Move the writeOutSamples function to save_files.r

R-package/R/save_files.r

@@ -130,4 +130,89 @@ saveSamplePoints <-
         overwrite_layer = TRUE
       )
     }
+  }
+
+
+#' 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 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 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: 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(in_path, step, class_name, output_format = c("shp", "geojson")) {
+  run1 <- get(load(paste(in_path, "Run", step, sep = "")))
+  load(paste(in_path, "threshold_step_", step, sep = ""))
+  dummy_sample <-
+    raster::raster(paste(in_path, "step_", step, "_", class_name, ".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") {
+    raster::crs(res) <- sp::proj4string(dummy_sample)
+    res <- sp::spTransform(res, sp::CRS("+init=epsg:4326"))
+    
+    rgdal::writeOGR(
+      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 {
+    raster::crs(res) <- sp::proj4string(dummy_sample)
+    
+    rgdal::writeOGR(
+      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
+    )
+  }
 }
\ No newline at end of file

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 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 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: 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 (in_path, step, class_name, output_format = c("shp", "geojson")) {
-
-  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(in_path, "step_", step, "_", class_name, ".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") {
-    raster::crs(res) <- sp::proj4string(dummy_sample)
-    res <- sp::spTransform(res, sp::CRS("+init=epsg:4326"))
-
-    rgdal::writeOGR(
-      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 {
-     raster::crs(res) <- sp::proj4string(dummy_sample)
-     
-      rgdal::writeOGR(
-        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/saveSamplePoints.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/save_files.r
+\name{saveSamplePoints}
+\alias{saveSamplePoints}
+\title{Save Sample Points}
+\usage{
+saveSamplePoints(
+  in_path,
+  step,
+  class_name,
+  output_format = c("shp", "geojson"),
+  ref_samples,
+  ref_switch,
+  dummy_raster
+)
+}
+\arguments{
+\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{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}
+
+\item{ref_samples}{list of reference sample points}
+
+\item{ref_switch}{vector with switch values}
+
+\item{dummy_raster}{raster with classified pixels marked as 1}
+}
+\value{
+ESRI shapefiles/GeoJSON with name: SamplePoints_step_classname.shp/SamplePoints_step_classname.geojson
+\enumerate{
+\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{
+Saves the reference sample points
+}

R-package/man/writeOutSamples.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/writeOutSamples.r
+% Please edit documentation in R/save_files.r
 \name{writeOutSamples}
 \alias{writeOutSamples}
 \title{Sample Collection for Habitat Types}