USEPA · cristinamullin · Jul 28, 2025 · Jul 2, 2025 · Jul 3, 2025 · Jul 8, 2025
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -76,15 +76,14 @@ Imports:
     igraph,
     jsonlite, 
     openxlsx,
-    rExpertQuery,
     DT,
     dataRetrieval,
     dbscan,
-    janitor
+    janitor,
+    rExpertQuery
 Depends: 
     R (>= 3.5.0)
 Suggests:
-    StreamCatTools, 
     hydroloom,
     lwgeom,
     RColorBrewer,
@@ -104,9 +103,7 @@ Suggests:
     rvest,
     remotes
 Remotes:
-    DOI-USGS/dataRetrieval@develop,
-    USEPA/rExpertQuery@develop,
-    USEPA/StreamCatTools@master
+    USEPA/rExpertQuery@develop
 VignetteBuilder: knitr, rmarkdown
 Language: en-US
 Config/testthat/edition: 3

diff --git a/R/CensoredDataSuite.R b/R/CensoredDataSuite.R
@@ -305,7 +305,10 @@ TADA_IDCensoredData <- function(.data) {
 #'   )
 #' }
 #'
-TADA_SimpleCensoredMethods <- function(.data, nd_method = "multiplier", nd_multiplier = 0.5, od_method = "as-is", od_multiplier = "null") {
+TADA_SimpleCensoredMethods <- function(.data, nd_method = "multiplier",
+                                       nd_multiplier = 0.5,
+                                       od_method = "as-is",
+                                       od_multiplier = "null") {
   # check .data has all of the required columns
   expected_cols <- c(
     "ResultDetectionConditionText",
@@ -337,7 +340,13 @@ TADA_SimpleCensoredMethods <- function(.data, nd_method = "multiplier", nd_multi
     # split out over detects and non detects
     nd <- subset(cens.data, cens.data$TADA.CensoredData.Flag == "Non-Detect")
     od <- subset(cens.data, cens.data$TADA.CensoredData.Flag == "Over-Detect")
-    all_others <- subset(cens.data, !cens.data$ResultIdentifier %in% c(nd$ResultIdentifier, od$ResultIdentifier))
+    no.ref <- subset(cens.data, cens.data$TADA.CensoredData.Flag == "Detection condition is missing and required for censored data ID.")
+    missing.ref <- subset(cens.data, cens.data$TADA.CensoredData.Flag == "Detection condition or detection limit is not documented in TADA reference tables.")
+
+    all_others <- subset(cens.data, !cens.data$ResultIdentifier %in% c(nd$ResultIdentifier, od$ResultIdentifier,
+                                                                       no.ref$ResultIdentifier, missing.ref$ResultIdentifier))
+
+  # HRM note 7/15/2025 still need to add code to set no.ref.missing results to NA
 
     # ND handling
     if (dim(nd)[1] > 0) {
@@ -369,7 +378,22 @@ TADA_SimpleCensoredMethods <- function(.data, nd_method = "multiplier", nd_multi
       }
     }
 
-    .data <- plyr::rbind.fill(nd, od, all_others) %>%
+    # handling for results with missing detection conditions or with a detection condition or limit not in TADA ref table
+    if (dim(no.ref)[1] > 0) {
+        no.ref$TADA.ResultMeasureValue <- NA
+        no.refTADA.CensoredMethod <- "Result set to NA due to Missing Detection Condition"
+        no.ref$TADA.ResultMeasureValueDataTypes.Flag <- "Result Value/Unit Cannot Be Estimated From Detection Limit"
+    }
+
+    # handling for results with missing detection conditions or with a detection condition or limit not in TADA ref table
+    if (dim(missing.ref)[1] > 0) {
+      missing.ref$TADA.ResultMeasureValue <- NA
+      missing.ref$TADA.CensoredMethod <- "Result set to NA as Detection Conditon or Limit is not in TADA Ref Table"
+      missing.ref$TADA.ResultMeasureValueDataTypes.Flag <- "Result Value/Unit Cannot Be Estimated From Detection Limit"
+    }
+
+
+    .data <- plyr::rbind.fill(nd, od, all_others, no.ref, missing.ref) %>%
       TADA_CreateComparableID()
   }
   .data <- TADA_OrderCols(.data)

diff --git a/R/Transformations.R b/R/Transformations.R
@@ -6,7 +6,7 @@
 #' synonym table created from TADA_GetSynonymRef and reviewed/customized by the
 #' user (recommended), or the default TADA-provided synonym table, containing
 #' suggested synonym naming for some priority characteristics. Where a suggested
-#' characteristic name, fraction, speciation, or unit is present, the function
+#' characteristic name, fraction, or speciation is present, the function
 #' will convert the TADA.CharacteristicName, TADA.ResultSampleFractionText,
 #' and TADA.MethodSpeciationName to the target format. In cases where a target
 #' speciation differs from the existing speciation, the reference table will
@@ -24,8 +24,8 @@
 #'   NO3 will be converted to as N using molecular weight conversion factors.
 #'
 #' @return The input TADA dataframe with the TADA.CharacteristicName,
-#'   TADA.ResultSampleFractionText, TADA.MethodSpeciationName, and
-#'   TADA.ResultMeasure.MeasureUnitCode columns converted to the target values,
+#'   TADA.ResultSampleFractionText, and TADA.MethodSpeciationName columns 
+#'   converted to the target values,
 #'   if supplied. Also includes additional columns
 #'   TADA.CharacteristicNameAssumptions, TADA.FractionAssumptions, and
 #'   TADA.SpeciationAssumptions populated with additional notes about the conversion
@@ -94,11 +94,11 @@ TADA_HarmonizeSynonyms <- function(.data, ref, np_speciation = TRUE) {
     stop("TADA.ResultMeasureValue is not numeric. This column must be numeric before proceeding.")
   }
 
-  # Change NONE in unit, fraction, and speciation to NA for better harmonization
+  # Changes NONE in fraction and speciation to NA for better harmonization
+  # Should this be specified in the template instead? 7/25/25 cm
   .data <- .data %>% dplyr::mutate(
     TADA.ResultSampleFractionText = replace(TADA.ResultSampleFractionText, TADA.ResultSampleFractionText %in% c("NONE"), NA),
-    TADA.MethodSpeciationName = replace(TADA.MethodSpeciationName, TADA.MethodSpeciationName %in% c("NONE"), NA),
-    TADA.ResultMeasure.MeasureUnitCode = replace(TADA.ResultMeasure.MeasureUnitCode, TADA.ResultMeasure.MeasureUnitCode %in% c("NONE"), NA)
+    TADA.MethodSpeciationName = replace(TADA.MethodSpeciationName, TADA.MethodSpeciationName %in% c("NONE"), NA)
   )
 
   # define harm.ref
@@ -313,7 +313,7 @@ TADA_CalculateTotalNP <- function(.data, sum_ref, daily_agg = c("max", "min", "m
     "ActivityMediaSubdivisionName",
     "TADA.ActivityMediaName",
     "TADA.ComparableDataIdentifier",
-    "TADA.ResultMeasure.MeasureUnitCode",
+    # "TADA.ResultMeasure.MeasureUnitCode",
     depths
   )