More o.o.s.

synoptic/L1_normalize.qmd

@@ -80,6 +80,7 @@ files_to_process <- list.files(L0, pattern = "*.csv$", full.names = TRUE)
 L1_NORMALIZE <- file.path(params$DATA_ROOT, params$L1_NORMALIZE)
 
 source("helpers.R")
+source("out-of-service.R")
 
 # Read the Aquatroll out-of-service table
 troll <- read_csv(file.path(params$DATA_ROOT, params$OOS,
@@ -203,9 +204,17 @@ f <- function(fn, out_dir, design_table) {
  
  message("\tAdding OOB flags")
  dat <- merge(dat, bt, by = c("research_name", "units"))
- dat$OOB <- as.integer(with(dat, value < low_bound | value > high_bound))
+ dat$F_OOB <- as.integer(with(dat, value < low_bound | value > high_bound))
  smry$`OOB%` <- round(sum(dat$OOB) / nrow(dat) * 100, 1)
  
+ # ------------- Out-of-service flags
+
+ message("\tAdding OOS flags")
+ x <- separate(dat, design_link, sep = "-", 
+ into = c("What", "Site", "Location", "Sensor"))
+ browser()
+ 
+ 
  # Remove unneeded columns unless needed for debugging
  if(!params$debug) {
  message("\tDropping bounds columns")

synoptic/helpers.R

@@ -352,7 +352,9 @@ ret <- valid_entries(objects = c(1, 1),
 stopifnot(ret == c(TRUE, FALSE))
 
 
-
+# We read in a version of the Aquatroll Calibration/Removal Log
+# (in Monitoring Documents on the COMPASS Google Drive) and restructure it
+# into a form ready for out-of-service calculations in L1_normalize.qmd
 prep_troll_oos_table <- function(troll) {
  # If no time_pulled given, assume 6 AM
  tp <- troll$Time_pulled
@@ -372,5 +374,7 @@ prep_troll_oos_table <- function(troll) {
  # Per Peter R., we throw out all data for 24 hours after replacement
  troll$oos_end <- troll$oos_end + 60 * 60 * 24
 
- troll[c("Site", "Location", "Troll", "oos_begin", "oos_end")]
+ troll$Sensor <- troll$Troll
+ troll$What <- "GW_BattV"
+ troll[c("Site", "Location", "Sensor", "oos_begin", "oos_end")]
 }