R/nodesfile.R

In connectscape/Makurhini: Makurhini: Analyzing landscape connectivity

#' Creation of nodefile attribute.
#'
#' Generates a table with the Core ID and the their attribute value (e.g. area in km²), using a shapefile with these values.
#' @param nodes sp, sf object, RasterLaryer or SpatRaster (terra package). It must be in a projected coordinate system.
#' @param id character. If nodes is a shappefile then you must specify the column name with the node ID
#'  in the shapefile data table. If nodes is a raster layer then raster values (Integer) will be taken as "id".
#' @param attribute character or vector. If nodes is a shappefile then you must specify the column name
#'  with the attribute in the data table selected for the nodes.
#'  If nodes is a raster layer then it must be a numeric vector with the node's attribute. The length of the vector must be equal to the number of nodes.
#'   The numeric vector is multiplied by the area of each node to obtain a weighted habitat index.
#'   If NULL the \bold{node area} will be used as a node attribute, the unit area can be selected using the "area_unit" argument.
#' @param area_unit character. If attribute is NULL you can set an area unit, ?unit_covert
#' compatible unit ("m2", "Dam2, "km2", "ha", "inch2", "foot2", "yard2", "mile2"). Default equal to "m2".
#' @param weighted logical. If the nodes are of raster type, you can weight the estimated area of each node by the attribute. When using this parameter the attribute, which must be a vector of length equal to the number of nodes, usually has values between 0 and 1.
#' @param restoration character or vector. If nodes is a shapefile then you must specify the name of the column
#' with restoration value. If nodes is a raster layer then must be a numeric vector with restoration values
#' to each node in the raster. Binary values (0,1), where 1 = existing nodes in the landscape, and 0 = a new node
#'  to add to the initial landscape (restored).
#' @param write character. Output folder path if you use the name option, otherwise, place the output path, with the name and extension ".txt"
#' @return nodo file in .txt format
#' @export
#' @importFrom raster res
#' @importFrom sf st_zm st_as_sf st_area
#' @importFrom methods as
#' @importFrom utils write.table
nodesfile <- function(nodes, id = NULL,
                      attribute = NULL, area_unit = "m2",
                      restoration = NULL, weighted = FALSE,
                      write = NULL) {
  if (missing(nodes)) {
    stop("error missing file of nodes")
  } else {
    if (is.numeric(nodes) | is.character(nodes)) {
      stop("error missing file of nodes")
    }
  }

  if (!is.null(write)) {
    if (!dir.exists(dirname(write))) {
      stop("error, output folder does not exist")
    }
  }

  if(class(nodes)[1] == "sf" | class(nodes)[1] == "SpatialPolygonsDataFrame"){
    if(is.null(id)){
      stop("Error, missing id argument")
    }

    if(class(nodes)[1] == "sf") {
      nodes <- st_zm(nodes)
    } else {
      nodes <- st_as_sf(nodes) |> st_zm(nodes)
    }

    if (is.null(attribute)){
      nodes$Area <- as.numeric(st_area(nodes)); attribute <- "Area"
      if (area_unit != "m2"){
        nodes$Area <- unit_convert(nodes$Area, "m2", area_unit)
      }
    }

    nodes <- nodes[ ,c(which(names(nodes) == id),
                       which(names(nodes) == attribute),
                       which(names(nodes) == restoration))] |> st_drop_geometry() |> as.data.frame()

  } else if (class(nodes)[1] == "RasterLayer" | class(nodes)[1] == "SpatRaster"){
    if(!is.null(attribute)){
      if(isTRUE(weighted)){
        nres <- unit_convert(res(nodes)[1]^2, "m2", area_unit);nodes <- as.data.frame(table(nodes[]));nodes$Freq <- nodes$Freq * nres
        nodes$Freq <- nodes$Freq * attribute
      } else {
        nodes <- as.data.frame(table(nodes[])); nodes$Freq <- attribute
      }
    } else {
      nres <- unit_convert(res(nodes)[1]^2, "m2", area_unit)
      nodes <- as.data.frame(table(nodes[]));nodes$Freq <- nodes$Freq * nres
    }

    names(nodes)[1:2] <- c("Id", "attribute"); nodes <- nodes[,1:2]; id = "Id"
    if(!is.null(restoration)){
      nodes$restoration <- restoration
    }
  } else {
    stop("error missing file of nodes. Check the nodes class")
  }

  if(!is.null(levels(nodes[[id]]))){
    nodes[,1] <- as.numeric(as.character(nodes[[id]]))
  }

  if(!is.null(write)){
    if (dim(nodes)[1] > 1){
      write.table(nodes, write, sep="\t", row.names = FALSE, col.names = FALSE)
      return(nodes)
    } else {
      stop("Error only one node")
    }
  }

  return(nodes)
}