Title: Accessing the Red List of Montane Tree Species of the Tropical Andes
Version: 0.0.0.1
Description: Access the 'Red List of Montane Tree Species of the Tropical Andes' Tejedor Garavito et al.(2014, ISBN:978-1-905164-60-8). This package allows users to search for globally threatened tree species within the andean montane forests, including cloud forests and seasonal (wet) forests above 1500 m a.s.l.
License: MIT + file LICENSE
Suggests: dplyr, forcats, ggplot2, janitor, knitr, rmarkdown, stringr, testthat, tibble, tidyr
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
Date: 2023-09-16
RoxygenNote: 7.2.3
Maintainer: Paul E. Santos Andrade <paulefrens@gmail.com>
URL: https://github.com/PaulESantos/mtsta
BugReports: https://github.com/PaulESantos/mtsta/issues
VignetteBuilder: knitr
Depends: R (≥ 2.10)
NeedsCompilation: no
Packaged: 2023-09-19 01:13:22 UTC; user
Author: Paul E. Santos Andrade ORCID iD [aut, cre]
Repository: CRAN
Date/Publication: 2023-09-19 14:20:02 UTC

mtsta_distribution: Distribution Data for Species in mtsta_tab

Description

This dataset contains distribution data for species included in A Regional Red List of Montane Tree Species of the Tropical Andes - 2014. It provides information on the current accepted names, distribution range, and taxonomic status for each species. The data is original diatribution data and the updated distribution information for the included species.

Usage

mtsta_distribution

Format

A tibble

accepted_name

Character vector with the current accepted name of the species.

distribution

Character vector indicating the distribution range of the species.

distribution_wcvp

Character vector indicating the distribution according to the World Checklist of Vascular Plants (WCVP).

taxonomic_status

Character vector indicating the taxonomic status of the species of the submitted name (e.g., "Accepted").

Details

The dataset contains information on the distribution of species in A Regional Red List of Montane Tree Species of the Tropical Andes - 2014. The distribution data includes the geographical range of each species, including countries where the species can be found.

Examples

# Load the mtsta_distribution dataset
data("mtsta_distribution")

Montane Tree Species of the Tropical Andes - Base Data

Description

This is the curated base data of montane tree species found in the Tropical Andes region. The data is stored as a tibble with 132 rows and 11 columns. Each row represents a species and contains information such as the species name, accepted name, accepted family, accepted genus, IUCN status, distribution, elevation range, assessor, description, and taxonomic status.

Usage

mtsta_tab

Format

A tibble with 132 rows and 11 columns.

Details

The columns in the base data tibble are as follows:

The base species list used in the mtsta package has been carefully reviewed and validated with the assistance of the Taxonomic Name Resolution Service (TNRS). By utilizing the TNRS, the base species list in the mtsta package guarantees accuracy and consistency in the representation of species names, enhancing the reliability of the package's functionalities.

Source

The data for this package was obtained from A Regional Red List of Montane Tree Species of the Tropical Andes - 2014.

See Also

Use search_mtsta() function to search and match species names using this base data.

Examples

data("mtsta_tab")

Search for Matching Species Names in the Red List of Montane Tree Species of the Tropical Andes

Description

This function searches for matching species names in the Red List of Montane Tree Species of the Tropical Andes (mtsta package) based on a provided list of species names. The function performs approximate matching using the Levenshtein distance algorithm to find similar names within a specified maximum distance.

Usage

search_mtsta(splist, max_distance = 0.1, ...)

Arguments

splist

A character vector containing the species names to be matched.

max_distance

The distance used is a generalized Levenshtein distance that indicates the total number of insertions, deletions, and substitutions allowed to match the two names. It can be expressed as an integer or as the fraction of the binomial name. A value between 0 and 1 will be treated as a percentage of the string length. A value greater than 1 will be treated as an absolute number of allowed changes. For example, a name with length 10, and a max_distance = 0.1, allow only one change (insertion, deletion, or substitution). A max_distance = 2, allows two changes.

...

Additional arguments (currently unused).

Value

A data frame with the following columns:

If no match is found, the name_matched column will contain "nill", and the other columns will be empty.

See Also

mtsta::mtsta_tab

Examples

# Assuming you have the mtsta package loaded with the necessary data
search_result <- search_mtsta(c("Aphelandra acantasa",
                                "Saurauia lehmani",
                                "Saurauia bullosaa",
                                "Schinus meyerii",
                                "Ilex colombiana",
                                "Ilex rimbachii",
                                "Ilex scopulorum"),
                              max_distance = 0.1)

Search Species Distribution of A Regional Red List of Montane Tree Species of the Tropical Andes

Description

This function searches the Montane Tree Species of the Tropical Andes distribution database for a list of submitted species names and returns their distribution information. The search allows for approximate string matching within a given maximum distance.

Usage

search_mtsta_distribution(splist, max_distance = 0.1, typedf = "main")

Arguments

splist

Character vector of submitted plant species names for which distribution data is to be searched.

max_distance

Numeric value representing the maximum allowed distance for approximate string matching. The default value is 0.1.

typedf

"main" return a selected columns in from mtsta_distribution "full" return all data

Details

The function uses approximate string matching with a maximum distance specified by the max_distance argument. It searches the mtsta distribution database for submitted species names that match the provided names within the given distance. The function then retrieves distribution information, including the accepted name, distribution region, unsure distribution (if available), distribution from the World Check-list of Vascular Plants (WCVP), taxonomic status, and the Levenshtein distance between submitted and matched species names.

Value

A data frame with the following columns:

name_submitted

Character vector with the submitted species names.

name_matched

Character vector with the matched species names in the database.

accepted_name

Character vector with the accepted names of the matched species.

distribution

Character vector with the distribution of the matched species.

unsure_distribution

Character vector with information about unsure distribution (if available).

distribution_wcvp

Character vector with the distribution from the World Check-list of Vascular Plants (WCVP) database for the matched species.

taxonomic_status

Character vector indicating the taxonomic status of the matched species.

distance

Numeric vector with the Levenshtein distance between submitted and matched species names.

See Also

mtsta_distribution

Examples

# Example usage of search_mtsta_distribution function
species_list <- c("Escallonia mirtilloydes", "Ilex rimbachii", "Saurauia lehmannii")
distribution_data <- search_mtsta_distribution(species_list, max_distance = 0.2)
print(distribution_data)