R/clean_dup.R

In luismurao/ntbox: From Getting Biodiversity Data to Evaluating Species Distribution Models in a Friendly GUI Environment

#' Function to clean duplicated longitude and latitude data
#' @description Clean duplicated longitude and latitude data using threshold distance
#'              which is a distance (in grades) between points to be considered
#'              duplicates.
#' @param data A data.frame with longitude and latitude data
#' @param longitude A character vector of the column name of longitude.
#' @param latitude A character vector of the column name of latitude.
#' @param threshold A numeric value representing the Euclidean distance between coordinates
#'            to be considered a duplicate.
#' @return Returns a data.frame with coordinate data from species
#' @export
#' @examples
#' # Species genus
#' genus <- "ambystoma"
#' # Species name
#' species <- "tigrinum"
#' \dontrun{
#' # GBIF search
#' ambystoma_tigrinum <- searh_gbif_data(genus,species,
#'                                        occlim=100,
#'                                        writeFile=FALSE)
#' ambystoma_tigrinum_clean <- clean_dup(ambystoma_tigrinum,
#'                                     longitude = "longitude",
#'                                     latitude = "latitude",
#'                                     threshold=0.1666)
#' # Check the dimensions of  data
#' dim(ambystoma_tigrinum)
#' dim(ambystoma_tigrinum_clean)
#' }
#'
clean_dup <- function(data,longitude,latitude,threshold=0.0){
  data <- data[!is.na(data[,longitude]),]
  dat_sp <- sp::SpatialPointsDataFrame(data[,c(longitude ,
                                           latitude)],data)
  dat_sp1 <- sp::remove.duplicates(dat_sp, zero = threshold)
  return(dat_sp1@data)
}