, Lucely L. Vilca
Bustamante [aut] | Title: | Access and Analyze Data from the Red Book of Endemic Plants of Peru |
|---|---|
| Description: | Provides access to and analysis of data from "The Red Book of Endemic Plants of Peru" (León, B., Roque, J., Ulloa, C., Jorgensen, P.M., Pitman, N., Cano, A. 2006) <doi:10.15381/rpb.v13i2.1782>. This package offers comprehensive taxonomic, geographic, and conservation information about Peru's endemic plant species. It includes functions to verify species inclusion, obtain updated taxonomic details, and explore the dataset. |
| Authors: | Paul E. Santos Andrade [aut, cre]
, Lucely L. Vilca
Bustamante [aut] |
| Maintainer: | Paul E. Santos Andrade <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.0.3 |
| Built: | 2024-09-20 10:23:38 UTC |
| Source: | CRAN |
This function checks a list of species names against the Red Book of Endemic Plants of Peru database and provides information about whether a species was recorded as endemic, and checks for misspelling typos (fuzzy match).
check_redbooklist(splist, dist = 0.02)check_redbooklist(splist, dist = 0.02)
splist |
A character vector containing the species names to be checked. |
dist |
Maximum allowed distance for fuzzy matching of species names. |
This function checks each species name in the provided list against the
Red Book of Endemic Plants of Peru database using fuzzy matching based on
the specified maximum distance (dist). It provides information about the
endemic status of each species and flags if the recorded name needs updating.
It also counts the number of exact and fuzzy matches found.
A character vector indicating if each input species name is listed as "endemic" in the Red Book of Endemic Plants of Peru database. Returns "endemic" if the species name is listed and "not endemic" if no matching entry is found.
Red Book of Endemic Plants of Peru The World Checklist of Vascular Plants, a continuously updated resource for exploring global plant diversity. Taxonomic Name Resolution Service - TNRS Plants of the World Online - Facilitated by the Royal Botanic Gardens - Kew.
# Example usage of the function splist <- c("Aphelandra cuscoenses", "Piper stevensi", "Sanchezia ovata", "Verbesina andina", "Festuca dentiflora", "Eucrosia bicolor var. plowmanii", "Hydrocotyle bonplandii var. hirtipes", "Persea americana") # Basic usage check_redbooklist(splist = splist, dist = 0.2) # Using base R with a data frame plant_list <- data.frame(splist = splist) plant_list$label <- check_redbooklist(plant_list$splist, dist = 0.2) plant_list# Example usage of the function splist <- c("Aphelandra cuscoenses", "Piper stevensi", "Sanchezia ovata", "Verbesina andina", "Festuca dentiflora", "Eucrosia bicolor var. plowmanii", "Hydrocotyle bonplandii var. hirtipes", "Persea americana") # Basic usage check_redbooklist(splist = splist, dist = 0.2) # Using base R with a data frame plant_list <- data.frame(splist = splist) plant_list$label <- check_redbooklist(plant_list$splist, dist = 0.2) plant_list
This function retrieves comprehensive information from the Red Book of Endemic Plants of Peru database for a provided list of species. It associates the provided species names with their corresponding updated taxonomic information and descriptions recorded in the original publication.
get_redbook_data(splist, dist = 0.1)get_redbook_data(splist, dist = 0.1)
splist |
A character vector containing the species names to be queried. |
dist |
Maximum allowed distance for fuzzy matching of species names. |
This function checks each species name in the provided list against the
Red Book of Endemic Plants of Peru database using fuzzy matching based on
the specified maximum distance (dist). For each species, it retrieves and
combines taxonomic information (accepted name, accepted family, accepted name author)
with additional descriptive data recorded in the original publication, such as
IUCN conservation category, bibliographic reference, collector, herbariums,
common name, departmental registrations, ecological regions, protected natural
areas (SINANPE), Peruvian herbaria, and additional remarks.
A data frame containing comprehensive information about the provided species, including updated taxonomic details and descriptions.
Red Book of Endemic Plants of Peru The World Checklist of Vascular Plants, a continuously updated resource for exploring global plant diversity. Taxonomic Name Resolution Service - TNRS Plants of the World Online - Facilitated by the Royal Botanic Gardens - Kew.
check_redbooklist function for a more focused check of species endemic status.
