renamed

R-package/R/WriteOutSamples.r

-#' Sample Collection for Habitat Types
-#'
-#'Writes out a set of samples (SpatialPointsDataFrame) into ESRI shapefiles or a GeoJSON file for a selected habitat type. Each point represents a valid sample location that identifies the selected habitat type.
-#'
-#' @param inPath file path (character) for results of habitat type sampling and probability mapping (same as outPath from function multi_Class_Sampling)
-#' @param step step number (numeric)
-#' @param className name (character) of habitat type for which samples should be selected
-#' @param output_format format (character) of output; whether shp (default) or geojson
-#'
-#' @return ESRI shapefiles/GeoJSON with name: SamplePoints_step_classname.shp/SamplePoints_step_classname.geojson
-#' 1) Point Shape/GeoJSON represents pixel that belong to selected habitat type and can be used as reference for further model building.
-#'    ESRI shapefiles have the same CRS as the input raster. GeoJSON files are in the standard CRS of GeoJSON (EPSG:4326).
-#'
-#'
-#' @export
-
-###write out selected samples
-writeOutSamples <- function (inPath, step, className, output_format = c("shp", "geojson")) {
-
-  paste(inPath, "step_", step, "_", className, ".tif", sep = "")
-  run1 <- get(load(paste(inPath, "Run", step, sep = "")))
-  load(paste(inPath, "threshold_step_", step, sep = ""))
-  dummy_sample <-
-    raster::raster(paste(inPath, "step_", step, "_", className, ".tif", sep =
-                           ""))
-
-  length_threshold <- length(threshold)
-  thres <- threshold[length_threshold]
-  dummy_sample[dummy_sample < thres] <- NA
-  dummy_sample[dummy_sample >= thres] <- 1
-
-  collect <- list()
-  j <- 0
-
-  ###extract only class samples
-  for (i in 1:length(run1@ref_samples)) {
-    if (length(dim(run1@ref_samples[[i]])) != 0)
-    {
-      if (is.na(run1@switch[i]) == F) {
-        j = j + 1
-        collect[[j]] <-
-          run1@ref_samples[[i]][which(run1@ref_samples[[i]]@data == 1), ]
-      } else
-      {
-        j = j + 1
-        collect[[j]] <-
-          run1@ref_samples[[i]][which(run1@ref_samples[[i]]@data == 2), ]
-      }
-    }
-  }
-  
-  result <- do.call(rbind, collect)
-
-  res <- raster::extract(dummy_sample, result)
-  if (length(which(is.na(res))) > 0) {
-    res <- result[-which(is.na(res)), ]
-  }
-  
-  output_format <- match.arg(output_format)
-  
-  if (output_format == "geojson") {
-    crs_dummy <- sp::proj4string(dummy_sample)
-    raster::crs(res) <- crs_dummy
-    res <- sp::spTransform(res, sp::CRS("+init=epsg:4326"))
-
-    rgdal::writeOGR(
-      obj = res,
-      layer = paste("SamplePoints_step_", step, "_", className, sep = ""),
-      dsn = paste(inPath, "SamplePoints_step_", step, "_", className, ".geojson", sep = ""),
-      driver = "GeoJSON",
-      check_exists = TRUE,
-      overwrite_layer = TRUE
-    ) 
-   } else {
-      crs_dummy <- sp::proj4string(dummy_sample)
-      raster::crs(res) <- crs_dummy
-      
-      rgdal::writeOGR(
-        obj = res,
-        layer = paste("SamplePoints_step_", step, "_", className, sep = ""),
-        dsn = paste(inPath, "SamplePoints_step_", step, "_", className, ".shp", sep = ""),
-        driver = "ESRI Shapefile",
-        check_exists = TRUE,
-        overwrite_layer = TRUE
-      )
-     }
-}