Changes per MR 72

workspace/02_NHD_navigate.Rmd

@@ -13,9 +13,6 @@ knitr::opts_chunk$set(error = TRUE, cache = FALSE)
 ```
 
 ```{r setup}
-#  Load data and libraries ----------------------
-VPU <- "18"
-
 # Load custom functions
 source("R/utils.R")
 source("R/NHD_navigate.R")
@@ -25,12 +22,12 @@ source("R/hyrefactor_funs.R")
 source("R/config.R")
 
 # Load NHDPlus Data if precprocessed to RDS format
-# nhdplus_path(data_paths$nhdplus_gdb)
-# staged_nhd <- stage_national_data(nhdplus_data = data_paths$nhdplus_gdb,
-#                                   output_path  = data_paths$nhdplus_dir)
+nhdplus_path(data_paths$nhdplus_gdb)
+staged_nhd <- stage_national_data(nhdplus_data = data_paths$nhdplus_gdb,
+                                  output_path  = data_paths$nhdplus_dir)
 
-# nhd_rds <- fix_headwaters(staged_nhd$flowline, gsub("flowline.rds", "flowline_update.rds", staged_nhd$flowline), 
-#                new_atts = data_paths$new_nhdp_atts, nhdpath = data_paths$nhdplus_gdb)
+nhd_rds <- fix_headwaters(staged_nhd$flowline, gsub("flowline.rds", "flowline_update.rds", staged_nhd$flowline),
+               new_atts = data_paths$new_nhdp_atts, nhdpath = data_paths$nhdplus_gdb)
 ```
 
 ```{r huc12 POIs}
@@ -39,7 +36,7 @@ if(needs_layer(nav_gpkg, nav_poi_layer)) {
   
   if (needs_layer(nav_gpkg, nhd_flowline)){
     # Subset NHD by VPU
-    nhd <- VPU_Subset(file.path(data_paths$nhdplus_dir, "nhdplus_flowline_update.rds"), VPU)
+    nhd <- VPU_Subset(nhd_rds, VPU)
     
     if("arbolate_sum" %in% names(nhd)) nhd <- rename(nhd, ArbolateSu = arbolate_sum)