config updates

workspace/02_NHD_navigate.Rmd

@@ -35,9 +35,9 @@ nhd_rds <- fix_headwaters(staged_nhd$flowline, gsub("flowline.rds", "flowline_up
 ```{r huc12 POIs}
 #  Derive or load HUC12 POIs ----------------------
 # Still need to deal with some duplicate HUC12s
-if(needs_layer(nav_gpkg, temp_POIs)) {
+if(needs_layer(nav_gpkg, nav_poi_layer)) {
   
-  if (needs_layer(nav_gpkg, nhdflowline)){
+  if (needs_layer(nav_gpkg, nhd_flowline)){
     # Subset NHD by VPU
     nhd <- VPU_Subset(nhd_rds, VPU) 
     
@@ -53,9 +53,9 @@ if(needs_layer(nav_gpkg, temp_POIs)) {
       mutate(dend = ifelse(!COMID %in% non_dend, 1, 0),
              poi = ifelse(!COMID %in% non_dend & TotDASqKM >= min_da_km, 1, 0))
       
-    write_sf(nhd, nav_gpkg, nhdflowline)
+    write_sf(nhd, nav_gpkg, nhd_flowline)
   } else {
-     nhd <- read_sf(nav_gpkg, nhdflowline)
+     nhd <- read_sf(nav_gpkg, nhd_flowline)
      try(nhd <- select(nhd, -c(minNet, WB, struct_POI, struct_Net, POI_ID)))
   }
 
@@ -72,13 +72,13 @@ if(needs_layer(nav_gpkg, temp_POIs)) {
   huc12_POIs <- POI_creation(st_drop_geometry(HUC12_COMIDs), filter(nhd, poi == 1), "HUC12")
 
   # Write out geopackage layer representing POIs for given theme
-  write_sf(huc12_POIs, nav_gpkg, temp_POIs)
+  write_sf(huc12_POIs, nav_gpkg, nav_poi_layer)
   tmp_POIs <- huc12_POIs
   
 } else {
   # Load HUC12 POIs as the tmpPOIs if they already exist
-  tmp_POIs <- read_sf(nav_gpkg, temp_POIs) 
-  nhd <- read_sf(nav_gpkg, nhdflowline)
+  tmp_POIs <- read_sf(nav_gpkg, nav_poi_layer) 
+  nhd <- read_sf(nav_gpkg, nhd_flowline)
 }
 ```
 
@@ -103,9 +103,9 @@ if(all(is.na(tmp_POIs$Type_Gages))) {
     addType(., tmp_POIs, "Gages")
 
   # Write out geopackage layer representing POIs for given theme
-  write_sf(tmp_POIs, nav_gpkg, temp_POIs)
+  write_sf(tmp_POIs, nav_gpkg, nav_poi_layer)
 } else {
-  tmp_POIs <- read_sf(nav_gpkg, temp_POIs)
+  tmp_POIs <- read_sf(nav_gpkg, nav_poi_layer)
 }
 ```
 
@@ -129,10 +129,10 @@ if(all(is.na(tmp_POIs$Type_TE))) {
     addType(., tmp_POIs, "TE")
 
   # Write out geopackage layer representing POIs for given theme
-  write_sf(tmp_POIs, nav_gpkg, temp_POIs)
+  write_sf(tmp_POIs, nav_gpkg, nav_poi_layer)
 } else {
   # Load TE POIs if they already exist
-  tmp_POIs <- read_sf(nav_gpkg, temp_POIs)
+  tmp_POIs <- read_sf(nav_gpkg, nav_poi_layer)
 }
 ```
 
@@ -163,11 +163,11 @@ if(all(is.na(tmp_POIs$Type_Conf))) {
   tmp_POIs <- POI_creation(conf_COMIDs, filter(nhd, dend ==1), "Conf") %>%
     addType(., tmp_POIs, "Conf")
   
-  write_sf(nhd, nav_gpkg, nhdflowline)
-  write_sf(tmp_POIs, nav_gpkg, temp_POIs)
+  write_sf(nhd, nav_gpkg, nhd_flowline)
+  write_sf(tmp_POIs, nav_gpkg, nav_poi_layer)
 } else {
-  nhd <- read_sf(nav_gpkg, nhdflowline)
-  tmp_POIs <- read_sf(nav_gpkg, temp_POIs)
+  nhd <- read_sf(nav_gpkg, nhd_flowline)
+  tmp_POIs <- read_sf(nav_gpkg, nav_poi_layer)
 }
 ```
 
@@ -187,10 +187,10 @@ if(all(is.na(tmp_POIs$Type_NID))) {
     addType(., tmp_POIs, "NID", bind = FALSE)
 
   # Write out geopackage layer representing POIs for given theme
-  write_sf(tmp_POIs, nav_gpkg, temp_POIs)
+  write_sf(tmp_POIs, nav_gpkg, nav_poi_layer)
 } else {
   # Load NID POIs if they already exist
-  tmp_POIs <- read_sf(nav_gpkg, temp_POIs)
+  tmp_POIs <- read_sf(nav_gpkg, nav_poi_layer)
 }
 ```
 
@@ -207,7 +207,7 @@ if(all(is.na(tmp_POIs$Type_WBOut))) {
     st_sf()
 
