R/iucnn_prepare_features.R

In azizka/IUCNN: Neural Networks to Approximate IUCN Red List Conservation Assessments

#'Prepare features for an IUCNN model
#'
#'A wrapper function to prepare all default features included in IUCNN:
#'geographic, biomes, climate, human footprint.
#'If desired, bias features need to be calculated separately with ft_bias.
#'For more control over feature preparation, you can use the
#'\code{\link{iucnn_geography_features}}, \code{\link{iucnn_biome_features}}, \code{\link{iucnn_climate_features}},
#'\code{\link{iucnn_footprint_features}} functions.
#'
#'Without internet access, only geographic features are calculated,
#'
#'@param x a data.frame of species occurrence records including three columns with
#'species name, longitudinal coordinates and latitudinal coordinates (both decimal).
#'@param species a character string. The name of the column with the species names.
#'@param lon a character string. The name of the column with the longitude.
#'@param lat a character string. The name of the column with the latitude.
#'@param type character. The type of features to calculate. Possible options are
#'\dQuote{geographic}, \dQuote{biome}, \dQuote{climate},
#'\dQuote{human footprint}.
#'@param download_folder character string. The folder were to save the
#'data used for feature extraction. Relative to the working directory.
#'Set to NULL for the working directory
#'@param impute_features logical. Should NA values be imputed for features? If TRUE
#'NA values are filled using multiple imputation using missForest. If set to FALSE
#'species with missing values are removed during the training process.
#'
#'@return a data.frame of features
#'
#' @keywords Feature preparation
#' @family Feature preparation
#'
#' @examples
#' \dontrun{

#' dat <- data.frame(species = c("A","B"),
#'                   decimallongitude = runif (200,10,15),
#'                   decimallatitude = runif (200,-5,5))
#'
#' iucnn_prepare_features(dat)
#'}
#'@export
#' @importFrom checkmate assert_character assert_data_frame assert_logical
#' @importFrom dplyr left_join

iucnn_prepare_features <- function(x,
                                   species = "species",
                                   lon = "decimallongitude",
                                   lat = "decimallatitude",
                                   type = c("geographic",
                                            "biomes",
                                            "climate",
                                            "humanfootprint"),
                                   download_folder = tempdir(),
                                   impute_features = TRUE){

  # assertions
  assert_data_frame(x)
  assert_numeric(x[[lon]], any.missing = FALSE, lower = -180, upper = 180)
  assert_numeric(x[[lat]], any.missing = FALSE, lower = -90, upper = 90)
  assert_character(type)
  assert_character(download_folder, null.ok = TRUE)

  # generate folder fore data
  if (is.null(download_folder)) {
    download_folder <- getwd()
  }

  if (!dir.exists(download_folder)) {
    dir.create(download_folder)
  }

  # else{
  #   download_folder<- file.path(getwd(), download_folder)
  # }

  #prepare geographic features
  if ("geographic" %in% type) {
    message("Calculating geographic features.")
    out <- iucnn_geography_features(x,
                                    species = species,
                                    lon = lon,
                                    lat = lat)
  }



  if (curl::has_internet()) {

    #biomes
    if ("biomes" %in% type) {
      message("Calculating biome features.")
      bio <- iucnn_biome_features(x,
                                  species = species,
                                  lon = lon,
                                  lat = lat,
                                  download_folder = download_folder)

      if (exists("out")) {
        out <- out %>%
          left_join(bio, by = species)
      }else{
        out <- bio
      }
    }

    #climate
    if ("climate" %in% type) {
      message("Calculating climate features.")
      clim <- iucnn_climate_features(x,
                                     species = species,
                                     lon = lon,
                                     lat = lat,
                                     download_folder = download_folder)

      if (exists("out")) {
        out <- out %>%
          left_join(clim, by = species)
      }else{
        out <- clim
      }
    }

    # human footprint
    if ("humanfootprint" %in% type) {
      message("Calculating human footprint features.")
      foot <- iucnn_footprint_features(x,
                                       species = species,
                                       lon = lon,
                                       lat = lat,
                                       download_folder = download_folder)

      if (exists("out")) {
        out <- out %>%
          left_join(foot, by = species)
      }else{
        out <- foot
      }
    }
  }else{
    warning("No internet connection, only geographic features created")
  }

  class(out) <- c("iucnn_features", class(out))
  # do imputation if argument is TRUE
  if (impute_features) {
    warning("Imputing NA values in features using missForest. Set impute_features=FALSE to suppress imputation.")
    final_out <- impute_missing_values(out)
  }else{
    final_out = out
  }

  return(final_out)
}