R/remove.dups.R

In diogosbr/spfilt: Species data cleaning

#' @title Remove duplicated and NAs
#' @name remove.dups
#'
#' @description A function to check whether the coordinates are consistent with the name of the polygon.
#'
#' @param pts Data.frame. Table with points of occurrence, including the municipalities informed on the label.
#' @param na.rm String. Name of pts column containing the standard to be searched for.
#' @param mask String.Name of shape column containing the standard to be searched for.
#' @param dup logical. If TRUE, remove duplicated coordinates
#'
#' @details The
#'
#' @return a data frame
#'
#' @author Diogo S. B. Rocha
#'
#' @examples
#'
#' eug <- remove.dups(Eugenia_aurata, mask = example, na.rm = FALSE, dup = FALSE)
#' eug
#'
#' @importFrom raster cellFromXY extract
#'
#' @export

remove.dups  <-  function(pts,
                          mask = example,
                          na.rm = FALSE,
                          dup = TRUE) {
  if (names(pts)[1] == "sp"  &
      names(pts)[2] == "lon" & names(pts)[3] == "lat") {
    species <- as.vector(unique(pts$sp))
    
    if (dup == T) {
      message("cleaning duplicates")
      dupls <- !duplicated(pts[, c('sp', 'lon', 'lat')])
      pts <- pts[dupls, ]
    }
    
    if (exists("mask")) {
      if (length(species > 1)) {
        # Selecionar pontos espacialmente únicos #
        cell <- cellFromXY(mask, pts[, c("lon", "lat")])  # get the cell number for each point
        dupls <- !duplicated(cbind(pts[, 'sp'],cell))
        pts1 <- pts[dupls, ]
        
        if (na.rm == TRUE) {
          message("\n Removing NA \n")
          pts1 <-
            pts1[!is.na(extract(mask, pts1[, c('lon', 'lat')])), ]  #selecionando apenas pontos que tem valor de raster
        }
      } else{
        # Selecionar pontos espacialmente únicos #
        cell <-
          cellFromXY(mask, pts[, c("lon", "lat")])  # get the cell number for each point
        dup <- duplicated(cell)
        pts1 <-
          pts[!dup, ]  # select the records that are not duplicated
        
        if (na.rm == TRUE) {
          pts1 <-
            pts1[!is.na(extract(mask, pts1[, c('lon', 'lat')])), ]  #selecionando apenas pontos que tem valor de raster
        }
      }
      
      cat(dim(pts)[1] - dim(pts1)[1], "points removed\n")
      cat(dim(pts1)[1], "spatially unique points\n")
    } else
      (cat("Indicate the object with the predictive variables"))
  } else{
    stop("The first three columns should be 'sp', 'lon' and 'lat' necessarily in this order")
  }
  
  message("Finished ...\n")
  
  invisible(pts1)
}