R/csv_to_wege.R

In harithmorgadinho/wege:

#' @title csv_to_wege
#' @description A function to add iucn data to species and coordinates df.
#' @param input  df: species/coordinates
#' @examples
#' csv_to_wege(df)
#' @export

csv_to_wege=function(input){

  input=input[complete.cases(input), ]
  input=df_organizer(input)


  flpth <- system.file('terrestrial_animals_status.RData', package = 'wege')
  iucn_statuses <- readRDS(file = flpth)
  # iucn_statuses <- list('amphibian' = amphibian_status,
  #                       'bird' = bird_status,
  #                       'mammal' = mammal_status,
  #                       'reptile' = reptile_status)
  # saveRDS(object = iucn_statuses, file = 'inst/terrestrial_animals_status.RData', compress = 'xz')
  amphibian_status <- iucn_statuses[['amphibian']]
  bird_status <- iucn_statuses[['bird']]
  mammal_status <- iucn_statuses[['mammal']]
  reptile_status <- iucn_statuses[['reptile']]
  rm(iucn_statuses)

  df_final=input
  df2=rbind(amphibian_status,bird_status,mammal_status,reptile_status)

  df_final$status <- df2$status[match(df_final$species,df2$species)]


colnames(df_final)=c("species", "longitude"   ,  "latitude"   ,   "status")


df_final=df_final[complete.cases(df_final), ]
return(df_final)
}