README.md
In redbookperu: Access and Analyze Data from the Red Book of Endemic Plants of Peru

redbookperu

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 0.0.3

To determine if a species of interest is listed in the Red Book of Endemic Plants of Peru, we provide the check_redbooklist() function. This function verifies whether the species of interest is included in the book’s species list.When the species of interest doesn’t match the species list, the response is “Not endemic”.


splist <- c("Aphelandra cuscoenses", 
            "Sanchezia capitata",
            "Sanchezia ovata", 
            "Piper stevensi",
            "Verbesina andinaa", 
            "Verbesina andina", 
            "Weinmania nubigena")

redbookperu::check_redbooklist(splist, dist = 0.2)
#> Total exact matches: 2
#> Total fuzzy matches: 3
#> [1] "endemic"     "endemic"     "not endemic" "endemic"     "endemic"    
#> [6] "endemic"     "not endemic"

Function 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_redbooklist() function is designed to work seamlessly with tibble, allowing users to easily analyze species data within a tabular format.

tibble::tibble(splist = splist) |> 
  dplyr::mutate(endemic = redbookperu::check_redbooklist(splist,
                                                         dist = 0.2))
#> Total exact matches: 2
#> Total fuzzy matches: 3
#> # A tibble: 7 × 2
#>   splist                endemic    
#>   <chr>                 <chr>      
#> 1 Aphelandra cuscoenses endemic    
#> 2 Sanchezia capitata    endemic    
#> 3 Sanchezia ovata       not endemic
#> 4 Piper stevensi        endemic    
#> 5 Verbesina andinaa     endemic    
#> 6 Verbesina andina      endemic    
#> 7 Weinmania nubigena    not endemic

If 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"), 
                   dist = 0.2)
#>                name_subitted              accepted_name accepted_name_author
#> 1         Sanchecia capitata                        ---                  ---
#> 2         Weinmania nubigena                        ---                  ---
#> 3 Macroclinium christensonii Macroclinium christensonii            D.E.Benn.
#> 4       Weberbauera violacea       Weberbauera violacea           Al-Shehbaz
#>   accepted_family               redbook_name        iucn
#> 1             ---                        ---         ---
#> 2             ---                        ---         ---
#> 3     Orchidaceae Macroclinium christensonii CR, B1abiii
#> 4    Brassicaceae       Weberbauera violacea          DD
#>                                publication                            collector
#> 1                                      ---                                  ---
#> 2                                      ---                                  ---
#> 3 Brittonia 46(3): 249 - 251, f. 13. 1994. O. del Castillo ex D.E. Bennett 5160
#> 4      Novon 14(3): 266 - 268, f. 3. 2004.        A. Sagástegui A. et al. 11175
#>   herbariums  common_name dep_registry ecological_regions      sinampe
#> 1        ---          ---          ---                ---          ---
#> 2        ---          ---          ---                ---          ---
#> 3        NY. Desconocido.           JU      BMHM; 1800 m. Sin registro
#> 4  MO; HUT!. Desconocido.           CA       PAR; 3800 m. Sin registro
#>   peruvian_herbariums
#> 1                 ---
#> 2                 ---
#> 3            Ninguno.
#> 4      HUT (isotipo).
#>                                                                                                                                                                                                                                             remarks
#> 1                                                                                                                                                                                                                                               ---
#> 2                                                                                                                                                                                                                                               ---
#> 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.

The code for the new version of the redbookperu package is based on the lcvplants package, with modifications specifically tailored to work with the data from the Red Book of Endemic Plants of Peru.