R/importStreams.R

In apear9/SSNdesign: An R Package for Optimal and Adaptive Sampling Designs on Stream Networks

#' Import a shapefile of stream edges without observed or predicted sites as a SpatialStreamNetwork
#' 
#'@description
#'
#'Imports a SpatialStreamNetwork without loading the observed and predicted sites. 
#'
#'@param filepath a path to a folder containing a stream network. The folder should have the extension .ssn. 
#'@param o.write a logical value indicating whether the binaryID.db inside the folder should be overwritten if it already exists. Note that, if no binaryID.db exists, that database will be generated by this function.
#'@return An object of class SpatialStreamNetwork, with nothing in obspoints and predpoints slots.
#'
#'@details
#'
#'The purpose of this function is to allow users to ingest stream shapefiles with no observed or prediction sites into R as a SpatialStreamNetwork. This will then allow them to use their data with functions like \code{generateSites}, which will allow them to explore various designs on their stream network.
#' 
#'@export
importStreams <- function(filepath, o.write = FALSE){
  old.wd <- getwd()
  Path <- dirname(filepath)
  ssn.obj <- basename(filepath)
  if (Path == ".") {
    Path = old.wd
  }
  setwd(paste(Path, "/", ssn.obj, sep = ""))
  on.exit(setwd(old.wd))
  edges <- readOGR(".", "edges", verbose = FALSE, stringsAsFactors = FALSE, integer64 = "allow.loss")
  rownames(edges@data) <- edges@data[, "rid"]
  if (exists("edges") == 0) {
    stop("edges.shp is missing from ", Path, " folder")
  }
  if (getinfo.shape("edges.shp")[[2]] != 3 & getinfo.shape("edges.shp")[[2]] != 13) {
    stop("edges.shp does not have polyline geometry")
  }
  ind1 <- colnames(edges@data) == c("netID")
  ind2 <- colnames(edges@data) == c("rid")
  ind3 <- colnames(edges@data) == c("upDist")
  if (sum(ind1) == 0) {
    stop("netID is missing from streams attribute table")
  }
  if (sum(ind2) == 0) {
    stop("rid is missing from streams attribute table")
  }
  if (sum(ind3) == 0) {
    stop("upDist is missing from streams attribute table")
  }
  if (is.factor(edges@data$netID)) {
    edges@data$netID <- anum(edges@data$netID)
  }
  network.line.coords <- data.frame(edges@data$netID, edges@data[, "rid"], edges@data[, "upDist"])
  colnames(network.line.coords) <- c("NetworkID", "SegmentID", "DistanceUpstream")
  network.line.coords <- as.data.frame(network.line.coords)
  row.names(network.line.coords) <- row.names(edges@data)
  network.line.coords[, 1] <- as.factor(network.line.coords[, 1])
  network.line.coords[, 2] <- as.factor(network.line.coords[, 2])
  rm(ind1, ind2, ind3)
  op <- new("SSNPoint", network.point.coords = data.frame(NULL), 
            point.coords = matrix(nrow = 1, ncol=2), point.data = data.frame(NULL), 
            points.bbox = matrix(nrow = 2, ncol = 2))
  ops <- new("SSNPoints")
  ops@SSNPoints[[1]] <- op
  ops@ID[[1]] <- "Obs"
  ssn <- new(
    "SpatialStreamNetwork", 
    edges, network.line.coords = network.line.coords, 
    obspoints = ops, 
    path = paste(Path, "/", ssn.obj, sep = "")
  )
  ssn@obspoints@SSNPoints[[1]]@point.data$netID <- as.factor(ssn@obspoints@SSNPoints[[1]]@point.data$netID)
  ssn@data$netID <- as.factor(ssn@data$netID)
  rm(network.line.coords, edges)
  SSN:::createBinaryID(ssn, o.write = o.write)
  return(ssn)
}