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                  x...sciName_col.        Genus    Epithet
#> 1              2858              Cordylanthus ramosus Cordylanthus    ramosus
#> 2              2829          Scutellaria nana A. Gray  Scutellaria       nana
#> 3              2861                Astragalus filipes   Astragalus    filipes
#> 4              2859              Sphaeralcea munroana  Sphaeralcea   munroana
#> 5              2928                    Diplacus nanus     Diplacus      nanus
#> 6              2834 Bromus sitchensis var. marginatus       Bromus sitchensis
#>         Binomial_authority       Name_authority Infraspecific_rank Infraspecies
#> 1     Cordylanthus ramosus Cordylanthus ramosus               <NA>         <NA>
#> 2 Scutellaria nana A. Gray              A. Gray               <NA>         <NA>
#> 3       Astragalus filipes   Astragalus filipes               <NA>         <NA>
#> 4     Sphaeralcea munroana Sphaeralcea munroana               <NA>         <NA>
#> 5           Diplacus nanus       Diplacus nanus               <NA>         <NA>
#> 6        Bromus sitchensis    Bromus sitchensis               <NA>         <NA>
#>   Infraspecific_authority
#> 1                    <NA>
#> 2                    <NA>
#> 3                    <NA>
#> 4                    <NA>
#> 5                    <NA>
#> 6                    <NA>
split_scientificName(ce, sciName_col = 'Binomial') |> head()
#>   Collection_number                  x...sciName_col.        Genus    Epithet
#> 1              2858              Cordylanthus ramosus Cordylanthus    ramosus
#> 2              2829          Scutellaria nana A. Gray  Scutellaria       nana
#> 3              2861                Astragalus filipes   Astragalus    filipes
#> 4              2859              Sphaeralcea munroana  Sphaeralcea   munroana
#> 5              2928                    Diplacus nanus     Diplacus      nanus
#> 6              2834 Bromus sitchensis var. marginatus       Bromus sitchensis
#>         Binomial_authority       Name_authority Infraspecific_rank Infraspecies
#> 1     Cordylanthus ramosus Cordylanthus ramosus               <NA>         <NA>
#> 2 Scutellaria nana A. Gray              A. Gray               <NA>         <NA>
#> 3       Astragalus filipes   Astragalus filipes               <NA>         <NA>
#> 4     Sphaeralcea munroana Sphaeralcea munroana               <NA>         <NA>
#> 5           Diplacus nanus       Diplacus nanus               <NA>         <NA>
#> 6        Bromus sitchensis    Bromus sitchensis               <NA>         <NA>
#>   Infraspecific_authority
#> 1                    <NA>
#> 2                    <NA>
#> 3                    <NA>
#> 4                    <NA>
#> 5                    <NA>
#> 6                    <NA>