   # Write out waterbodies
-  write_sf(st_transform(WBs_VPU, 4269), nav_gpkg, WBs)
+  write_sf(st_transform(WBs_VPU, 4269), nav_gpkg, WBs_layer)
 
   # Segments that are in waterbodies
   nhd <- mutate(nhd, WB = ifelse(WBAREACOMI > 0 & WBAREACOMI %in% WBs_VPU$COMID, 1, 0))
@@ -233,11 +233,11 @@ if(all(is.na(tmp_POIs$Type_WBOut))) {
   tmp_POIs <- POI_creation(filter(wbin_COMIDs, !COMID %in% wbout_COMIDs$COMID), filter(nhd, poi == 1), "WBIn") %>%
     addType(., tmp_POIs, "WBIn")
 
-  write_sf(nhd, nav_gpkg, nhdflowline)
-  write_sf(tmp_POIs, nav_gpkg, temp_POIs)
+  write_sf(nhd, nav_gpkg, nhd_flowline)
+  write_sf(tmp_POIs, nav_gpkg, nav_poi_layer)
 } else {
-  tmp_POIs <- read_sf(nav_gpkg, temp_POIs)
-  nhd <- read_sf(nav_gpkg, nhdflowline)
+  tmp_POIs <- read_sf(nav_gpkg, nav_poi_layer)
+  nhd <- read_sf(nav_gpkg, nhd_flowline)
 }
 ```
 
@@ -281,7 +281,7 @@ if(needs_layer(nav_gpkg, pois_all)) {
 
 ```{r Final segments}
 # Derive first cut of segments ----------------------
-if(needs_layer(nav_gpkg, n_segments)) {
+if(needs_layer(nav_gpkg, nsegments_layer)) {
 
   # Sort POIs by Levelpath and Hydrosequence in upstream to downstream order
   seg_POIs <-  filter(st_drop_geometry(nhd), COMID %in% tmp_POIs$COMID, COMID %in% filter(nhd, minNet == 1)$COMID) 
@@ -303,13 +303,13 @@ if(needs_layer(nav_gpkg, n_segments)) {
     mutate(struct_POI = ifelse(COMID %in% strucFeat$struc_POIs$COMID, 1, 0),
            struct_Net = ifelse(COMID %in% strucFeat$structnet$COMID, 1, 0))
   
-  write_sf(nhd_Final, nav_gpkg, nhdflowline)
-  write_sf(nsegments, nav_gpkg, n_segments)
+  write_sf(nhd_Final, nav_gpkg, nhd_flowline)
+  write_sf(nsegments, nav_gpkg, nsegments_layer)
 } else {
   # Read in NHDPlusV2 flowline simple features and filter by vector processing unit (VPU)
   final_POIs <- read_sf(nav_gpkg, pois_all)
-  nhd_Final <- read_sf(nav_gpkg, nhdflowline)
-  nsegments <- read_sf(nav_gpkg, n_segments)
+  nhd_Final <- read_sf(nav_gpkg, nhd_flowline)
+  nsegments <- read_sf(nav_gpkg, nsegments_layer)
 }
 
 # Ensure that all the problem POIs have been taken care of
@@ -331,11 +331,11 @@ if(needs_layer(nav_gpkg, pois_merge)) {
 
   # Write out geopackage layer representing POIs for given theme
   write_sf(out_HUC12$allPOIs, nav_gpkg, pois_merge)
-  write_sf(nhd_Final, nav_gpkg, nhdflowline)
-  write_sf(out_HUC12$segs, nav_gpkg, n_segments)
+  write_sf(nhd_Final, nav_gpkg, nhd_flowline)
+  write_sf(out_HUC12$segs, nav_gpkg, nsegments_layer)
 } else {
   final_POIs <- read_sf(nav_gpkg, pois_merge)
-  nhd_Final <- read_sf(nav_gpkg, nhdflowline)
-  nsegments <- read_sf(nav_gpkg, n_segments)
+  nhd_Final <- read_sf(nav_gpkg, nhd_flowline)
+  nsegments <- read_sf(nav_gpkg, nsegments_layer)
 }
 ```

workspace/05_hyRefactor_flines.Rmd

@@ -37,7 +37,7 @@ Load and filter source NHD Flowline network.
 if(needs_layer(out_gpkg, nhd_flowline)) {
   
   # Determine which Flowlines are in scope, previously implemented in NHD_Navigate
-  nhd <- read_sf(gf_gpkg, "NHDFlowline") %>%
+  nhd <- read_sf(gf_gpkg, "nhd_flowline") %>%
     subset_rpu(rpu_code, run_make_standalone = TRUE) %>%
     st_sf()
   

workspace/R/config.R

@@ -41,6 +41,8 @@ if(!nchar(cache_split <- Sys.getenv("CACHE_SPLIT")) > 5)
 if(!nchar(lookup_table_file <- Sys.getenv("LOOKUP_TABLE")) > 5) 
   lookup_table_file <- file.path("cache", paste0(rpu_code, "_lookup.csv"))
 
+options(scipen = 9999)
+
 # Source Data
 crs <- 5070
 data_paths <- jsonlite::read_json(file.path("cache", "data_paths.json"))