The filter, like in other save functions should be done inside the function.

R-package/R/save_files.r

@@ -66,7 +66,8 @@ 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 dummy_raster raster with classified pixels marked as 1
+#' @param threshold threshold
+#' @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.
@@ -81,9 +82,12 @@ saveSamplePoints <-
            output_format = c("shp", "geojson"),
            ref_samples,
            ref_switch,
+           threshold,
            dummy_raster) {
     collect <- list()
     j <- 0
+    dummy_raster[dummy_raster < threshold] <- NA
+    dummy_raster[dummy_raster >= threshold] <- 1
     
     ###extract only class samples
     for (i in 1:length(ref_samples)) {

R-package/man/saveSamplePoints.Rd

@@ -11,6 +11,7 @@ saveSamplePoints(
   output_format = c("shp", "geojson"),
   ref_samples,
   ref_switch,
+  threshold,
   dummy_raster
 )
 }
@@ -27,7 +28,9 @@ saveSamplePoints(
 
 \item{ref_switch}{vector with switch values}
 
-\item{dummy_raster}{raster with classified pixels marked as 1}
+\item{threshold}{threshold}
+
+\item{dummy_raster}{raster with probabilities for each pixel}
 }
 \value{
 ESRI shapefiles/GeoJSON with name: SamplePoints_step_classname.shp/SamplePoints_step_classname.geojson