split out a scientific input column to pieces — split

This function attempts to split a scientific name into it's component pieces. Given an input scientific, or scientific with scientific authorities and infraspecies this function will parse them into the columns used in the BarnebyLives pipeline.

Usage

split_scientificName(x, sciName_col, overwrite)

Arguments

x: Dataframe with collection information.
sciName_col: Character. Column containing the data to parse
overwrite: Boolean. Whether to overwrite the original input columns, or simply append the spell checked columns.

Examples

library(BarnebyLives)
ce <- collection_examples
ce <- data.frame(
  Collection_number = ce$Collection_number[sample(1:nrow(ce), size = 100, replace = FALSE)],
  Binomial = c(ce$Full_name, ce$Name_authority)[sample(1:nrow(ce)*2, size = 100, replace = FALSE)],
  Binomial_authority = ce$Binomial_authority[sample(1:nrow(ce), size = 100, replace = FALSE)]
) # extra columns to challenge name search - values are meaningless

split_scientificName(ce)|> head()
#> `sciName_col` argument not supplied, using: Binomial
#>   Collection_number
#> 1              2859
#> 2              2933
#> 3              2927
#> 4              2834
#> 5              2901
#> 6              2863
#>                                                           x...sciName_col.
#> 1                                                Crepis occidentalis Nutt.
#> 2                                                     Ipomopsis polycladon
#> 3                                                            Allium parvum
#> 4                                                         Allium nevadense
#> 5 Bromus sitchensis Trin. var. marginatus (Piper) Otting and R.E. Brainerd
#> 6                                                      Lupinus brevicaulis
#>       Genus      Epithet        Binomial_authority       Name_authority
#> 1    Crepis occidentalis Crepis occidentalis Nutt.                Nutt.
#> 2 Ipomopsis   polycladon      Ipomopsis polycladon Ipomopsis polycladon
#> 3    Allium       parvum             Allium parvum        Allium parvum
#> 4    Allium    nevadense          Allium nevadense     Allium nevadense
#> 5    Bromus   sitchensis   Bromus sitchensis Trin.                Trin.
#> 6   Lupinus  brevicaulis       Lupinus brevicaulis  Lupinus brevicaulis
#>   Infraspecific_rank Infraspecies Infraspecific_authority
#> 1               <NA>         <NA>                    <NA>
#> 2               <NA>         <NA>                    <NA>
#> 3               <NA>         <NA>                    <NA>
#> 4               <NA>         <NA>                    <NA>
#> 5               <NA>         <NA>                    <NA>
#> 6               <NA>         <NA>                    <NA>
split_scientificName(ce, sciName_col = 'Binomial') |> head()
#>   Collection_number
#> 1              2859
#> 2              2933
#> 3              2927
#> 4              2834
#> 5              2901
#> 6              2863
#>                                                           x...sciName_col.
#> 1                                                Crepis occidentalis Nutt.
#> 2                                                     Ipomopsis polycladon
#> 3                                                            Allium parvum
#> 4                                                         Allium nevadense
#> 5 Bromus sitchensis Trin. var. marginatus (Piper) Otting and R.E. Brainerd
#> 6                                                      Lupinus brevicaulis
#>       Genus      Epithet        Binomial_authority       Name_authority
#> 1    Crepis occidentalis Crepis occidentalis Nutt.                Nutt.
#> 2 Ipomopsis   polycladon      Ipomopsis polycladon Ipomopsis polycladon
#> 3    Allium       parvum             Allium parvum        Allium parvum
#> 4    Allium    nevadense          Allium nevadense     Allium nevadense
#> 5    Bromus   sitchensis   Bromus sitchensis Trin.                Trin.
#> 6   Lupinus  brevicaulis       Lupinus brevicaulis  Lupinus brevicaulis
#>   Infraspecific_rank Infraspecies Infraspecific_authority
#> 1               <NA>         <NA>                    <NA>
#> 2               <NA>         <NA>                    <NA>
#> 3               <NA>         <NA>                    <NA>
#> 4               <NA>         <NA>                    <NA>
#> 5               <NA>         <NA>                    <NA>
#> 6               <NA>         <NA>                    <NA>