Renamed sites to correspond with monitoring site IDs. Changed catchme…

code/get_flow_network.R

@@ -11,17 +11,21 @@
 library(sf)
 library(nhdplusTools)
 library(tidyverse)
+library(mapview)
+library(mapedit)
+library(leaflet)
+library(leafpm)
 
 # Identify the COMID ------------------------------------------------------
 
 # comid for confluence segment Shasta-Little Shasta
-peace <- st_sfc(st_point(c(-122.51016, 41.70364)), crs=4326) # peacemaker gage
-uspt <- st_sfc(st_point(c(-122.34792, 41.73355)), crs=4326) # upstream gage
+PMK <- st_sfc(st_point(c(-122.51016, 41.70364)), crs=4326) # peacemaker gage
+LSR <- st_sfc(st_point(c(-122.34792, 41.73355)), crs=4326) # upstream gage
 
-(peace_comid <- discover_nhdplus_id(point = peace))
-(uspt_comid <- discover_nhdplus_id(point = uspt))
+(PMK_comid <- discover_nhdplus_id(point = PMK))
+(LSR_comid <- discover_nhdplus_id(point = LSR))
 
-pts <- tibble("site"=c("peace","uspt"), "comid"=c(peace_comid, uspt_comid))
+pts <- tibble("site"=c("PMK","LSR"), "comid"=c(PMK_comid, LSR_comid))
 
 # what sources of data?
 # discover_nldi_sources()$source
@@ -91,22 +95,65 @@ sf::st_layers("data/nhdplus_little_shasta.gpkg")
 
 # QUICK PLOTS -------------------------------------------------------------
 
-library(mapview)
-mapviewOptions(fgb=FALSE)
+#mapviewOptions(fgb=FALSE) #This argument didn't mean anything when Ann ran the code
 
 # read data in: flowlines
 flowlines <- sf::read_sf("data/nhdplus_little_shasta.gpkg", "NHDFlowline_Network")
 catchment <- sf::read_sf("data/nhdplus_little_shasta.gpkg", "CatchmentSP")
 
 # quick plot
-plot(catchment$geom,  lwd = 4, border = "gray30")
+plot(catchment$geom,  lwd = 4, border = "maroon3")
 plot(sf::st_geometry(flowlines), lwd = 7, col = alpha("blue", 0.5), add=TRUE)
 plot(lshasta_ut$geometry, lwd = 1.2, col = "dodgerblue", add = TRUE)
 
 # mapview
-mapview(catchment, color="gray50", col.regions="gray50", alpha.regions=0, alpha=0.5, lwd=2) +
+lshasta_rawmap <- mapview(catchment, color="maroon3", col.regions="gray50", alpha.regions=0, alpha=0.9, lwd=2) +
   mapview(flowlines, zcol="ftype") +
-  mapview(lshasta_ut, color="dodgerblue", lwd=0.75, alpha=0.9)
+  mapview(lshasta_ut, color="dodgerblue", lwd=2, alpha=0.9)
+
+lshasta_rawmap
+# so mainstem seems to be ok, but the associated tributaries are a jumble of diversions, canals, etc
+# Also, catchment outline is incomplete. See map in Little Shasta Report, figure 1 for the HUC catchment
+
+
+# Clean streamlines -------------------------------------------------------
+
+# First, create a list of all segments using their comids so we can add an attribute to them describing whether they are a stream channel (natural) or canal/ditch (canal)
+
+all_segments_w_sf <- rbind(lshasta_um,lshasta_ut)
+
+all_segments <- st_set_geometry(all_segments_w_sf,NULL)
+
+all_segments$channel_type <- with(all_segments, ifelse(type=="UM","natural",""))
+
+# Add another column to indicate whether the natural channel is altered (e.g., the runoff is natural, but it's been run into a ditch that's routed to the stream), unaltered (e.g., the natural channel), or NA (e.g., it's a canal)
+
+all_segments$altered <- with(all_segments, ifelse(type=="UM","unaltered",""))
+
+# Review each segment individually and update all_segments df
+
+natural_unaltered_segs <- as.character(c("3917194", "3917136", "3917138", "3917914", "3917916", "3917082", "3917114", "3917154", "3917156", "3917172", "3917164", "3917158", "3917160", "3917922", "3917364","3917372", "3917326", "3917330", "3917328", "3917374","3917392", "3917084", "3917084", "3917106", "3917130", "3917162", "3917176", "3917178", "3917198", "3917200", "3917244", "3917912", "3917918", "3917946", "3917948", "3917950"))
+
+natural_altered_segs <- as.character(c("948010089", "3917920"))
+
+canal_segs <- as.character(c("3917230", "3917954", "3918004", "3917382", "3917266", "3917222", "3917212", "3917214", "3917218", "3917228", "3917270", "3917250", "3917256", "3917268", "3917284", "3917282", "3917274", "3917278", "3917276", "3917958", "3917960", "3917384",  "3917370",  "3917376"))
+
+all_segments <- all_segments %>%
+  mutate(channel_type = case_when(nhdplus_comid %in% natural_unaltered_segs ~ "natural",
+                                  nhdplus_comid %in% natural_altered_segs ~ "natural",
+                                  nhdplus_comid %in% canal_segs ~ "canal"))
+
+all_segments <- all_segments %>%
+  mutate(altered = case_when(nhdplus_comid %in% natural_unaltered_segs ~ "unaltered",
+                                  nhdplus_comid %in% natural_altered_segs ~ "altered",
+                                  nhdplus_comid %in% canal_segs ~ "NA"))
+
+# filter all_segments df so that only natural channels w/in the Little Shasta watershed are included; UM segments are duplicated in the UT record, so filter out duplicate comids
+
+lshasta_stream_network <- all_segments %>%
+  filter(channel_type == "natural", type == "UT")
+
+#write out Little Shasta stream network as csv
 
+write_csv(lshasta_stream_network, path = "data/lshasta_stream_network.csv")
 
-# so mainstem seems to be ok, but the associated tributaries are a jumble of diversions, canals, etc.

data/lshasta_stream_network.csv

@@ -0,0 +1,38 @@
+nhdplus_comid,type,channel_type,altered
+3917946,UT,natural,unaltered
+3917244,UT,natural,unaltered
+3917950,UT,natural,unaltered
+3917948,UT,natural,unaltered
+3917200,UT,natural,unaltered
+3917198,UT,natural,unaltered
+948010089,UT,natural,altered
+3917918,UT,natural,unaltered
+3917920,UT,natural,altered
+3917922,UT,natural,unaltered
+3917364,UT,natural,unaltered
+3917372,UT,natural,unaltered
+3917176,UT,natural,unaltered
+3917164,UT,natural,unaltered
+3917160,UT,natural,unaltered
+3917158,UT,natural,unaltered
+3917178,UT,natural,unaltered
+3917172,UT,natural,unaltered
+3917374,UT,natural,unaltered
+3917392,UT,natural,unaltered
+3917912,UT,natural,unaltered
+3917156,UT,natural,unaltered
+3917328,UT,natural,unaltered
+3917330,UT,natural,unaltered
+3917162,UT,natural,unaltered
+3917154,UT,natural,unaltered
+3917326,UT,natural,unaltered
+3917130,UT,natural,unaltered
+3917114,UT,natural,unaltered
+3917106,UT,natural,unaltered
+3917916,UT,natural,unaltered
+3917084,UT,natural,unaltered
+3917082,UT,natural,unaltered
+3917914,UT,natural,unaltered
+3917194,UT,natural,unaltered
+3917136,UT,natural,unaltered
+3917138,UT,natural,unaltered