gagesiii to swim in gage_info

workspace/00_gage_info.Rmd

@@ -40,11 +40,11 @@ gages_ii_ref <- read_sf(data_paths$gagesii_lyr) %>%
   st_drop_geometry()
 ```
 
-Get data from Gages III 
-```{r gagesiii}
-### read GagesIII data file from DBF file
-allsites <- read.dbf(file.path(data_paths$gagesiii_points_path,
-                               "GAGESIII_gages.dbf"), 
+Get data from SWIM
+```{r swim}
+### read swim data file from DBF file
+allsites <- read.dbf(file.path(data_paths$SWIM_points_path,
+                               "SWIM_gage_loc.dbf"), 
                      as.is = TRUE)
 
 allsites_dup <- group_by(allsites, Gage_no) %>%
@@ -70,8 +70,8 @@ if(file.exists(tempf)) {
 ```
 
 
-Provide some initial POR coverage for GAGES III
-```{r analysis_gagesiii}
+Provide some initial POR coverage for SWIM
+```{r analysis_swim}
 #Calculate number of days between begin date and end date
 dailydata$TPdays <- difftime(dailydata$end_date,
                              dailydata$begin_date,
@@ -111,10 +111,10 @@ dailydata <- dailydata %>%
 dailydata$TPdays1 <- as.numeric(dailydata$TPdays1)
 dailydata$missing_days<-as.numeric(dailydata$missing_days)
 
-gagesiii_all <- full_join(siteinfo, dailydata, by = "site_no") %>%
+swim_all <- full_join(siteinfo, dailydata, by = "site_no") %>%
   left_join(gages_ii_ref, by = c("site_no" = "STAID"))
 
-mapview(st_as_sf(gagesiii_all, coords = c("dec_long_va", "dec_lat_va"), crs = 4326), layer.name = "GAGES-III sites with daily Q") 
+mapview(st_as_sf(swim_all, coords = c("dec_long_va", "dec_lat_va"), crs = 4326), layer.name = "SWIM sites with daily Q") 
 ```
 
 Evaluate the NHDPlus GageLoc dataset
@@ -123,7 +123,7 @@ Evaluate the NHDPlus GageLoc dataset
 
 GageLocAll <- sf::read_sf(data_paths$nhdplus_gdb, "Gage") 
 
-#get rid of gages that are also in GagesIII
+#get rid of gages that are also in SWIM
 GageLoc<-anti_join(GageLocAll, gages, by = c("SOURCE_FEA"="Gage_no"))#16719 gages
 
 tempf <- "temp/gages_gagloc_nwis_daily.rds"
@@ -182,7 +182,7 @@ GLmdays_tojoin <- mostGLmdays %>%
 GLmdays_tojoin$TPdays1<-as.numeric(GLmdays_tojoin$TPdays1)
 GLmdays_tojoin$missing_days<-as.numeric(GLmdays_tojoin$missing_days)
 
-#rearrange column order so the same as previous file with gages 3 data.
+#rearrange column order so the same as previous file with SWIM data.
 gageloc_all <- full_join(GLSI_tojoin, GLmdays_tojoin, by = "site_no") %>%
   select(site_no, drain_area_va, contrib_drain_area_va, agency_cd,  station_nm,
          site_tp_cd, dec_lat_va, dec_long_va, coord_acy_cd, huc_cd, 
@@ -191,19 +191,19 @@ gageloc_all <- full_join(GLSI_tojoin, GLmdays_tojoin, by = "site_no") %>%
   filter(!is.na(dec_lat_va)) %>%
   left_join(gages_ii_ref, by = c("site_no" = "STAID"))
 
-mapview(st_as_sf(gagesiii_all, coords = c("dec_long_va", "dec_lat_va"), crs = 4326), layer.name = "GAGES-III sites with daily Q") +
-  mapview(st_as_sf(filter(gageloc_all, !site_no %in% gagesiii_all$site_no), 
+mapview(st_as_sf(swim_all, coords = c("dec_long_va", "dec_lat_va"), crs = 4326), layer.name = "SWIM sites with daily Q") +
+  mapview(st_as_sf(filter(gageloc_all, !site_no %in% swim_all$site_no), 
           coords = c("dec_long_va", "dec_lat_va"), crs = 4326), layer.name = "GageLoc sites with daily Q", col.regions = "orange") 
 ```
 
 
 Retrieve streamgages that were a part of GFv1.1.  This ensures all past locations used for modeling work are included in GFV2.0.
 
