Merge branch 'WriteOutSamples' into 'master'

renamed the function and output names and put in missing packages for functions used

See merge request !19

R-package/NAMESPACE

@@ -12,5 +12,5 @@ export(sample_nb)
 export(save_class_tiff)
 export(save_kml)
 export(save_run)
-export(write_Out_Samples)
+export(writeOutSamples)
 exportClasses(Habitat)

R-package/R/WriteOutSamples.r → R-package/R/writeOutSamples.r

@@ -2,25 +2,26 @@
 #'
 #'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 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)
-#' @param className name (character) of habitat type for which samples should be selected
+#' @param class_name 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: RefHaSa_step_classname.shp/RefHaSa_step_classname.geojson
-#' 1) Point Shape represents pixel that belong to selected habitat type and can be used as reference for further model building
+#' @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
-write_Out_Samples <- function (inPath, step, className, output_format = c("shp", "geojson")) {
+writeOutSamples <- function (in_path, step, class_name, 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 = ""))
+  paste(in_path, "step_", step, "_", class_name, ".tif", sep = "")
+  run1 <- get(load(paste(in_path, "Run", step, sep = "")))
+  load(paste(in_path, "threshold_step_", step, sep = ""))
   dummy_sample <-
-    raster::raster(paste(inPath, "step_", step, "_", className, ".tif", sep =
+    raster::raster(paste(in_path, "step_", step, "_", class_name, ".tif", sep =
                            ""))
 
   length_threshold <- length(threshold)
@@ -58,27 +59,24 @@ write_Out_Samples <- function (inPath, step, className, output_format = c("shp",
   output_format <- match.arg(output_format)
   
   if (output_format == "geojson") {
-    crs_dummy <- sp::proj4string(dummy_sample)
-    crs(res) <- crs_dummy
-    res <- sp::spTransform(res, CRS("+proj=longlat +datum=WGS84 +init=epsg:4326"))
+    raster::crs(res) <- sp::proj4string(dummy_sample)
+    res <- sp::spTransform(res, sp::CRS("+init=epsg:4326"))
 
     rgdal::writeOGR(
-      res,
-      layer = paste("RefHaSa_step_", step, "_", className, sep = ""),
-      dsn = paste(inPath, "RefHaSa_step_", step, "_", className, ".geojson", sep = ""),
+      obj = res,
+      layer = paste("SamplePoints_step_", step, "_", class_name, sep = ""),
+      dsn = paste(in_path, "SamplePoints_step_", step, "_", class_name, ".geojson", sep = ""),
       driver = "GeoJSON",
       check_exists = TRUE,
       overwrite_layer = TRUE
     ) 
    } else {
-      crs_dummy <- sp::proj4string(dummy_sample)
-      crs(res) <- crs_dummy
-      res <- sp::spTransform(res, CRS("+proj=longlat +datum=WGS84 +init=epsg:4326"))
+     raster::crs(res) <- sp::proj4string(dummy_sample)
      
       rgdal::writeOGR(
-        res,
-        layer = paste("RefHaSa_step_", step, "_", className, sep = ""),
-        dsn = paste(inPath, "RefHaSa_", className, "_", step, ".shp", sep = ""),
+        obj = res,
+        layer = paste("SamplePoints_step_", step, "_", class_name, sep = ""),
+        dsn = paste(in_path, "SamplePoints_step_", step, "_", class_name, ".shp", sep = ""),
         driver = "ESRI Shapefile",
         check_exists = TRUE,
         overwrite_layer = TRUE

R-package/man/write_Out_Samples.Rd → R-package/man/writeOutSamples.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/WriteOutSamples.r
-\name{write_Out_Samples}
-\alias{write_Out_Samples}
+% Please edit documentation in R/writeOutSamples.r
+\name{writeOutSamples}
+\alias{writeOutSamples}
 \title{Sample Collection for Habitat Types}
 \usage{
-write_Out_Samples(inPath, step, className, output_format = c("shp", "geojson"))
+writeOutSamples(in_path, step, class_name, output_format = c("shp", "geojson"))
 }
 \arguments{
-\item{inPath}{file path (character) for results of habitat type sampling and probability mapping (same as outPath from function multi_Class_Sampling)}
+\item{in_path}{file path (character) for results of habitat type sampling and probability mapping (same as outPath from function multi_Class_Sampling)}
 
 \item{step}{step number (numeric)}
 
-\item{className}{name (character) of habitat type for which samples should be selected}
+\item{class_name}{name (character) of habitat type for which samples should be selected}
 
 \item{output_format}{format (character) of output; whether shp (default) or geojson}
 }
 \value{
-ESRI shapefiles/GeoJSON with name: RefHaSa_step_classname.shp/RefHaSa_step_classname.geojson
+ESRI shapefiles/GeoJSON with name: SamplePoints_step_classname.shp/SamplePoints_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
+\item 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).
 }
 }
 \description{