https://github.com/pakillo/taxonomy.tools
R package to work with taxonomic data
https://github.com/pakillo/taxonomy.tools
Last synced: 7 months ago
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R package to work with taxonomic data
- Host: GitHub
- URL: https://github.com/pakillo/taxonomy.tools
- Owner: Pakillo
- License: gpl-3.0
- Created: 2024-12-17T22:51:27.000Z (over 1 year ago)
- Default Branch: master
- Last Pushed: 2024-12-28T23:57:07.000Z (over 1 year ago)
- Last Synced: 2025-10-09T04:06:21.742Z (8 months ago)
- Language: R
- Homepage: https://pakillo.github.io/taxonomy.tools/
- Size: 1.06 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE.md
Awesome Lists containing this project
README
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# taxonomy.tools
[](https://github.com/Pakillo/taxonomy.tools/actions/workflows/R-CMD-check.yaml)
`r badger::badge_repostatus("Active")`
taxonomy.tools is an R package to help working with taxonomic data.
By now, it builds upon [rWCVP package](https://matildabrown.github.io/rWCVP) to match plant taxonomic names against the [World Checklist of Vascular Plants (WCVP)](https://powo.science.kew.org/about-wcvp).
## Installation
You can install the development version of taxonomy.tools from [R-universe](https://pakillo.r-universe.dev/taxonomy.tools):
``` r
install.packages("taxonomy.tools", repos = c("https://pakillo.r-universe.dev", "https://cloud.r-project.org"))
```
or from [GitHub](https://github.com/) with:
``` r
# install.packages("pak")
pak::pak("Pakillo/taxonomy.tools")
```
## Usage
```{r}
library(taxonomy.tools)
```
### Matching plant taxonomic names against WCVP
[wcvp_match_names_parallel](https://pakillo.github.io/taxonomy.tools/reference/wcvp_match_names_parallel.html) runs [rWCVP::wcvp_match_names](https://matildabrown.github.io/rWCVP/reference/wcvp_match_names.html) in parallel to speed up matching with large taxonomic lists.
```{r message=FALSE}
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)
```
```{r }
dplyr::glimpse(out)
```
## Citation
```{r}
citation("taxonomy.tools")
```