R/generateGBuffers.R

In GapAnalysis: Conservation Indicators Using Spatial Information

#' @title Generate buffer of G type occurrences
#' @name generateGBuffers
#' @description
#' Produces a terra vect object representing the area around the G type occurrences
#'
#' @param taxon A character object that defines the name of the species as listed in the occurrence dataset
#' @param occurrenceData a data frame of values containing columns for the taxon, latitude, longitude, and type
#' @param bufferDistM Distance in meters. Used to set the size of the buffered objects.
#'
#' @return A list object containing
#' 1. data : a terra vect object showing all the buffered areas around the G type occurrences
#' 2. map : a leaflet object showing the spatial results of the function
#'

#' @examples
#' ##Obtaining occurrences from example
#' data(CucurbitaData)
#'
#' # convert the dataset for function
#' taxon <- "Cucurbita_cordata"
#' occurrenceData <- CucurbitaData
#'
#' #Running generateGBuffers
#' gBuffer <- generateGBuffers(taxon = taxon,
#'                     occurrenceData = occurrenceData,
#'                     bufferDistM = 50000
#'                     )
#'
#'
#'
#' @references
#' Khoury et al. (2019) Ecological Indicators 98:420-429. \doi{10.1016/j.ecolind.2018.11.016}
#' Carver et al. (2021) GapAnalysis: an R package to calculate conservation indicators using spatial information
#' @importFrom dplyr filter
#' @importFrom terra vect crs buffer
#' @importFrom leaflet addTiles addPolygons addLegend addRasterImage addCircleMarkers
#' @export

generateGBuffers <- function(taxon, occurrenceData, bufferDistM) {
  # filter the occurrence data to the species of interest
  d1 <- occurrenceData |>
    dplyr::filter(species == taxon & type == "G") |>
    terra::vect(geom = c("longitude", "latitude"))
  terra::crs(d1) <- "epsg:4326"
  # test to see if g points are present
  if (nrow(d1) > 0) {
    # Buffer object
    d2 <- d1 |>
      terra::buffer(width = bufferDistM)
    # leaflet map of results
    map_title <- "<h3 style='text-align:center; background-color:rgba(255,255,255,0.7); padding:2px;'>Buffered G Occurrences</h3>"
    map <- leaflet::leaflet(d2) |>
      leaflet::addTiles() |>
      leaflet::addPolygons(
        color = "#444444",
        weight = 1,
        opacity = 1.0,
        fillOpacity = 0.5,
        fillColor = "#6300f0"
      ) |>
      leaflet::addCircleMarkers(
        data = d1,
        color = "#000",
        radius = 2,
        opacity = 1
      ) |>
      leaflet::addControl(html = map_title, position = "bottomleft")
  } else {
    #
    d2 <- "No G points present"
    # generate a empty map
    map <- leaflet::leaflet(d2)
  }

  return(list(
    data = d2,
    map = map
  ))
}