adjusted docu and deleted unnessecary lines in function writeOutSamples.r

R-package/R/WriteOutSamples.r

@@ -14,41 +14,32 @@
 
 ###write out selected samples
 write_Out_Samples <- function (inPath, step, className) {
-  
-  print("function started")
-  
+
   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 =
                            ""))
-  
-  print("problem zone 0")
-  
+
   length_threshold <- length(threshold)
   thres <- threshold[length_threshold]
   dummy_sample[dummy_sample < thres] <- NA
   dummy_sample[dummy_sample >= thres] <- 1
-  
-  print("problem zone 1")
 
   collect <- list()
   j <- 0
 
   ###extract only class samples
   for (i in 1:length(run1@ref_samples)) {
-    print("problem zone 1.1")
     if (length(dim(run1@ref_samples[[i]])) != 0)
     {
-      print("problem zone 1.2")
       if (is.na(run1@switch[i]) == F) {
         j = j + 1
         collect[[j]] <-
           run1@ref_samples[[i]][which(run1@ref_samples[[i]]@data == 1), ]
       } else
       {
-        print("problem zone 1.3")
         j = j + 1
         collect[[j]] <-
           run1@ref_samples[[i]][which(run1@ref_samples[[i]]@data == 2), ]
@@ -56,8 +47,6 @@ write_Out_Samples <- function (inPath, step, className) {
     }
   }
   
-  print("problem zone 2")
-  
   result <- do.call(rbind, collect)
 
   res <- raster::extract(dummy_sample, result)
@@ -65,43 +54,10 @@ write_Out_Samples <- function (inPath, step, className) {
     res <- result[-which(is.na(res)), ]
   }
   
-  print("problem zone 3")
-  ### save the points as .shp with crs
-  # crs_dummy <- proj4string(dummy_sample)
-  # proj4string(res) <- crs_dummy
-  # print(str(res))
-  # print(proj4string(res))
-  # 
-  # rgdal::writeOGR(
-  #   res,
-  #   layer = "result",
-  #   dsn = paste(inPath, "RefHaSa_", className, "_", step, ".shp", sep = ""),
-  #   driver = "ESRI Shapefile",
-  #   check_exists = TRUE,
-  #   overwrite_layer = TRUE
-  # )
-
-  #### this approach is for a shape file in a Geopackage (.dpkg) container
-  # print(proj4string(res))
-  # 
-  # crs_dummy <- proj4string(dummy_sample)
-  # proj4string(res) <- crs_dummy
-  # 
-  # print(proj4string(res))
-  # 
-  # rgdal::writeOGR(
-  #   res,
-  #   layer = paste("RefHaSa_step_", step, "_", className, sep = ""),
-  #   dsn = paste(inPath, "RefHaSa_step_", step, "_", className, ".gpkg", sep = ""),
-  #   driver = "ESRI Shapefile",
-  #   check_exists = TRUE,
-  #   overwrite_layer = TRUE
-  # )
-  
-  crs_dummy <- proj4string(dummy_sample)
+  crs_dummy <- sp::proj4string(dummy_sample)
   crs(res) <- crs_dummy
-  res <- spTransform(res, CRS("+proj=longlat +datum=WGS84 +init=epsg:4326"))
-  
+  res <- sp::spTransform(res, CRS("+proj=longlat +datum=WGS84 +init=epsg:4326"))
+
   rgdal::writeOGR(
     res,
     layer = paste("RefHaSa_step_", step, "_", className, sep = ""),
@@ -110,6 +66,4 @@ write_Out_Samples <- function (inPath, step, className) {
     check_exists = TRUE,
     overwrite_layer = TRUE
   )
-
-  print("finished")
 }

R-package/man/write_Out_Samples.Rd

@@ -14,11 +14,11 @@ write_Out_Samples(inPath, step, className)
 \item{className}{name (character) of habitat type for which samples should be selected}
 }
 \value{
-ESRI shapefile with name: RefHaSa_className_step.shp
+GeoJSON file with name: RefHaSa_step_classname.geojson
 \enumerate{
 \item Point Shape represents pixel that belong to selected habitat type and can be used as reference for further model building
 }
 }
 \description{
-Writes out a set of samples (SpatialPointsDataFrame) into an ESRI shapefile for a selected habitat type. Each point represents a valid sample location that identifies the selected habitat type.
+Writes out a set of samples (SpatialPointsDataFrame) into an GeoJSON file for a selected habitat type. Each point represents a valid sample location that identifies the selected habitat type.
 }