R/GapSPDF.R

In ForestGapR: Tropical Forest Canopy Gaps Analysis

#' Forest Canopy Gaps as Spatial Polygons
#'
#' @description This function converts forest canopy gaps as [`raster::RasterLayer-class`] to
#' [`sp::SpatialPointsDataFrame-class`] objects
#'
#' @usage GapSPDF(gap_layer)
#'
#' @param gap_layer ALS-derived gap layer (output of [getForestGaps()] function).
#' An object of the class RasterLayer.
#' @return A [`sp::SpatialPointsDataFrame-class`] object of the forest canopy gaps.
#' The output file can be exported as a ESRI shapefile using
#' [rgdal::writeOGR()] function in the \emph{rgdal} package.
#' @author Carlos Alberto Silva.
#'
#' @examples
#' # Loading raster and viridis libraries
#' library(raster)
#' library(viridis)
#'
#' # ALS-derived CHM over Adolpho Ducke Forest Reserve - Brazilian tropical forest
#' data(ALS_CHM_DUC)
#'
#' # set height thresholds (e.g. 10 meters)
#' threshold <- 10
#' size <- c(1, 10^4) # m2
#'
#' # Detecting forest gaps
#' gaps_duc <- getForestGaps(chm_layer = ALS_CHM_DUC, threshold = threshold, size = size)
#'
#' # Converting raster layer to SpatialPolygonsDataFrame
#' gaps_spdf <- GapSPDF(gap_layer = gaps_duc)
#'
#' # Plotting ALS-derived CHM and forest gaps
#' plot(ALS_CHM_DUC, col = viridis(10), xlim = c(173025, 173125), ylim = c(9673100, 96731200))
#' plot(gaps_spdf, add = TRUE, border = "red", lwd = 2)
#'
#' # Populating the attribute table of Gaps_spdf with gaps statistics
#' gaps_stats <- GapStats(gap_layer = gaps_duc, chm_layer = ALS_CHM_DUC)
#' gaps_spdf <- merge(gaps_spdf, gaps_stats, by = "gap_id")
#' head(gaps_spdf@data)
#' @export
GapSPDF <- function(gap_layer) {
  names(gap_layer) <- "gap_id"
  gaps_spdf <- raster::rasterToPolygons(x = gap_layer, fun = NULL, n = 4, na.rm = TRUE, digits = 12, dissolve = TRUE)
  gaps_spdf@data <- cbind(sp::coordinates(gaps_spdf), gaps_spdf@data)
  colnames(gaps_spdf@data) <- c("x", "y", "gap_id")
  return(gaps_spdf)
}