Merge branch 'main' into 'main'

Clean up and fix issues in reference flowline creation

See merge request !171

workspace/00_get_data.Rmd

@@ -278,7 +278,7 @@ if(!file.exists(ref_cat)){
 
   for (vpu in possible_vpu){
     vpu_gpkg <- paste0(vpu, "_reference_features.gpkg")
-    sbtools::item_file_download("61295190d34e40dd9c06bcd7", names = vpu_gpkg, 
+    sbtools::item_file_download("6317a72cd34e36012efa4e8a", names = vpu_gpkg, 
                                 destinations = file.path(ref_fab_path, vpu_gpkg))
   }
   
@@ -545,22 +545,6 @@ out_list <- c(out_list, out)
 
 ```
 
-```{r nhdplus_attributes}
-
-out <- list(new_nhdp_atts = file.path("cache", (sb_f <- "enhd_nhdplusatts.csv")))
-
-if(!file.exists(out$new_nhdp_atts)) {
-  if(is.null(sbtools::current_session()))
-    authenticate_sb()
-
-  sbtools::item_file_download("63cb311ed34e06fef14f40a3",
-                              names = sb_f,
-                              destinations = out$new_nhdp_atts)
-}
-
-out_list <- c(out_list, out)
-```
-
 ```{r GFv1.1}
 GFv11_dir <- file.path(data_dir, "GFv11")
 out <- list(GFv11_gages_lyr = file.path(data_dir, "GFv11/GFv11_gages.rds"),

workspace/02_NHD_navigate.Rmd

@@ -260,7 +260,7 @@ if(!"Type_WBOut" %in% names(tmp_POIs)) {
   tmp_POIs <- read_sf(temp_gpkg, nav_poi_layer)
   nhd <- read_sf(nav_gpkg, nhd_flowline)
   ref_WB <- read_sf(temp_gpkg, WBs_layer)
-  resops_POIs_df <- read.csv(file.path("data/reservoir_Data", paste0("resops_POIs_",vpu,".csv")))
+  resops_POIs_df <- read.csv(file.path("data/reservoir_Data", paste0("resops_POIs_", VPU,".csv")))
 }
 
 mapview(filter(tmp_POIs, !is.na(Type_WBOut)), layer.name = "Waterbody outlet POIs", col.regions = "red")

workspace/05_hyRefactor_flines.Rmd

@@ -183,7 +183,7 @@ if(needs_layer(out_refac_gpkg, outlets_layer)) {
 check_dups_poi <- final_outlets %>%
   group_by(reconciled_ID) %>%
   filter(n() > 1) %>%
-  ungroup
+  ungroup()
 
 if(nrow(check_dups_poi) > 1){
   print("Double-check for double POIs")

workspace/06-2_aggregate_cats.Rmd

@@ -92,7 +92,7 @@ if(needs_layer(out_agg_gpkg, agg_cats_layer)){
     mutate(type = ifelse(type == "terminal" & !is.na(toID), "outlet", type)) %>%
     select(-toID)
   
-  outlets <- unique(outlets)
+  outlets <- distinct(outlets)
   agg_cats <- aggregate_catchments(flowpath = reconciled,
                                    divide = divides,
                                    outlets = outlets,

workspace/R/NHD_navigate.R

@@ -1135,7 +1135,7 @@ wbin_POIcreation <- function(nhd, WBs_VPU, data_paths, crs,
     # Drive the inlet events
     nhd_inlet <- filter(nhd_WBs, !COMID %in% wb_outlet_events$COMID)
     
-    if(unique(nhd$VPUID) == "12"){
+    if("12" %in% unique(nhd$VPUID)){
       nhd_inlet <- rbind(nhd_inlet, filter(nhd_WBs, COMID == 1304709))
     }
     

workspace/R/utils.R

@@ -27,8 +27,8 @@ fix_headwaters <- function(nhd_rds, out_gpkg, new_atts = NULL,
   ble <- sf::st_zm(sf::st_as_sf(ble))
   nhd <- sf::st_zm(nhd)
   
-  sf::st_geometry(nhd)[!sf::st_is_empty(sf::st_geometry(ble)) & (nhd$StartFlag == 1 | nhd$Divergence == 2)] <- 
-    sf::st_geometry(ble)[!sf::st_is_empty(sf::st_geometry(ble)) & (nhd$StartFlag == 1 | nhd$Divergence == 2)]
+  sf::st_geometry(nhd)[!sf::st_is_empty(sf::st_geometry(ble)) & (nhd$StartFlag == 1)] <- 
+    sf::st_geometry(ble)[!sf::st_is_empty(sf::st_geometry(ble)) & (nhd$StartFlag == 1)]
   
   if(!is.null(new_atts)) {
     new_atts <- data.table::fread(new_atts, 
@@ -109,6 +109,12 @@ fix_headwaters <- function(nhd_rds, out_gpkg, new_atts = NULL,
   
   nhd <- select(nhd, -override_tocomid)
   
+  # remove remnant attributes
+  nhd <- select(nhd, -FromNode, -ToNode, -StartFlag -StreamCalc, -Divergence, -DnMinorHyd)
+  
+  warning("naive duplication!")
+    nhd <- nhd[!duplicated(nhd$COMID), ]
+  
   sf::write_sf(nhd, out_gpkg, "reference_flowlines")
   
   }