From 207dd76021bf1b2e39c8df82b6342c171f983204 Mon Sep 17 00:00:00 2001
From: David Blodgett <dblodgett@usgs.gov>
Date: Mon, 25 Nov 2024 14:21:34 -0600
Subject: [PATCH] resolve minor issues
---
workspace/02_NHD_navigate.Rmd | 4 +++-
workspace/03_hyRefactor_flines.Rmd | 5 -----
workspace/05-2_NonDend.Rmd | 12 ++++++------
workspace/R/NHD_navigate.R | 8 ++++----
workspace/R/non_dend.R | 4 ++--
workspace/R/poi_move.R | 2 ++
workspace/R/user_vars.R | 6 +++---
7 files changed, 20 insertions(+), 21 deletions(-)
diff --git a/workspace/02_NHD_navigate.Rmd b/workspace/02_NHD_navigate.Rmd
index fd0e904..6c1edc8 100644
--- a/workspace/02_NHD_navigate.Rmd
+++ b/workspace/02_NHD_navigate.Rmd
@@ -211,7 +211,7 @@ if(needs_layer(temp_gpkg, "WBs_layer_orig")){
ref_WB <- WBs_VPU_all %>%
group_by(wb_id, GNIS_NAME) %>%
sfheaders::sf_remove_holes() %>%
- summarize(do_union = T, member_comid = paste(COMID, collapse = ",")) %>%
+ summarize(do_union = TRUE, member_comid = paste(COMID, collapse = ",")) %>%
st_make_valid() %>%
ungroup() %>%
mutate(area_sqkm = as.numeric(st_area(.)) / 1000000) %>%
@@ -236,6 +236,7 @@ if(!"Type_resops" %in% names(tmp_POIs)){
mutate(member_comid = as.character(member_comid)) %>%
distinct()
+ # TODO: get this file from data.json
# ResOpsUS locations with attributes from the VPU NHDv2 wb set
resops_wb_df <- read.csv("data/reservoir_data/istarf_xwalk_final_48_gfv11.csv") %>%
# Subset to VPU, only one DAMID per waterbody
@@ -925,6 +926,7 @@ final_POIs_prec <- mutate(final_POIs, id = row_number(), moved = NA) %>%
write_sf(nav_gpkg, nav_poi_layer)
collapse <- TRUE
+# TODO: document what this is doing!
source("R/poi_move.R")
check_dups <- final_POIs %>%
diff --git a/workspace/03_hyRefactor_flines.Rmd b/workspace/03_hyRefactor_flines.Rmd
index d23d0b3..cabb6c3 100644
--- a/workspace/03_hyRefactor_flines.Rmd
+++ b/workspace/03_hyRefactor_flines.Rmd
@@ -177,11 +177,6 @@ if(needs_layer(out_refac_gpkg, outlets_layer)) {
filter(member_COMID == max(member_COMID)) %>%
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")
write_sf(outlets_ref_COMID, out_refac_gpkg, outlets_layer)
} else {
diff --git a/workspace/05-2_NonDend.Rmd b/workspace/05-2_NonDend.Rmd
index 77f64e4..e700887 100644
--- a/workspace/05-2_NonDend.Rmd
+++ b/workspace/05-2_NonDend.Rmd
@@ -183,7 +183,7 @@ if(needs_layer(ND_gpkg, divides_nd)){
if(debug) {
protoHRUs <- divides_lu %>%
group_by("POI_ID") %>%
- summarize(do_union = T) %>%
+ summarize(do_union = TRUE) %>%
sfheaders::sf_remove_holes(.) %>%
st_make_valid()
write_sf(protoHRUs, ND_gpkg, HRU_layer)
@@ -223,7 +223,7 @@ if(!"HUC_12" %in% unique(divides_lu$aggStep)){
# HRU layer
protoHRUs <- divides_lu %>%
group_by(POI_ID) %>%
- summarize(do_union = T) %>%
+ summarize(do_union = TRUE) %>%
sfheaders::sf_remove_holes(.) %>%
st_make_valid()
write_sf(protoHRUs, ND_gpkg, HRU_layer)
@@ -259,7 +259,7 @@ if("Coastline" %in% unique(vpu_nhd$FTYPE)){
# HRU layer
protoHRUs <- divides_lu %>%
group_by(POI_ID) %>%
- summarize(do_union = T) %>%
+ summarize(do_union = TRUE) %>%
sfheaders::sf_remove_holes(.) %>%
st_make_valid()
# Write out updates
@@ -370,7 +370,7 @@ if(needs_layer(ND_gpkg, missing_cats)){
# Prob HRU - filter(all_hrus, POI_ID == 140402000209)
all_hrus <- filter(divides_lu, !is.na(POI_ID)) %>%
group_by(POI_ID) %>%
- summarize(do_union = T) %>%
+ summarize(do_union = TRUE) %>%
sfheaders::sf_remove_holes(.) %>%
nhdplusTools:::check_valid(.)
