbl> <chr>         <chr>           <chr>         <chr>      <dbl>   <dbl>
#> 1 fbd1b4fe-f8ed-5390-9cb1-e0f798691b1e Quadrella steyermar…           2 Quadrella st… Quadrella stey… Quadrella st… (Standl.)…    NA       4
#> 2 e4e1d462-d332-583d-97a1-09735712f04d Parus major Linnaeu…           2 Parus maior   Parus major     Parus major   Linnaeus …  1788       1
#> 3 e571bae4-9e3f-5481-9b53-f614d536066c Helianthus annuus v…           3 Helianthus a… Helianthus ann… Helianthus a… <NA>          NA       1

It’s pretty fast, thanks to gnparser of course

n <- 10000L
# get random scientific names from taxize
spp <- taxize::names_list(rank = "species", size = n)
timed <- system.time(gn_parse_tidy(spp))
#> Rows: 10000 Columns: 9
#> ── Column specification ────────────────────────────────────────
#> Delimiter: ","
#> chr (5): Id, Verbatim, CanonicalStem, CanonicalSimple, CanonicalFull
#> dbl (2): Cardinality, Quality
#> lgl (2): Authorship, Year
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
timed
#>    user  system elapsed 
#>   0.458   0.091   0.244

Just 0.244 sec for 10000 names

gn_parse

output a list of lists with more detailed information

x <- c("Quadrella steyermarkii (Standl.) Iltis &amp; Cornejo",
  "Parus major Linnaeus, 1788", "Helianthus annuus var. texanus")
gn_parse(x)
#> [[1]]
#> [[1]]$parsed
#> [1] TRUE
#> 
#> [[1]]$quality
#> [1] 4
#> 
#> [[1]]$qualityWarnings
#>   quality       warning
#> 1       4 Unparsed tail
#> 
#> [[1]]$verbatim
#> [1] "Quadrella steyermarkii (Standl.) Iltis &amp; Cornejo"
#> 
#> [[1]]$normalized
#> [1] "Quadrella steyermarkii (Standl.) Iltis"
#> 
#> [[1]]$canonical
#> [[1]]$canonical$stemmed
#> [1] "Quadrella steyermark"
#> 
#> [[1]]$canonical$simple
#> [1] "Quadrella steyermarkii"
#> 
#> [[1]]$canonical$full
#> [1] "Quadrella steyermarkii"
#> 
#> 
#> [[1]]$cardinality
#> [1] 2
#> 
#> [[1]]$authorship
#> [[1]]$authorship$verbatim
#> [1] "(Standl.) Iltis"
#> 
#> [[1]]$authorship$normalized
#> [1] "(Standl.) Iltis"
#> 
#> [[1]]$authorship$authors
#> [1] "Standl." "Iltis"  
#> 
#> 
#> [[1]]$tail
#> [1] " &amp; Cornejo"
#> 
#> [[1]]$id
#> [1] "fbd1b4fe-f8ed-5390-9cb1-e0f798691b1e"
#> 
#> [[1]]$parserVersion
#> [1] "v1.7.1"
#> 
#> 
#> [[2]]
#> [[2]]$parsed
#> [1] TRUE
#> 
#> [[2]]$quality
#> [1] 1
#> 
#> [[2]]$verbatim
#> [1] "Parus major Linnaeus, 1788"
#> 
#> [[2]]$normalized
#> [1] "Parus major Linnaeus 1788"
#> 
#> [[2]]$canonical
#> [[2]]$canonical$stemmed
#> [1] "Parus maior"
#> 
#> [[2]]$canonical$simple
#> [1] "Parus major"
#> 
#> [[2]]$canonical$full
#> [1] "Parus major"
#> 
#> 
#> [[2]]$cardinality
#> [1] 2
#> 
#> [[2]]$authorship
#> [[2]]$authorship$verbatim
#> [1] "Linnaeus, 1788"
#> 
#> [[2]]$authorship$normalized
#> [1] "Linnaeus 1788"
#> 
#> [[2]]$authorship$year
#> [1] "1788"
#> 
#> [[2]]$authorship$authors
#> [1] "Linnaeus"
#> 
#> 
#> [[2]]$id
#> [1] "e4e1d462-d332-583d-97a1-09735712f04d"
#> 
#> [[2]]$parserVersion
#> [1] "v1.7.1"
#> 
#> 
#> [[3]]
#> [[3]]$parsed
#> [1] TRUE
#> 
#> [[3]]$quality
#> [1] 1
#> 
#> [[3]]$verbatim
#> [1] "Helianthus annuus var. texanus"
#> 
#> [[3]]$normalized
#> [1] "Helianthus annuus var. texanus"
#> 
#> [[3]]$canonical
#> [[3]]$canonical$stemmed
#> [1] "Helianthus annu texan"
#> 
#> [[3]]$canonical$simple
#> [1] "Helianthus annuus texanus"
#> 
#> [[3]]$canonical$full
#> [1] "Helianthus annuus var. texanus"
#> 
#> 
#> [[3]]$cardinality
#> [1] 3
#> 
#> [[3]]$id
#> [1] "e571bae4-9e3f-5481-9b53-f614d536066c"
#> 
#> [[3]]$parserVersion
#> [1] "v1.7.1"