Renamed

workspace/05_hyRefactor_flines.Rmd → workspace/03_hyRefactor_flines.Rmd

@@ -26,19 +26,22 @@ See `hyRefactory_config.R` for all constants.
 source("R/utils.R")
 source("R/hyRefactor_funs.R")
 source("R/config.R")
+source("R/user_vars.R")
 ```
 
 Load and filter source NHD Flowline network. Bring in POIs
 ```{r flowlines}
 nhd <- read_sf(out_refac_gpkg, nhd_flowline)
 
-cats <- read_sf(out_refac_gpkg, nhd_catchment)
+#cats <- read_sf(out_refac_gpkg, nhd_catchment)
   
 POIs_data <- read_sf(nav_gpkg, poi_data_table)
 
 POIs <- read_sf(nav_gpkg, poi_geometry_table)
 
 POI_id <- st_drop_geometry(POIs)
+
+events <- read_sf(nav_gpkg, event_geometry_table)
 ```
 
 Read POIs and add nhd outlets. Save to a non-spatial table.
@@ -72,15 +75,17 @@ nhdplus_flines <- sf::st_zm(filter(nhd, refactor == 1)) %>%
   st_as_sf() 
 
 if(!needs_layer(nav_gpkg, event_geometry_table)){
-  events <- read_sf(nav_gpkg, event_geometry_table) %>%
-    mutate(event_identifier = as.character(row_number()))
+  events <- read_sf(nav_gpkg, event_geometry_table) 
   
   events_ref <- filter(events, hy_id %in% nhdplus_flines$COMID) %>%
     rename(COMID = hy_id) %>%
-    distinct(COMID, REACHCODE, REACH_meas, event_identifier)
+    distinct(COMID, REACHCODE, REACH_meas, 
+             poi_id, geom) %>%
+    arrange(poi_id) %>%
+    mutate(event_identifier = row_number())
   
-  outlets <- filter(outlets, !poi_id %in% events$poi_id) %>%
-    rename(COMID = hy_id)
+  outlets <- rename(outlets, COMID = hy_id) %>%
+    filter(!poi_id %in% events_ref$poi_id)
 } else {
   events_ref <- NULL
 }
@@ -103,11 +108,12 @@ if(needs_layer(out_refac_gpkg, refactored_layer)) {
                    three_pass = TRUE, 
                    purge_non_dendritic = FALSE, 
                    events = events_ref,
-                   exclude_cats = c(outlets$COMID, avoid$COMID, POI_downstream$COMID),
+                   exclude_cats = c(outlets$COMID, 
+                                    avoid$COMID, POI_downstream$COMID),
                    warn = TRUE)
   
-  write_sf(st_transform(read_sf(tf), crs), out_refac_gpkg, refactored_layer)
-  write_sf(st_transform(read_sf(tr), crs), out_refac_gpkg, reconciled_layer)
+  write_sf(st_transform(read_sf(tf), proj_crs), out_refac_gpkg, refactored_layer)
+  write_sf(st_transform(read_sf(tr), proj_crs), out_refac_gpkg, reconciled_layer)
   
   unlink(list(tf, tr))
   rm(tf, tr)
@@ -126,7 +132,7 @@ refactor_lookup <- st_drop_geometry(read_sf(out_refac_gpkg, reconciled_layer)) %
 if(is.character(refactor_lookup$reconciled_ID)) refactor_lookup$reconciled_ID <- as.integer(refactor_lookup$reconciled_ID)
 
 lookup_table <- tibble::tibble(NHDPlusV2_COMID = unique(as.integer(refactor_lookup$member_COMID))) %>%
-    dplyr::left_join(refactor_lookup, by = "NHDPlusV2_COMID") 
+    dplyr::left_join(refactor_lookup, by = "NHDPlusV2_COMID")
 
 readr::write_csv(lookup_table, lookup_table_file)
 write_sf(lookup_table, out_refac_gpkg, lookup_table_refactor)
@@ -138,49 +144,54 @@ if(needs_layer(out_refac_gpkg, outlets_layer)) {
     select(member_COMID = COMID, Hydroseq, event_identifier, event_REACHCODE) %>%
