add_country_to_checklist.R

# This script assigns countries to a list of plants based on their geographical coordinates.
# It utilizes the 'terra' package for spatial operations and requires CSV files
# with plant information (these files can be generated by `create_plant_cheklist_by_beee.R`) 
# and a world boundary shapefile in WGS 84 (EPSG:4326) projection.

library(terra)
library(tidyverse)

config <- config::get()
DATA_FOLDER <- config$data_folder

# Find checklist data files
listado_archivos <- fs::dir_ls(path = DATA_FOLDER, glob="*_list.csv")

crs_wgs84 <- "+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0"

# Download country borders from https://www.naturalearthdata.com/downloads/50m-cultural-vectors/
world_info <- vect(config$country_borders_path)
attr_country <- c("ISO_A2", "NAME_ES")

for(f in listado_archivos) {
  cat("Procesando archivo", fs::path_file(f), "\n")
  data <- read_csv(f)
  if (nrow(data) == 0) {
    next
  }
  data_names <- names(data)
  data_names <- c(data_names, attr_country)
  
  data <- vect(
    as.matrix(select(data, longitude, latitude)),
    crs=crs_wgs84,
    atts=as.data.frame(select(data, -longitude, -latitude))
  )
  
  country_data <- terra::extract(
    world_info, data
  )
  
  data <- cbind(data, country_data)
  data <- as.data.frame(data, geom = "XY") %>%
    rename("longitude"=x, "latitude"=y) %>%
    select(any_of(data_names))
  write_csv(data, f)
}