taxonomy.tools

taxonomy.tools is an R package to help working with taxonomic data.

By now, it builds upon rWCVP package to match plant taxonomic names against the World Checklist of Vascular Plants (WCVP).

Installation

You can install the development version of taxonomy.tools from R-universe:

install.packages("taxonomy.tools", repos = c("https://pakillo.r-universe.dev", "https://cloud.r-project.org"))

or from GitHub with:

# install.packages("pak")
pak::pak("Pakillo/taxonomy.tools")

Usage

library(taxonomy.tools)

Matching plant taxonomic names against WCVP

wcvp_match_names_parallel runs rWCVP::wcvp_match_names in parallel to speed up matching with large taxonomic lists.

df <- data.frame(taxon = c("Laurus nobilis", "Laurus nobilis", "Laurus nobili"),
                 author = c(NA, "L.", NA))

out <- wcvp_match_names_parallel(df, 
                                 name_col = "taxon", 
                                 author_col = "author", 
                                 cores = 3)

dplyr::glimpse(out)
#> Rows: 3
#> Columns: 16
#> $ taxon                     <chr> "Laurus nobilis", "Laurus nobilis", "Laurus …
#> $ author                    <chr> NA, "L.", NA
#> $ match_type                <chr> "Exact (without author)", "Exact (with autho…
#> $ multiple_matches          <lgl> FALSE, FALSE, FALSE
#> $ match_similarity          <dbl> 1.000, 1.000, 0.929
#> $ match_edit_distance       <dbl> 0, 0, 1
#> $ wcvp_id                   <dbl> 2349094, 2349094, 2349094
#> $ wcvp_name                 <chr> "Laurus nobilis", "Laurus nobilis", "Laurus …
#> $ wcvp_authors              <chr> "L.", "L.", "L."
#> $ wcvp_rank                 <chr> "Species", "Species", "Species"
#> $ wcvp_status               <chr> "Accepted", "Accepted", "Accepted"
#> $ wcvp_homotypic            <lgl> NA, NA, NA
#> $ wcvp_ipni_id              <chr> "465049-1", "465049-1", "465049-1"
#> $ wcvp_accepted_id          <dbl> 2349094, 2349094, 2349094
#> $ wcvp_author_edit_distance <dbl> NA, 0, NA
#> $ wcvp_author_lcs           <int> -1, 2, -1

Citation

citation("taxonomy.tools")
#> To cite package 'taxonomy.tools' in publications use:
#> 
#>   Rodriguez-Sanchez F (2024). _taxonomy.tools: Tools to Work with
#>   Taxonomic Data_. <https://github.com/Pakillo/taxonomy.tools>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {taxonomy.tools: Tools to Work with Taxonomic Data},
#>     author = {Francisco Rodriguez-Sanchez},
#>     year = {2024},
#>     url = {https://github.com/Pakillo/taxonomy.tools},
#>   }