R/RL_threats.R

In matthewlewis896/redlistManipulatr: Obtain Red List habitat and elevation data and manipulate formats

#' Fetch Red List threats data
#' @description Download Red List threats data from the Red List API.
#' @author Matt Lewis, \email{matthewlewis896@@gmail.com}
#'
#' @param x List, vector, or dataframe with a column corresponding to binomial species names or IUCN Red List IDs.
#' @param col.name Character string. Column name if x is a dataframe. Not needed if x is a list or vector.
#' @param query Character string. 'name' if querying by species name; 'ID' if querying by IUCN Red List ID.
#' @param key Character string. IUCN Red List API key - available from https://apiv3.iucnredlist.org/api/v3/token
#' @param sleep_dur (optional) Numeric. Duration of sleep between API calls in seconds. Defaults to 2 seconds.
#' @param subset (optional). Numeric. Specify proportion of x to run for between 0 and 1. Defaults to 1.
#' @param parallel (optional) Logical. If TRUE uses multiple cores. Default is TRUE.
#' @param num.cores (optional) Numeric. Specify number of cores to use if running in parallel. Default is number of CPU cores available - 1.
#' @param verbose (optional) Numeric. If 0 gives no progress update, if 1 prints progress bar, if 2 prints 1 row per task completed. Default is 1.
#' @details A code value of "999" indicates that no information for that species could be found.
#' @return A dataframe in long format (one row per species-threat combination).
#' @export

RL_threats <-
  function(x,
           col.name,
           key,
           query,
           subset = 1,
           sleep_dur = 2,
           parallel = TRUE,
           num.cores = parallel::detectCores() - 1,
           verbose = 1) {

    # Checking needed packages are installed.

    packTest("rredlist")

    # Testing if API key is valid.
    if(is.character(key) == F){
      stop("Please supply a valid API key. API keys should be provided as a character string.")
    }
    # Testing if sleep duration is valid
    if(is.numeric(sleep_dur) == F){
      stop("Please supply a valid sleep duration. This should be a numeric input.")
    }
    # Handles verbose option
    if(is.numeric(verbose) == FALSE){
      stop("Please supply a valid value for 'verbose'.")
    }else if(!(verbose %in% c(0:2))){
      stop("Please supply a valid value for 'verbose'.")
    }

    if(is.data.frame(x) == TRUE){
      if(!is.character(col.name)){
        stop("Please supply a valid value for 'col.name'. 'col.name' should be a character input.")
      }else{
        x <- x[,col.name]
      }
    }
    if(is.list(x) == TRUE){
      x <- unlist(x)
    }
    #handles subset
    if(!is.numeric(subset)){
      stop("Please supply a valid value for 'subset'. 'subset' should be between 0 and 1.")
    }else if(subset <0 | subset > 1){
      stop("Please supply a valid value for 'subset'. 'subset' should be between 0 and 1.")
    }else{
      subset <- round(subset * length(x))
      message("\nFetching data for a subset of ", subset, "/", length(x), " (", round((100*subset/length(x)),2), "%) of the data.")
    }
    #handles query
    if(!is.character(query)){
      stop("Please supply a valid value for 'query'. 'query' should be between a character input.")
    }else if(!(query %in% c("name", "ID"))){
      stop("Please supply a valid value for 'query'. 'query' should be between a character input of 'name' or 'ID'.")
    }

    if(is.numeric(num.cores) == FALSE){
      stop("Please supply a valid number of cores as an integer number.")
    }else if(num.cores %% 1 != 0){
      stop("Please supply a valid number of cores as an integer number.")
    }else if(num.cores > parallel::detectCores()){
      stop("You have supplied a number of CPU cores greater than the number available.")
    }

    message("Using Red List version ", rredlist::rl_version(key = key))
    # Getting data (parallel or not)

    df <- list()
    batches <- c(seq(0, subset, 99), subset)
    for(a in 1:(length(batches) - 1)) {
      batch <- (batches[a] + 1):batches[a + 1]
      batch_to_run <- batch
      batch_to_run <- batch_to_run - diff(c(1, batch_to_run[1]))
      message("\nFetching ",length(batch),  " data records for batch number ",   a,  " of ", (length(batches) - 1))
      if (parallel == TRUE) {
        df[[a]] <-
          threats_par(
            x = x[batch],
            key = key,
            query = query,
            subset = batch_to_run,#subset,
            sleep_dur = sleep_dur,
            num.cores = num.cores,
            verbose = verbose
          )
      } else{
        df[[a]] <-
          threats_nopar(
            x = x[batch],
            key = key,
            query = query,
            subset = batch_to_run,#subset,
            sleep_dur = sleep_dur,
            verbose = verbose
          )
      }
    }
    df <-
      df %>%
      do.call(what = "rbind") %>%
      #tidyr::drop_na("iucn_id") %>%
      as.data.frame()

    return(df)
  }