added examples and started vignette

Author: dkopp3

.gitignore

@@ -2,3 +2,4 @@
 .Rhistory
 .RData
 .Ruserdata
+Example_Data/NHDPlus/

Example_Data/Sample_Locations.csv

@@ -1,9 +1,4 @@
 SiteName,StreamName,N,W,VPU
-SC2,Sycamore Creek,33.86396,-111.4655,15
-SC3,Sycamore Creek,33.78711,-111.50788,15
-WC1,Workman Creek,33.83373,-110.95091,15
-WC2,Workman Creek,33.84628,-110.9681,15
-WC3,Workman Creek,33.84776,-110.98302,15
 CC2,Carrizo Creek,37.16442,-103.03109,11
 CC3,Carrizo Creek,37.13483,-103.01728,11
 MC1,Jimmy Creek,34.81536,-98.58271,11
@@ -12,7 +7,3 @@ MC3,Medicine Creek,34.77091,-98.58141,11
 KR1,Upper Kiamichi River,34.67789,-94.46922,11
 KR2,Upper Kiamichi River,34.67746,-94.48624,11
 KR3,Upper Kiamichi River,34.66721,-94.535,11
-SS1,Troublesome Branch,32.9778,-87.4146,03W
-SS2,Mayfield Creek,32.9683,-87.408,03W
-SS3,South Sandy Creek,32.9661,-87.3919,03W
-TC,Terlingua Creek,29.20012,-103.60625,13

StreamNetworkTools/vignettes/SNT_Examples.R

@@ -1,26 +1,102 @@
 # example workflow for StreamNetworkTools
-remove.packages("StreamNetworkTools")
 
 # install devtools if not already
-#install.packages(devtools)
+# install.packages(devtools)
 library("devtools")
-#install StreamNetworkTools from github repository
-#install_git("https://github.com/dkopp3/StreamNetworkTools_git.git", subdir = "StreamNetworkTools")
+
+# install StreamNetworkTools from github repository
+# install_git("https://github.com/dkopp3/StreamNetworkTools_git.git", subdir = "StreamNetworkTools")
 library(StreamNetworkTools)
 
-#check package help
-help(package="StreamNetworkTools")
+#check SNT package help for avaialble functions
+help(package ="StreamNetworkTools")
 
 # to begin download NHDPlusV2 data for Vector Processing Unit (VPU) of interest
 # here we are using VPU 11 which includes Arkansas, Red and White River basins
 # check function documentation for further details
 # setwd to example folder - where NHDPlusV2 data will be downloaded
-# this is mostly to keep myself organized
+
 setwd("C:/Users/Darin/Dropbox/Dissertation/Chapter_2_StreamNetworkTools/StreamNetworkTools_git/Example_Data")
 
-?net_nhdplus
-net_nhdplus(nhdplus_path = getwd(), download = "http",
-            vpu = 11, files = ALL, zip_7 = "C:/Program Files/7-Zip")
+# check documentation
+# net_nhdplus
+# can download all available data for vpu but sppecified only files needed to run streamNetworkTools
+# this can be time consuming, be patient it only has to be done once
+# data for VPU is already present in example data folder
+
+#net_nhdplus(nhdplus_path = getwd(), download = "http",
+ #           vpu = 11, files = c("NHDPlusAttributes", "NHDSnapshot",
+  #                              "NHDPlusCatchment", "VPUAttributeExtension",
+   #                             "VogelExtension", "EROMExtension"),
+    #        zip_7 = "C:/Program Files/7-Zip")
+
+# can run with for loop to download all VPU in CONUS
+# recommend running overnight
+
+#vpus<- c("01","02","03N","03S","03W","04","05","06","07","08","09","10U",
+ #        "10L","11","12","13","14","15","16","17","18")
+
+# for (i in vpus){
+  # net_nhdplus(nhdplus_path = getwd(), download = "http",
+   #            vpu = i, files = c("NHDPlusAttributes", "NHDSnapshot",
+    #                               "NHDPlusCatchment", "VPUAttributeExtension",
+     #                              "VogelExtension", "EROMExtension"),
+      #         zip_7 = "C:/Program Files/7-Zip")
+#}
+
+# net_sample randomly selects comid's of specified stream order from a vector processing unit
+# below identifies 3, fifth order comid's from VPU 11
+
+rmd_comid <- net_sample(nhdplus_path = getwd(), vpu = "11", ws_order = 5, n = 3)
+print(rmd_comid)
+
+# net_delin queries all COMID's upsteam comid's from root
+# inpput group_comids must be character
+rmd_netdelin <- net_delin(group_comid = as.character(rmd_comid),
+                          nhdplus_path = getwd(),
+                          vpu = "11")
+# output is list of 3
+str(rmd_netdelin)
+
+# can write network as shapefile with
+library(sf)
+write_sf(rmd_netdelin$SF_Obj, paste(getwd(),"/rmd_netdelin.shp", sep = ""))
+
+# value added attribute queries for NHDPlusV2
+# landcover percentage are for sub-catchments
+rmd_netlc <- net_lc(netdelin = rmd_netdelin, vpu = "11", nhdplus_path = getwd())
+# field headings follow https://www.mrlc.gov/nlcd11_leg.php
+head(rmd_netlc)
+
+# climate variables follow world clim, bioclim variables and were calculated from 1971-2001 PRISM
+# where necessary units are in tempp in deg C and ppt in mm
+rmd_netclim <- net_clim (nhdplus_path = getwd(), vpu = "11", netdelin = rmd_netdelin)
+head(rmd_netclim)
+
+# flow variables were calculated using the Mean Annual and Mean Monthly EROM
+rmd_netflow <- net_flow(nhdplus_path = getwd(), vpu = "11", netdelin = rmd_netdelin)
+head(rmd_netflow)
+
+# network scale topology
+rmd_netclac <- net_calc(netdelin = rmd_netdelin, vpu = "11", nhdplus_path = getwd())
+head(rmd_netclac)
+
+# net_hort M values are not included here
+rmd_nethort <- net_hort(netdelin = rmd_netdelin, vpu = "11", nhdplus_path = getwd())
+str(rmd_nethort)
 
+# net sinu gives values for each reach (comid) within a network
+rmd_netsinu <- net_sinu (netdelin = rmd_netdelin, nhdplus_path = getwd(), vpu = "11")
+head(rmd_netsinu)
 
+# can be aggregated as a network mean
+mean.sinu <- aggregate(rmd_netsinu[,"sinuosity"],
+                       by = list(group.comid = rmd_netsinu[,"group.comid"]),
+                       mean)
+head(mean.sinu)
 
+# net_conflu resullts are given by each confluence
+# this takes a while - ended
+#rmd_netconflu <- net_conflu(netdelin = rmd_netdelin,
+ #                           nhdplus_path = getwd(),
+  #                          vpu = "11")