all SamplePoints are saved now, not only those in the actual classified habitat

R-package/R/save_files.r

@@ -66,11 +66,11 @@ save_kml <- function(outPath, step, raster, overwrite) {
 #' @param output_format format (character) of output; whether shp (default) or geojson
 #' @param ref_samples list of reference sample points
 #' @param ref_switch vector with switch values
-#' @param threshold threshold
+#' @param num_models number of models used for the classification of a habitat
 #' @param dummy_raster raster with probabilities for each pixel
 #'
 #' @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.
+#' 1) Point Shape/GeoJSON represents the pixels which were used to train the models for that habitat.
 #'    ESRI shapefiles have the same CRS as the input raster. GeoJSON files are in the standard CRS of GeoJSON (EPSG:4326).
 #'
 #'
@@ -82,13 +82,13 @@ saveSamplePoints <-
            output_format = c("shp", "geojson"),
            ref_samples,
            ref_switch,
-           threshold,
+           num_models,
            dummy_raster) {
     collect <- list()
     j <- 0
-    dummy_raster[dummy_raster < threshold] <- NA
-    dummy_raster[dummy_raster >= threshold] <- 1
-    
+    dummy_raster[dummy_raster == num_models] <- NA
+    dummy_raster[dummy_raster > num_models] <- 1
+
     ###extract only class samples
     for (i in 1:length(ref_samples)) {
       if (length(dim(ref_samples[[i]])) != 0)
@@ -113,6 +113,7 @@ saveSamplePoints <-
       result <- result[-which(is.na(res)), ]
     }
     raster::crs(result) <- raster::crs(dummy_raster)
+
     output_format <- match.arg(output_format)
     if (output_format == "geojson") {
       # Only transform is there points to be saved.
@@ -140,9 +141,11 @@ saveSamplePoints <-
   }
 
 
-#' Sample Collection for Habitat Types
+#' Selected 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.
+#' 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. Only those points are selected
+#' which lay in the habitat type selected by the user's input threshold.
 #'
 #' @param in_path 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)
@@ -150,7 +153,7 @@ saveSamplePoints <-
 #' @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.
+#' 1) Point Shape/GeoJSON represents the pixels which 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).
 #'
 #'