From a629b02e1d0ba965e0aacdc5507b49365e346a09 Mon Sep 17 00:00:00 2001
From: David Blodgett <dblodgett@usgs.gov>
Date: Fri, 14 May 2021 16:21:54 -0500
Subject: [PATCH] config updates
---
workspace/02_NHD_navigate.Rmd | 62 +++++++++++++++---------------
workspace/05_hyRefactor_flines.Rmd | 2 +-
workspace/R/config.R | 2 +
3 files changed, 34 insertions(+), 32 deletions(-)
diff --git a/workspace/02_NHD_navigate.Rmd b/workspace/02_NHD_navigate.Rmd
index 5732fd0..26a8ed7 100644
--- a/workspace/02_NHD_navigate.Rmd
+++ b/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)
}
```
diff --git a/workspace/05_hyRefactor_flines.Rmd b/workspace/05_hyRefactor_flines.Rmd
index 6bba6b1..514c7cc 100644
--- a/workspace/05_hyRefactor_flines.Rmd
+++ b/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()
diff --git a/workspace/R/config.R b/workspace/R/config.R
index c737f5d..65cff81 100644
--- a/workspace/R/config.R
+++ b/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"))
--
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