R_examples.qmd

# Using the API to retreive a species range as a zipped shapefile via R

For this example, we'll use the species *Pinus arizonica*.  Note that when submitting to the API, the space between the Genus and specific epithet needs to be replaced with an underscore.

```{r}

# Load required packages

library(httr)
library(sf)

# Create a temporary directory

temp_dir <- tempdir()

# Getting the ranges and metadata via a .zip file

# Download the data from the API 

  pinus_zip <- GET(url = "https://biendata.org/api/download/range?species=Pinus_arizonica") |>
    
  #convert to a manageable format  
    
              content(as = "raw")|> 
    
  # write to a zip file  
    
    writeBin(con = file.path(temp_dir,"pinus_arizonica.zip"))
  
  # Unzip the file
  
    unzip(zipfile = file.path(temp_dir,"pinus_arizonica.zip"),
          exdir = temp_dir)

  # list the files
  
    files <- list.files(temp_dir,full.names = TRUE,recursive = TRUE)

  # read and plot file  
    
    sf::st_read(dsn = files[5]) |> plot()

  # clean up
  
    unlink(temp_dir,recursive = TRUE,force = TRUE)
  
```  

# Using the API to download a species range as well-known text in R

In this example, we download the range for *Acer rubrum* in well-known text.  This approach can load the range directly into R without having to save an intermediate .zip file.

```{r}

library(httr)
library(jsonlite)
library(sf)

  species <- "Acer rubrum"

  # Fix the name for the API

    species <- gsub(pattern = " ",
                    replacement = "_",
                    x = species)

  #make the URL
    
    url <- paste0("https://biendata.org/api/range/range-data?species=", species)
  
  # Download the data from the API
    
    req <- GET(url = url)
  
  # convert to raw - this throws an error
    
    raw_content <- rawToChar(req$content)
  
  # convert raw content from JSON to R object
    
    df <- fromJSON(raw_content)
  
  # convert well-known text to sf geometry

    sp_range <- st_as_sf(x = df,
                         wkt = "st_astext",
                         crs = "epsg:4326")
          
  # plot data
    
    plot(sp_range[1])


```