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# ppendemic <a href='https://github.com/PaulESantos/ppendemic'><img src='man/figures/ppendemic_logo.png' align="right" height="180" width="160" /></a>

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## Overview

This package offers convenient access to a new and extensive database
containing a list of 7892 endemic plant species found in Peru. This
comprehensive collection provides detailed botanical information,
including accepted names, family, genus, species, infraspecific
taxonomy, authorship, publication details, and temporal information
including both actual and nominal publication years for each species.

The construction of the `ppendemic` package is built upon valuable data
sourced from the renowned **World Checklist of Vascular Plants (WCVP)**
database. The WCVP is an international collaborative programme initiated
in 1988 by Rafaël Govaerts that provides high-quality expert-reviewed
taxonomic data on all vascular plants. As a highly authoritative
resource updated daily, WCVP offers comprehensive information on plant
taxonomy and occurrence worldwide, serving as the taxonomic backbone for
World Flora Online (WFO) and being incorporated into the Catalogue of
Life Checklist via GBIF. Leveraging this data, the ppendemic package
aims to present an up-to-date and novel compilation of Peru’s endemic
plant species, tailored to the diverse ecosystems of the region.

By incorporating meticulously curated data from WCVP following the
International Code of Nomenclature for algae, fungi, and plants (ICN),
this package offers users a reliable and accurate resource to explore,
analyze, and gain deeper insights into the rich diversity of Peru’s
endemic flora. The latest version (V-15, dated 06-01-2026) includes
enhanced temporal bibliographic information with sophisticated year
extraction capabilities, distinguishing between actual and nominal
publication years for improved citation accuracy.

Representing a significant advancement in our understanding of Peru’s
endemic plant species, the ppendemic package update the previously known
list of 5,507 species presented in the Red Book of Endemic Plants of
Peru, bringing the total to an impressive 7892 species. This substantial
increase in documented endemic species is a testament to the continuous
integration of updated taxonomic data and the commitment to presenting
the most current information available. With this expanded and current
database, researchers, conservationists, and nature enthusiasts alike
can now delve into a more comprehensive and accurate account of Peru’s
unique and diverse plant biodiversity.

The database spans a total of 165 families, with particular richness
observed in the Orchidaceae, Asteraceae, Piperaceae, Fabaceae,
Bromeliaceae, Solanaceae, Melastomataceae, Cactaceae, Araceae, Rubiaceae
families, all of which boast the highest number of endemic species in
Peru. The enhanced dataset now includes 159 records where actual and
nominal publication years differ, providing valuable insights into
historical botanical publishing practices.

<img src="man/figures/README-unnamed-chunk-2-1.png" alt="" width="100%" />

## Installation

You can install the `ppendemic` package from CRAN using:

``` r
install.packages("ppendemic")
# or
pak::pak("ppendemic")
```

Also you can install the `ppendemic` package from GitHub using the
following command:

``` r
pak::pak("PaulESantos/ppendemic")
```

## Getting Started

After installing the `ppendemic` package, you can load it into your R
session using:

``` r
library(ppendemic)
#> ── Access Peruvian plant endemic data ─────────────────────── ppendemic 0.2.0 ──
```

- Use `is_ppendemic()` to check if taxa are endemic

``` r
splist <- c("Aa aurantiaca", 
             "Aa aurantiaaia",
             "Werneria nubigena", 
             "Dasyphyllum brasiliense var. barnadesioides",
             "Miconia firma",
             "Festuca densiflora")
is_ppendemic(splist)
#> [1] "Endemic"     "Endemic"     "Not endemic" "Endemic"     "Endemic"    
#> [6] "Endemic"
```

- The `is_ppendemic()` function is designed to work seamlessly with
  tibbles, allowing users to easily analyze and determine the endemic
  status of species within a tabular format.

``` r

tibble::tibble(splist = splist) |> 
  dplyr::mutate(endemic = is_ppendemic(splist))
#> # A tibble: 6 × 2
#>   splist                                      endemic    
#>   <chr>                                       <chr>      
#> 1 Aa aurantiaca                               Endemic    
#> 2 Aa aurantiaaia                              Endemic    
#> 3 Werneria nubigena                           Not endemic
#> 4 Dasyphyllum brasiliense var. barnadesioides Endemic    
#> 5 Miconia firma                               Endemic    
#> 6 Festuca densiflora                          Endemic
```

## Citation

To cite the `ppendemic` package, please use:

``` r
citation("ppendemic")
#> To cite ppendemic in publications use:
#> 
#>   Santos-Andrade PE, Vilca-Bustamante LL (2025). ppendemic: A glimpse
#>   at the diversity of Peru's endemic plants.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     author = {Paul E. Santos Andrade and Lucely L. Vilca Bustamante},
#>     title = {ppendemic: A glimpse at the diversity of Peru's endemic plants},
#>     year = {2025},
#>     doi = {10.5281/zenodo.5106619},
#>     url = {https://paulesantos.github.io/ppendemic/},
#>   }
```
