output paths update

src/R/urban-forest-classification-and-individual-crown-parameterization.Rmd

@@ -26,7 +26,8 @@ if (!requireNamespace("imager", quietly = TRUE))
   install.packages("imager")
 if (!require("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
-BiocManager::install("EBImage")
+if (!require("EBImage", quietly = TRUE))
+    BiocManager::install("EBImage")
 if (!requireNamespace("terra", quietly = TRUE))
   install.packages("terra")
 if (!requireNamespace("ForestTools", quietly = TRUE))
@@ -285,7 +286,7 @@ ws_segments_cleaned <- terra::subset(ws_segments_cleaned,  ws_segments_cleaned$t
 ndsm_grid <- terra::mask(ndsm_grid, ws_segments_cleaned, inverse=FALSE, updatevalue=NA, touches=FALSE)
 
 # store as raster GeoTIFF
-ndsm_grid_out_path <- here::here("results/urban_forest_classification", paste0("chm_grid.tif"))
+ndsm_grid_out_path <- here::here("results/urban_forest_classification", "chm_grid.tif")
 terra::writeRaster(ndsm_grid, ndsm_grid_out_path, overwrite = TRUE)
 
 # merge CHM to point cloud
@@ -295,7 +296,7 @@ lidar_surface_points <- lidR::merge_spatial(lidar_surface_points, ndsm_grid, att
 lidar_surface_points <- lidR::filter_poi(lidar_surface_points, !is.na(CHM))
 
 # store LiDAR point cloud as LAS
-lidar_chm_points_out_path <- here::here("results/urban_forest_classification", "lidar_chm_points.las"))
+lidar_chm_points_out_path <- here::here("results/urban_forest_classification", "lidar_chm_points.las")
 lidR::writeLAS(lidar_surface_points, lidar_chm_points_out_path)
 
 # delete intermediate data
@@ -478,11 +479,11 @@ tree_positions_point <- terra::merge(tree_positions_point, tree_attribs_df, by =
 crowns_convex_hull_poly <- terra::merge(crowns_convex_hull_poly, tree_attribs_df, by = "treeID")
 
 # store tree positions as geojson
-tree_positions_out_path <-  here::here("results/parameterized_tree_crowns",paste0("tree_positions_parameterized.geojson"))
+tree_positions_out_path <-  here::here("results/parameterized_tree_crowns", "tree_positions_parameterized.geojson")
 terra::writeVector(tree_positions_point, tree_positions_out_path, filetype = "GeoJSON", overwrite = TRUE)
 
 # store tree crowns as geojson
-crowns_convex_hull_parameterized_out_path <-  here::here("results/parameterized_tree_crowns",paste0("crowns_convex_hull_parameterized.geojson"))
+crowns_convex_hull_parameterized_out_path <-  here::here("results/parameterized_tree_crowns", "crowns_convex_hull_parameterized.geojson")
 terra::writeVector(crowns_convex_hull_poly, crowns_convex_hull_parameterized_out_path, filetype = "GeoJSON", overwrite = TRUE)
 ```