Overview
The mtsta package provides a powerful tool for searching and matching species names in the montane forests of the Tropical Andes region. It allows users to input a list of species names and find the closest matching names from a curated base data of montane tree species in the region. The matching process takes into account both exact matches and fuzzy matches based on a user-defined maximum distance threshold.
Installation
You can install the mtsta package from GitHub using the devtools library:
pak::pak("PaulESantos/mtsta")Usage
To use the mtsta package, simply load it and call the search_mtsta() function with your list of species names as the input:
library(mtsta)
# Example species list
splist <- c("Aphelandra acantasa",
"Saurauia lehmani",
"Saurauia bullosaa",
"Schinus meyerii",
"Ilex colombiana",
"Ilex rimbachii",
"Ilex scopulorum")
mtsta::search_mtsta(splist, max_distance = 0.1) |>
dplyr::select(name_submitted, name_matched, accepted_name, accepted_family,
taxonomic_status, distance) |>
tibble::as_tibble()
#> # A tibble: 7 × 6
#> name_submitted name_matched accepted_name accepted_family taxonomic_status
#> <chr> <chr> <chr> <chr> <chr>
#> 1 Aphelandra acanta… nill nill nill nill
#> 2 Saurauia lehmani Saurauia le… Saurauia leh… Actinidiaceae Accepted
#> 3 Saurauia bullosaa Saurauia bu… Saurauia bul… Actinidiaceae Accepted
#> 4 Schinus meyerii Schinus mey… Schinus meye… Anacardiaceae Accepted
#> 5 Ilex colombiana Ilex colomb… Ilex colombi… Aquifoliaceae Accepted
#> 6 Ilex rimbachii Ilex rimbac… Ilex rimbach… Aquifoliaceae Accepted
#> 7 Ilex scopulorum Ilex scopul… Ilex scopulo… Aquifoliaceae Accepted
#> # ℹ 1 more variable: distance <chr>- Species distribution
mtsta::search_mtsta_distribution(splist = splist) |>
tibble::as_tibble()
#> # A tibble: 7 × 6
#> name_submitted name_matched accepted_name distribution_wcvp taxonomic_status
#> <chr> <chr> <chr> <chr> <chr>
#> 1 Aphelandra acan… nill nill nill nill
#> 2 Saurauia lehmani Saurauia le… Saurauia leh… Colombia - Ecuad… Accepted
#> 3 Saurauia bullos… Saurauia bu… Saurauia bul… Colombia - Ecuad… Accepted
#> 4 Schinus meyerii Schinus mey… Schinus meye… Argentina - Boli… Accepted
#> 5 Ilex colombiana Ilex colomb… Ilex colombi… Colombia - Ecuad… Accepted
#> 6 Ilex rimbachii Ilex rimbac… Ilex rimbach… Ecuador - Peru Accepted
#> 7 Ilex scopulorum Ilex scopul… Ilex scopulo… Ecuador - Peru -… Accepted
#> # ℹ 1 more variable: distance <chr>Description
The search_mtsta() and search_mtsta_distribution() functions takes a list of species names (splist) and a maximum distance value (max_distance) as input. It performs fuzzy matching and exact matching to find the closest matching species names in the curated base data of montane tree species in the Tropical Andes region. The output is a data frame with data for the submitted species name. If no match is found within the specified maximum distance, the result will show "nill" for the matched species name.
Acknowledgments
A team of Regional Red List of Montane Tree Species of the Tropical Andes (2014). The research was carried out by Natalia Tejedor Garavito from Bournemouth University in collaboration with BGCI and over 20 regional experts. Source data here
The curated base data used in this package was reviewed and validated using the Taxonomic Name Resolution Service TNRS. The TNRS is a computer-assisted tool for standardizing plant scientific names, correcting spelling errors, and resolving out-of-date names to the current accepted names. We are grateful for the contribution of the TNRS in validating the accuracy of the base data.