| Title: | Accessing the Red List of Montane Tree Species of the TropicalAndes |
| 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 [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 RegionalRed List of Montane Tree Species of the Tropical Andes - 2014.It provides information on the current accepted names, distribution range, andtaxonomic status for each species. The data is original diatribution data and theupdated distribution information for the included species.
Usage
mtsta_distributionFormat
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 WorldChecklist 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 RegionalRed List of Montane Tree Species of the Tropical Andes - 2014.The distribution data includes the geographical range of each species, including countries wherethe species can be found.
Examples
# Load the mtsta_distribution datasetdata("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_tabFormat
A tibble with 132 rows and 11 columns.
Details
The columns in the base data tibble are as follows:
species_name: The scientific name of the species.accepted_name: The currently accepted name for the species.accepted_family: The family to which the species belongs.accepted_genus: The genus to which the species belongs.taxonomic_status: The taxonomic status of the species.iucn: The conservation status of the species according to the IUCN Red List Categories.distribution: The distribution range of the species.unsure_distribution: Information about the uncertainty in the distribution data.elevation: The elevation range where the species is found.assessor: The person or group responsible for assessing the species.description: Additional information or description of the species.
The base species list used in the mtsta package has been carefully reviewed andvalidated with the assistance of the Taxonomic Name Resolution Service (TNRS).By utilizing the TNRS, the base species list in the mtsta package guaranteesaccuracy and consistency in the representation of species names, enhancing thereliability of the package's functionalities.
Source
The data for this package was obtained fromA Regional Red List of Montane Tree Species of the Tropical Andes - 2014.
See Also
Usesearch_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 ofthe Tropical Andes
Description
This function searches for matching species names in the Red List of MontaneTree Species of the Tropical Andes (mtsta package) based on a providedlist of species names. The function performs approximate matching using theLevenshtein distance algorithm to find similar names within a specifiedmaximum 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 indicatesthe total number of insertions, deletions, and substitutions allowed tomatch the two names. It can be expressed as an integer or as the fraction ofthe 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 onechange (insertion, deletion, or substitution). A max_distance = 2, allows two changes. |
... | Additional arguments (currently unused). |
Value
A data frame with the following columns:
name_submitted: The submitted species names.name_matched: The matched species names from the mtsta data.accepted_name: The accepted scientific name of the matched species.accepted_family: The accepted family name of the matched species.accepted_genus: The accepted genus name of the matched species.taxonomic_status: The taxonomic status of the matched species.iucn: The conservation status of the matched species according to the IUCN Red List Categories.distribution: The distribution range of the matched species.unsure_distribution: Information about the uncertainty in the distribution data.elevation: The elevation range where the species is found.assessor: The person or group responsible for assessing the species.description: Additional information or description of the species.distance: The Levenshtein distance between the submitted name and the matched name.
If no match is found, thename_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 datasearch_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 distributiondatabase 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 distributiondata is to be searched. |
max_distance | Numeric value representing the maximum allowed distance for approximatestring 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 bythemax_distance argument. It searches themtsta distribution database for submittedspecies names that match the provided names within the given distance. The function thenretrieves distribution information, including the accepted name, distribution region, unsuredistribution (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-listof 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
Examples
# Example usage of search_mtsta_distribution functionspecies_list <- c("Escallonia mirtilloydes", "Ilex rimbachii", "Saurauia lehmannii")distribution_data <- search_mtsta_distribution(species_list, max_distance = 0.2)print(distribution_data)