# Example illustrating how to use the get_redbook_data function species_list <- c("Aphelandra cuscoensis", "Sanchezia ovata", "Piper stevensii") redbook_data <- get_redbook_data(species_list) head(redbook_data)# Example illustrating how to use the get_redbook_data function species_list <- c("Aphelandra cuscoensis", "Sanchezia ovata", "Piper stevensii") redbook_data <- get_redbook_data(species_list) head(redbook_data)
The 'redbook_position' reports the position (in term of number of rows) of the first three letters (triphthong) for the plant names stored in the variable 'accepted_name' of the table 'redbook_tab'. This indexing system speeds up of the search on the largest list using the package.
redbook_positionredbook_position
A data frame with 978 observations on the following 3 variables:
A character vector. The position of the first three letters of the species name in the redbook_tab.
A character vector. The first three letters of the species name in the redbook_tab.
A character vector. The corresponding genus name.
Positions of Species Names in The Red Book of Endemic Plants of Peru
The redbook_position dataset provides the positions of the first three letters of each species name listed in the redbook_tab.
data("redbook_position") head(redbook_position)data("redbook_position") head(redbook_position)
This database contains comprehensive information regarding the endemic plant species listed in the Red Book of Endemic Plants of Peru. Each endemic taxon is accompanied by corresponding variables that detail its taxonomic status, IUCN conservation category, bibliographic references, type collection details, common names, departmental registrations, ecological regions, protected natural areas (SINANPE), and Peruvian herbaria where the specimens are deposited, as recorded in the original book.
redbook_sp_dataredbook_sp_data
A data frame with the following variables:
Unique identifier for each species in the Red Book of Endemic Plants of Peru.
Scientific name of the endemic species.
Conservation category assigned according to IUCN.
Bibliographic reference where the taxon was originally described.
Name(s) of the collector(s) of the type specimen.
Acronyms of the institutions where the type specimens of the taxon are deposited.
Common names of the species as mentioned in the literature.
Abbreviations of the departments where the taxon has been recorded.
Abbreviations of the ecological regions proposed by Zamora (1996).
Abbreviation of the Protected Natural Area where the taxon was recorded.
Acronyms of the Peruvian institutions where both type and non-type specimens are deposited.
Observations and additional information about the endemic taxon.
This database provides essential information for research and conservation efforts related to Peru's endemic flora, offering access to the data presented in the corresponding book.
León, Blanca, et.al. 2006. “The Red Book of Endemic Plants of Peru”. Revista Peruana De Biología 13 (2): 9s-22s. https://revistasinvestigacion.unmsm.edu.pe/index.php/rpb/issue/view/153
# Example illustrating how to load and explore the database data("redbook_sp_data") head(redbook_sp_data)# Example illustrating how to load and explore the database data("redbook_sp_data") head(redbook_sp_data)
The redbook_sps_class dataset includes all species names separated by genus,
epithet, author, subspecies, variety, and their position (ID) in the
redbook_tab.
redbook_sps_classredbook_sps_class
A data.frame with the following columns:
A character vector. The full species name.
A character vector. The genus of the species.
A character vector. The specific epithet of the species.
A character vector. The infraspecific epithet of the species, if applicable.
A character vector. The taxonomic rank (e.g., "species", "subspecies", "variety").
A character vector. The subspecies name, if applicable.
A character vector. The variety name, if applicable.
A character vector. Indicates if the species is a hybrid.
A character vector. The ID of the species in the redbook_tab.
data("redbook_sps_class") head(redbook_sps_class)data("redbook_sps_class") head(redbook_sps_class)
The redbook_tab contains records for all species listed in The Red Book of Endemic Plants of Peru.
redbook_tabredbook_tab
A tibble with the following columns:
The fixed species ID of the input taxon in The Red Book of Endemic Plants of Peru.
A character vector. The species name as listed in The Red Book of Endemic Plants of Peru.
A character vector. The input genus of the corresponding species name listed.
A character vector. The specific epithet of the corresponding species name listed.
A character vector. The taxonomic rank (e.g., "species", "subspecies", "variety") of the corresponding species name listed.
A character vector. The infraspecific epithet of the corresponding species name listed, if applicable.
A character vector. The accepted plant taxa names according to the World Checklist of Vascular Plants (WCVP).
A character vector. The corresponding family name of the accepted name.
A character vector. The author of the accepted name.
A character vector. The rank of the accepted name (e.g., species, subspecies).
A character vector. A tag indicating if the subspecies is recognized in the WCVP.
A character vector. The genus part of the name according to the WCVP.
A character vector. The specific epithet part of the name according to the WCVP.
A character vector. The infraspecific epithet part of the name according to the WCVP, if applicable.
León, Blanca, et.al. 2006. “The Red Book of Endemic Plants of Peru”. Revista Peruana De Biología 13 (2): 9s-22s. https://doi.org/10.15381/rpb.v13i2.1782.
data("redbook_tab") head(redbook_tab)data("redbook_tab") head(redbook_tab)