-These will overlap with GAGES III and GageLoc but will sort out redundancy later
+These will overlap with SWIM and GageLoc but will sort out redundancy later
 ```{r Gages_GFv1.1}
 # Read in data layer, 373 non-EC gages
 GFv11_gage <- readRDS(data_paths$GFv11_gages_lyr) %>% 
-  filter(!Type_Gage %in% c(gageloc_all$site_no, gagesiii_all$site_no) &
+  filter(!Type_Gage %in% c(gageloc_all$site_no, swim_all$site_no) &
            # Exclude GFv11 gages
            nchar(NHD_Unit) < 4)
 
@@ -265,7 +265,7 @@ Gv11mdays_tojoin <- mostGv11mdays %>%
 Gv11mdays_tojoin$TPdays1 <- as.numeric(Gv11mdays_tojoin$TPdays1)
 Gv11mdays_tojoin$missing_days <- as.numeric(Gv11mdays_tojoin$missing_days)
 
-#rearrange column order so the same as previous file with gages 3 data.
+#rearrange column order so the same as previous file with SWIM data.
 gagev11_all <- full_join(Gv11SI_tojoin, Gv11mdays_tojoin, by = "site_no") %>%
   select(site_no, drain_area_va, contrib_drain_area_va, agency_cd,  station_nm,
          site_tp_cd, dec_lat_va, dec_long_va, coord_acy_cd, huc_cd, 
@@ -281,10 +281,10 @@ mapview(st_as_sf(gagev11_all, coords = c("dec_long_va", "dec_lat_va"), crs = 432
 ```{r write}
 write.dbf(as.data.frame(gagev11_all), "data/GFV11.dbf")
 write.dbf(gageloc_all, "data/GageLocGFinfo.dbf")
-write.dbf(gagesiii_all, "data/gages3GFinfo.dbf")
+write.dbf(swim_all, "data/SWIMGFinfo.dbf")
 
 ### ONLY RUN IF CHANGED ###
 # sbtools::authenticate_sb()
 # sbtools::item_replace_files("5dcd5f96e4b069579760aedb", c("data/GageLocGFinfo.dbf",
-#                                                          "data/gages3GFinfo.dbf"))
+#                                                          "data/SWIMGFinfo.dbf"))
 ```
\ No newline at end of file

workspace/00_get_data.Rmd

@@ -71,7 +71,8 @@ if(!file.exists(SWIM_points_path)) {
   g3gf <- "gages3GFinfo.dbf"
   
   sbtools::item_file_download("5dcd5f96e4b069579760aedb", names = g3gf, 
-                              destinations = file.path(data_dir, g3gf))
+                              destinations = file.path(data_dir, g3gf), 
+                              overwrite_file = TRUE)
 }
 
 out_list <- c(out_list, list(SWIM_points_path = SWIM_points_path))
@@ -547,14 +548,14 @@ out_list <- c(out_list, out)
 
 ```{r Gages_II}
 # Download the GFv1.1 geodatabase
-if(!dir.exists(gagesiii_points_path)) 
-  dir.create(gagesiii_points_path, recursive = TRUE)
+if(!dir.exists(SWIM_points_path)) 
+  dir.create(SWIM_points_path, recursive = TRUE)
 
-g2_out <- list(gagesii_lyr = file.path(gagesiii_points_path, "gagesII_9322_point_shapefile.shp"))
+g2_out <- list(gagesii_lyr = file.path(SWIM_points_path, "gagesII_9322_point_shapefile.shp"))
 
 gagesII_url <- "https://water.usgs.gov/GIS/dsdl/gagesII_9322_point_shapefile.zip"
 
-zip <- file.path(gagesiii_points_path, basename(gagesII_url))
+zip <- file.path(SWIM_points_path, basename(gagesII_url))
 
 if(!file.exists(g2_out$gagesii_lyr)) {
   

workspace/R/utils.R

@@ -101,7 +101,7 @@ retrieve_sb <- function(sbitem, out_dir){
            {
              
              out_file <- file.path(out_path, y$name)
-             download.file(y$downloadUri, out_file)
+             download.file(y$downloadUri, out_file, mode = "wb")
              
              list(fname = y$name,
                   url = y$downloadUri)
@@ -270,7 +270,7 @@ get_HUC12_Xwalk <- function(VPU, full_cats = FALSE, divides = FALSE, wbd = FALSE
     # Convert area to squaker kilometers 
     mutate(intArea = as.numeric(st_area(.)) * 0.000001,
            AreaHUC12 = ACRES * .00404686) %>%
-    rename(HUC_12_int = HUC_12.1)
+    rename(HUC_12_int = HUC_12)
   
   
   return(list(cats_HUC12 = cats_HUC12, divides_HUC12 = divides_HUC12))

workspace/cache/data_paths.json

 {
   "data_dir": "data",
   "hu12_points_path": "data/hu_outlets.gpkg",
-  "swim_points_path": "data/SWIM_gages",
+  "SWIM_points_path": "data/SWIM_gage_loc",
   "TE_points_path": "data/TE_points",
   "USGS_IT_path": "data/USGS_IT",
   "NID_points_path": "data/NID_points",
@@ -175,6 +175,6 @@
   "new_nwm_nhdp_atts": "cache/nwm_enhd_nhdplusatts.csv",
   "GFv11_gages_lyr": "data/GFv11/GFv11_gages.rds",
   "GFv11_gdb": "data/GFv11/GFv1.1.gdb",
-  "gagesii_lyr": "data/GAGESIII_gages/gagesII_9322_point_shapefile.shp",
+  "gagesii_lyr": "data/SWIM_gage_loc/gagesII_9322_point_shapefile.shp",
   "new_nhdp_rds": "data/NHDPlusNationalData/nhdplus_flowline_update.rds"
 }