The R package redbookperu provides convenient access to
the information contained in the Red
Book of Endemic Plants of Peru. This book represents a comprehensive
compilation of data on Peru’s endemic plant species, encompassing
records of 5,507 distinct taxa. Although this document marked a
milestone by consolidating an ambitious initiative focused on
understanding the diversity of Peru’s endemic plant species at the time
of its publication, it currently requires a review and update of the
presented taxonomic information.
The process of accessing data from the original publication can pose
challenges for researchers, particularly due to the large number of taxa
presented within it. The redbookperu package has the
primary objective of addressing these challenges by providing updated
taxonomic information. Additionally, it introduces functions designed to
enhance the accessibility and usefulness of the data presented in the
Red Book of Endemic Plants of Peru.
The information included in the redbookperu package is
built with the support of the Taxonomic Name Resolution Service
TNRS, in collaboration with the World Checklist of
Vascular Plants WCVP database. These resources are utilized to
ensure the validity and standardization of the taxonomic information
that we provide.
You can install the redbookperu package from CRAN
using:
install.packages("redbookperu")
# or
pak::pak("redbookperu")You can install the development version of redbookperu
from GitHub:
pak::pak("PaulESantos/redbookperu")After installing the redbookperu package, you can load
it into your R session using:
library(redbookperu)
#> This is redbookperu 0.0.2To determine if a species of interest is listed in the Red Book of
Endemic Plants of Peru, we provide the check_redbook()
function. This function verifies whether the species of interest is
included in the book’s species list. The function comes in two
variations:
check_redbook(splist, tax_status == TRUE): The
resulting information is structured as follows: “species name” -
“taxonomic status” - “validation information”.
splist <- c("Aphelandra cuscoenses", "Sanchezia capitata",
"Sanchezia ovata", "Piper stevensi",
"Verbesina andinaa", "Verbesina andina", "Weinmania nubigena")
redbookperu::check_redbook(splist, tax_status = TRUE)
#> [1] "Aphelandra cuscoensis - Accepted name - Fuzzy match"
#> [2] "Sanchezia ovata - Updated name"
#> [3] "Sanchezia ovata - Not endemic"
#> [4] "Piper stevensii - No opinion - Fuzzy match"
#> [5] "Verbesina andina - No info. available - Fuzzy match"
#> [6] "Verbesina andina - No info. available"
#> [7] "Weinmania nubigena - Not endemic"check_redbook(splist, tax_status == FALSE): The result
indicates whether the species is endemic or not, based on its match with
the species present in the database.redbookperu::check_redbook(splist, tax_status = FALSE)
#> [1] "Endemic - fuzzy match" "Endemic" "Not endemic"
#> [4] "Endemic - fuzzy match" "Endemic - fuzzy match" "Endemic"
#> [7] "Not endemic"Both functions indicate the presence of partial matches (fuzzy match) when the name of the species of interest varies compared to the information present in the database.
check_redbook() function is designed to work seamlessly
with tibbles, allowing users to easily analyze species data within a
tabular format.
tibble::tibble(splist = splist) |>
dplyr::mutate(endemic_tax_status = redbookperu::check_redbook(splist, tax_status = FALSE),
endemic = redbookperu::check_redbook(splist, tax_status = TRUE))
#> # A tibble: 7 × 3
#> splist endemic_tax_status endemic
#> <chr> <chr> <chr>
#> 1 Aphelandra cuscoenses Endemic - fuzzy match Aphelandra cuscoensis - Accepted …
#> 2 Sanchezia capitata Endemic Sanchezia ovata - Updated name
#> 3 Sanchezia ovata Not endemic Sanchezia ovata - Not endemic
#> 4 Piper stevensi Endemic - fuzzy match Piper stevensii - No opinion - Fu…
#> 5 Verbesina andinaa Endemic - fuzzy match Verbesina andina - No info. avail…
#> 6 Verbesina andina Endemic Verbesina andina - No info. avail…
#> 7 Weinmania nubigena Not endemic Weinmania nubigena - Not endemicIf you intend to access the information provided for each of the
species listed in the Red Book of Endemic Plants of Peru, you have the
option to use the get_redbook_data() function. This
function facilitates the association of updated taxonomic information
with the details concerning conservation status, distribution, and
descriptions presented in the original publication.
redbookperu::get_redbook_data(c("Sanchecia capitata",
"Weinmania nubigena",
"Macroclinium christensonii",
"Weberbauera violacea"))
#> name_subitted accepted_name accepted_family
#> 1 Sanchecia capitata Sanchezia ovata Acanthaceae
#> 2 Weinmania nubigena nill nill
#> 3 Macroclinium christensonii Macroclinium christensonii Orchidaceae
#> 4 Weberbauera violacea Weberbauera violacea Brassicaceae
#> accepted_name_author redbook_name iucn
#> 1 Ruiz & Pav. Sanchezia capitata DD
#> 2 nill nill nill
#> 3 D.E.Benn. Macroclinium christensonii CR, B1abiii
#> 4 Al-Shehbaz Weberbauera violacea DD
#> publication
#> 1 Bull. Herb. Boissier, ser. 2, 4: 315. 1904.
#> 2 nill
#> 3 Brittonia 46(3): 249 - 251, f. 13. 1994.
#> 4 Novon 14(3): 266 - 268, f. 3. 2004.
#> collector herbariums common_name dep_registry
#> 1 A. Mathews 1230 (K) <NA> Desconocido. JU - PA
#> 2 nill nill nill nill
#> 3 O. del Castillo ex D.E. Bennett 5160 NY. Desconocido. JU
#> 4 A. Sagástegui A. et al. 11175 MO; HUT!. Desconocido. CA
#> ecological_regions sinampe peruvian_herbariums
#> 1 BMHP, BHA; altitud desconocida. Sin registro Ninguno.
#> 2 nill nill nill
#> 3 BMHM; 1800 m. Sin registro Ninguno.
#> 4 PAR; 3800 m. Sin registro HUT (isotipo).
#> remarks
#> 1 Esta especie arbustiva es conocida de dos localidades. La colección tipo fue recolectada en la cuenca del Pangoa en el siglo XVIII. Probablemente la expansión urbana y las actividades agrícolas sean problemas para esta especie.
#> 2 nill
#> 3 Esta hierba epífita es conocida sólo de la colección tipo, proveniente del valle de Chanchamayo, en una subcuenca del Perené. Esta región ha sufrido continuas reducciones de sus áreas naturales debido a la ampliación de la frontera agrícola.
#> 4 Esta hierba paramuna es conocida de la localidad tipo, en la cuenca del Crisnejas, un tributario del Marañón. El ejemplar tipo fue recolectado en 1983, de una jalca poco herborizada.