Merge pull request #337 from USEPA/cristinamullin-updates

Contributing files, depth unit conversion update
USEPA · Sep 6, 2023 · 1d4292f · 1d4292f
2 parents 5fcd3f5 + a6a6020
commit 1d4292f
Show file tree

Hide file tree

Showing 21 changed files with 797 additions and 1,723 deletions.
diff --git a/R/Figures.R b/R/Figures.R
diff --git a/R/GenerateRefTables.R b/R/GenerateRefTables.R
@@ -66,8 +66,8 @@ TADA_GetWQXCharValRef <- function() {
   # # Convert all NONE to NA in Value and Value.Unit columns
   # WQXcharValRef = WQXcharValRef %>% dplyr::mutate(Value = replace(Value, Value%in%c("NONE"),NA),
   #                                                 Value.Unit = replace(Value.Unit, Value.Unit%in%c("NONE"),NA)) %>% dplyr::distinct()
-  # 
-  
+  #
+
   # Save updated table in cache
   WQXCharValRef_Cached <- WQXcharValRef
 
@@ -248,15 +248,20 @@ TADA_GetDetCondRef <- function() {
 
   # If the download failed fall back to internal data (and report it)
   if (is.null(raw.data)) {
-    message("Downloading latest Measure Unit Reference Table failed!")
+    message("Downloading latest Result Detection Condition Reference Table failed!")
     message("Falling back to (possibly outdated) internal file.")
     return(utils::read.csv(system.file("extdata", "WQXResultDetectionConditionRef.csv", package = "TADA")))
   }
 
+  # Add detection type for all domain values. New domains are automatically assigned to the
+  # Non-Detect category. Review this closely when updating the reference table when new domains are added.
   WQXDetCondRef <- raw.data %>%
     dplyr::mutate(TADA.Detection_Type = dplyr::case_when(
       Name %in% c("Above Operating Range", "Present Above Quantification Limit") ~ as.character("Over-Detect"),
-      Name %in% c("Value Decensored", "Reported in Raw Data (attached)", "High Moisture") ~ as.character("Other"),
+      Name %in% c(
+        "Value Decensored", "Reported in Raw Data (attached)", "High Moisture",
+        "Unable to Measure"
+      ) ~ as.character("Other"),
       TRUE ~ as.character("Non-Detect")
     )) %>%
     dplyr::distinct()
@@ -469,15 +474,17 @@ TADA_GetActivityTypeRef <- function() {
       TRUE ~ as.character("Non_QC")
     )) %>%
     dplyr::distinct()
-  
+
   # Hard-code add activity types from NWIS
   ## Add USGS limits not in WQX domain table
-  new.atcs = data.frame(Code = c("Quality Control Sample-Blind", "Unknown"),
-                        Description = c("Hard-coded activity type not in WQX domain","Hard-coded activity type not in WQX domain"),
-                        TADA.ActivityType.Flag = c("QC_duplicate","Non_QC"),
-                        Last.Change.Date = rep("8/11/2023 12:00:00 PM",2))
-
-  WQXActivityTypeRef = plyr::rbind.fill(WQXActivityTypeRef, new.atcs)
+  new.atcs <- data.frame(
+    Code = c("Quality Control Sample-Blind", "Unknown"),
+    Description = c("Hard-coded activity type not in WQX domain", "Hard-coded activity type not in WQX domain"),
+    TADA.ActivityType.Flag = c("QC_duplicate", "Non_QC"),
+    Last.Change.Date = rep("8/11/2023 12:00:00 PM", 2)
+  )
+
+  WQXActivityTypeRef <- plyr::rbind.fill(WQXActivityTypeRef, new.atcs)
 
   # Save updated table in cache
   WQXActivityTypeRef_Cached <- WQXActivityTypeRef
@@ -605,7 +612,7 @@ TADA_GetMeasureQualifierCodeRef <- function() {
     "RPO", "S2", "SCA", "SCF", "SCP", "SCX", "SD%EL", "SDROL", "SSR",
     "SUS", "V", "^", "F", "FEQ", "G", "UDL", "MDL"
   )
-  keep <- c(
+  pass <- c(
     "&", ")", "*", "=", "A", "AC", "AL", "ALK", "ALT",
     "AP", "B", "BAC", "C25", "CAJ", "CBG", "CBL", "CC",
     "CDI", "CG", "CKB", "CKBJ", "CKG", "CKJ", "CLC", "CNT", "CON", "CUG",
@@ -617,7 +624,7 @@ TADA_GetMeasureQualifierCodeRef <- function() {
     "O", "OA3", "OS3", "OTHER", "OUT", "PB", "PK", "PPD", "PQL", "PRE",
     "QCI", "RC", "REX", "RIN", "RLRS", "RMAX", "RNAF", "RP",
     "RPDX", "RR", "RV", "RVB", "SBB", "SLB", "SM", "SS", "SSRV", "T",
-    "TMLF", "TOC", "TT", "UNC", "VS", "VVRR", "VVRR2", "UDQ"
+    "TMLF", "TOC", "TT", "UNC", "VS", "VVRR", "VVRR2", "UDQ", "ZZ"
   )
   nondetect <- c("BQL", "2-5B", "RNON", "U", "LTGTE", "K", "IDL", "<2B", "BRL", "D>T", "DL")
   overdetect <- c("E", "EE", "GT")
@@ -627,10 +634,9 @@ TADA_GetMeasureQualifierCodeRef <- function() {
       Code %in% nondetect ~ "Non-Detect",
       Code %in% overdetect ~ "Over-Detect",
       Code %in% suspect ~ "Suspect",
-      Code %in% keep ~ "Pass",
+      Code %in% pass ~ "Pass",
       Code %in% NA ~ "Pass",
-      TRUE ~ as.character("Non-Detect"),
-      TRUE ~ as.character("Over-Detect")
+      TRUE ~ as.character("NewValue_NeedsReview")
     )) %>%
     dplyr::distinct()