@@ -399,7 +399,7 @@ if(all(!is.na(noagg_divides$POI_ID_noagg))){
# Prob HRU - filter(all_hrus, POI_ID == 140402000209)
all_hrus <- filter(divides_lu, !is.na(POI_ID)) %>%
group_by(POI_ID) %>%
- summarize(do_union = T) %>%
+ summarize(do_union = TRUE) %>%
sfheaders::sf_remove_holes(.) %>%
nhdplusTools:::check_valid(.)
@@ -409,4 +409,4 @@ if(all(!is.na(noagg_divides$POI_ID_noagg))){
print ("account for unaggregated divides")
}
-```
\ No newline at end of file
+```
diff --git a/workspace/R/NHD_navigate.R b/workspace/R/NHD_navigate.R
index 7a4d3f9..3aaacd5 100644
--- a/workspace/R/NHD_navigate.R
+++ b/workspace/R/NHD_navigate.R
@@ -740,7 +740,7 @@ WB_event <- function(WBs, nhd_wb, type){
arrange(desc(Hydroseq)) %>%
group_by(LevelPathI) %>%
# union together
- summarize(do_union = T) %>%
+ summarize(do_union = TRUE) %>%
st_cast("LINESTRING")
WBs_HR <- filter(WBs_layer, source == "HR ID AVAILABLE")
@@ -1288,7 +1288,7 @@ wb_inlet_collapse <- function(tmp_POIs, nhd, events){
gage_reach <- gage_ds %>%
group_by(REACHCODE) %>%
- summarize(do_union = T,
+ summarize(do_union = TRUE,
total_length = sum(LENGTHKM))
#print(nrow(gage_reach))
@@ -1433,7 +1433,7 @@ wb_poi_collapse <- function(tmp_POIs, nhd, events){
gage_reach <- gage_ds %>%
group_by(REACHCODE) %>%
- summarize(do_union = T,
+ summarize(do_union = TRUE,
total_length = sum(LENGTHKM))
#print(nrow(gage_reach))
@@ -1719,4 +1719,4 @@ cs_group <- function(a, athres) {
result = c(result, group)
}
return (result)
-}
\ No newline at end of file
+}
diff --git a/workspace/R/non_dend.R b/workspace/R/non_dend.R
index 008afdd..090819d 100644
--- a/workspace/R/non_dend.R
+++ b/workspace/R/non_dend.R
@@ -10,7 +10,7 @@ dissolve_holes <- function(divides_poi){
# HRU layer
protoHRUs <- filter(divides_poi, !is.na(POI_ID)) %>%
group_by(POI_ID) %>%
- summarize(do_union = T) %>%
+ summarize(do_union = TRUE) %>%
clean_geometry(., ID = "POI_ID")
agg_noholes <- sfheaders::sf_remove_holes(protoHRUs) %>%
@@ -502,7 +502,7 @@ NHD_sinks <- function(divides_poi, area_thresh, HUC12_table, NHD_sinks){
# Aggretate sink cats to HUC12 and add area
sink_cats_agg <- filter(sink_cats, is.na(POI_ID)) %>%
group_by(HUC_12_int) %>%
- summarize(do_union = T) %>%
+ summarize(do_union = TRUE) %>%
mutate(agg_id = row_number())
m_per_km <- 1000
diff --git a/workspace/R/poi_move.R b/workspace/R/poi_move.R
index 3edcde7..ebfdd7a 100644
--- a/workspace/R/poi_move.R
+++ b/workspace/R/poi_move.R
@@ -1,3 +1,5 @@
+## TODO: document this file!
+
# Load data
if(collapse){
diff --git a/workspace/R/user_vars.R b/workspace/R/user_vars.R
index d721dbd..980c4ff 100644
--- a/workspace/R/user_vars.R
+++ b/workspace/R/user_vars.R
@@ -1,7 +1,7 @@
if(Sys.getenv("sb_user") == "CHANGEME") stop("must set sb_user")
# Path mods
-path_mod <- TRUE
+path_mod <- FALSE
if (path_mod){
# 7-zip
old_path <- Sys.getenv("PATH")
@@ -9,11 +9,11 @@ if (path_mod){
# Mapshaper
old_path <- Sys.getenv("PATH")
- Sys.setenv(PATH = paste(old_path, "C:\\Users\\abock\\AppData\\Roaming\\npm", sep = ";"))
+ Sys.setenv(PATH = paste(old_path, paste0(Sys.getenv("USERPROFILE"), "AppData\\Roaming\\npm"), sep = ";"))
# Whitebox Tools
library(whitebox)
- wbt_init(exe_path = "C:\\Users\\abock\\AppData\\Roaming\\R\\data\\R\\whitebox\\WBT\\whitebox_tools.exe")
+ wbt_init(exe_path = paste0(Sys.getenv("USERPROFILE"), "AppData\\Roaming\\R\\data\\R\\whitebox\\WBT\\whitebox_tools.exe"))
}
# CRS for projected and geographic reference systems
--
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