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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.
You can install the mtsta package from GitHub using:
pak::pak("PaulESantos/mtsta")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>
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>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.
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.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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