     inner_join(select(st_drop_geometry(nhd), orig_COMID = COMID, Hydroseq), by = "Hydroseq") 
   
-  if(!is.null(events_ref)){
+  if(nrow(events_ref) > 0){
     # Subset for events
     refactored_events <- refactored %>%
-      filter(!is.na(event_REACHCODE), !is.na(event_identifier))
+      filter(!is.na(event_REACHCODE), !is.na(event_identifier)) %>%
+      mutate(event_identifier = as.numeric(event_identifier))
   
-    event_outlets <- events %>%
+    event_outlets <- events_ref %>%
       inner_join(st_drop_geometry(refactored_events), by = "event_identifier") %>%
-      select(hy_id, event_id, poi_id, member_COMID)
+      select(hy_id = COMID, event_id = event_identifier, poi_id, member_COMID)%>% 
+      inner_join(select(lookup_table, -NHDPlusV2_COMID), by = "member_COMID")
     
     # subset for refactored outlets (non-events)
-    refactored_outlets <- filter(refactored, !member_COMID %in% event_outlets$member_COMID)
+    refactored_outlets <- filter(refactored, 
+                                 !member_COMID %in% event_outlets$member_COMID) 
     
     # get ref_COMId for other outlets
     outlets_ref <- outlets %>%
-      left_join(select(st_drop_geometry(refactored_outlets), member_COMID, orig_COMID), 
-                by = c("COMID" = "orig_COMID")) %>%
+      filter(!poi_id %in% event_outlets$poi_id) %>%
+      inner_join(lookup_table, 
+                by = c("COMID" = "NHDPlusV2_COMID")) %>%
       group_by(COMID) %>%
       filter(member_COMID == max(member_COMID)) %>%
-      select(hy_id = COMID, poi_id, member_COMID, type) 
+      select(hy_id = COMID, poi_id, member_COMID, reconciled_ID, type) 
     
-    outlets_ref_COMID <- data.table::rbindlist(list(outlets_ref, event_outlets), fill = TRUE) %>%
+    outlets_ref_COMID <- data.table::rbindlist(list(outlets_ref, event_outlets), 
+                                               fill = TRUE) %>%
       st_as_sf()
   } else {
     # get ref_COMId for other outlets
     outlets_ref_COMID <- outlets %>%
-      left_join(select(st_drop_geometry(refactored), member_COMID, orig_COMID), 
-                by = c("COMID" = "orig_COMID")) %>%
+      inner_join(lookup_table, 
+                by = c("COMID" = "NHDPlusV2_COMID")) %>%
       group_by(COMID) %>%
       filter(member_COMID == max(member_COMID)) %>%
-      select(hy_id = COMID, poi_id, member_COMID, type) 
+      select(hy_id = COMID, poi_id, member_COMID, reconciled_ID, type) 
   }
 
-  final_outlets <-  outlets_ref_COMID %>%
-    st_as_sf() %>%
-    inner_join(select(lookup_table, member_COMID, reconciled_ID), 
-                      by = "member_COMID") 
+  # final_outlets <-  outlets_ref_COMID %>%
+  #   st_as_sf() %>%
+  #   inner_join(select(lookup_table, member_COMID, reconciled_ID), 
+  #                     by = "member_COMID") 
   
-  write_sf(final_outlets, out_refac_gpkg, outlets_layer)
+  write_sf(outlets_ref_COMID, out_refac_gpkg, outlets_layer)
 } else {
-  final_outlets <- read_sf(out_refac_gpkg, outlets_layer)
+  outlets_ref_COMID <- read_sf(out_refac_gpkg, outlets_layer)
 }
 
-check_dups_poi <- final_outlets %>%
+check_dups_poi <- outlets_ref_COMID %>%
   group_by(reconciled_ID) %>%
   filter(n() > 1) %>%
   ungroup()