ID nondetects based on specific text result values

USEPA · Dec 15, 2023 · 785c5e4 · 785c5e4
1 parent b9d22bb
commit 785c5e4
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Showing 2 changed files with 58 additions and 6 deletions.
diff --git a/R/CensoredDataSuite.R b/R/CensoredDataSuite.R
@@ -56,8 +56,11 @@ TADA_IDCensoredData <- function(.data) {
     ## Flag censored data that does not have det cond populated
     cens$TADA.Detection_Type <- ifelse(is.na(cens$ResultDetectionConditionText), "ResultDetectionConditionText missing", cens$TADA.Detection_Type)
 
-    ## Fill in detection type when result measure value = "ND"
-    cens$TADA.Detection_Type <- ifelse(cens$ResultMeasureValue %in% c("ND"), "Non-Detect", cens$TADA.Detection_Type)
+    ## Fill in detection type when text result measure value indicates it is a nondetect
+    cens$TADA.Detection_Type <- ifelse(cens$ResultMeasureValue %in% 
+                                         c("ND", "BPQL", "BDL"), 
+                                       "Non-Detect", 
+                                       cens$TADA.Detection_Type)
 
     ## Let user know when detection condition text is missing from one or more results
     # NOTE that at this point, TADA.Detection_Type may be NA if there are detection conditions in dataset that are not present in domain table

diff --git a/R/Utilities.R b/R/Utilities.R
@@ -149,10 +149,59 @@ TADA_AutoClean <- function(.data) {
   .data <- TADA_ConvertSpecialChars(.data, "DetectionQuantitationLimitMeasure.MeasureValue")
 
   # Move detection limit value and unit to TADA Result Measure Value and Unit columns
-  .data$TADA.ResultMeasureValue <- ifelse(is.na(.data$TADA.ResultMeasureValue) & !is.na(.data$TADA.DetectionQuantitationLimitMeasure.MeasureValue), .data$TADA.DetectionQuantitationLimitMeasure.MeasureValue, .data$TADA.ResultMeasureValue)
-  .data$TADA.ResultMeasure.MeasureUnitCode <- ifelse(is.na(.data$TADA.ResultMeasure.MeasureUnitCode) & !is.na(.data$TADA.DetectionQuantitationLimitMeasure.MeasureUnitCode), .data$TADA.DetectionQuantitationLimitMeasure.MeasureUnitCode, .data$TADA.ResultMeasure.MeasureUnitCode)
-  .data$TADA.ResultMeasureValueDataTypes.Flag <- ifelse(.data$TADA.ResultMeasureValueDataTypes.Flag == "Blank" & !is.na(.data$TADA.DetectionQuantitationLimitMeasure.MeasureValue), "Result Value/Unit Copied from Detection Limit", .data$TADA.ResultMeasureValueDataTypes.Flag)
-
+  # Consider moving this to ID censored data in the future?
+  # this first row copies all over when result is blank but 
+  # TADA.DetectionQuantitationLimitMeasure.MeasureValue is not and the 
+  # TADA.ResultMeasureValueDataTypes.Flag is not Text 
+  # Imp note: TADA result values are NA for text even though they are not NA in the original result value
+  .data$TADA.ResultMeasureValue <- ifelse(
+    is.na(.data$TADA.ResultMeasureValue)
+    & !is.na(.data$TADA.DetectionQuantitationLimitMeasure.MeasureValue)
+    & .data$TADA.ResultMeasureValueDataTypes.Flag != "Text",
+    .data$TADA.DetectionQuantitationLimitMeasure.MeasureValue, 
+    .data$TADA.ResultMeasureValue)
+  # this does the same as above for the units
+  .data$TADA.ResultMeasure.MeasureUnitCode <- ifelse(
+    is.na(.data$TADA.ResultMeasure.MeasureUnitCode)
+    & !is.na(.data$TADA.DetectionQuantitationLimitMeasure.MeasureUnitCode)
+    & .data$TADA.ResultMeasureValueDataTypes.Flag != "Text", 
+    .data$TADA.DetectionQuantitationLimitMeasure.MeasureUnitCode, 
+    .data$TADA.ResultMeasure.MeasureUnitCode)
+  .data$TADA.ResultMeasureValueDataTypes.Flag <- ifelse(
+    .data$TADA.ResultMeasureValueDataTypes.Flag == "Blank"
+    & !is.na(.data$TADA.DetectionQuantitationLimitMeasure.MeasureValue),
+    "Result Value/Unit Copied from Detection Limit",
+    .data$TADA.ResultMeasureValueDataTypes.Flag)
+
+  # this copies det lim result value and unit over to TADA result value and unit 
+  # when the result value is TEXT but there is a specific text value that indicates 
+  # the result is censored (BPQL, BDL, ND)
+  # and the TADA.DetectionQuantitationLimitMeasure.MeasureValue provided
+  .data$TADA.ResultMeasureValueDataTypes.Flag <- ifelse(
+    .data$TADA.ResultMeasureValueDataTypes.Flag == "Text" &
+      .data$ResultMeasureValue == "BPQL" |
+      .data$ResultMeasureValue == "BDL" |
+      .data$ResultMeasureValue == "ND" & 
+      !is.na(.data$TADA.DetectionQuantitationLimitMeasure.MeasureValue),
+    "Result Value/Unit Copied from Detection Limit", 
+    .data$TADA.ResultMeasureValueDataTypes.Flag)
+  .data$TADA.ResultMeasureValue <- ifelse(
+    is.na(.data$TADA.ResultMeasureValue)
+    & !is.na(.data$TADA.DetectionQuantitationLimitMeasure.MeasureValue)
+    & .data$ResultMeasureValue == "BPQL" |
+      .data$ResultMeasureValue == "BDL" |
+      .data$ResultMeasureValue == "ND" ,
+    .data$TADA.DetectionQuantitationLimitMeasure.MeasureValue, 
+    .data$TADA.ResultMeasureValue)
+  # this does the same as above for the units
+  .data$TADA.ResultMeasure.MeasureUnitCode <- ifelse(
+    !is.na(.data$TADA.DetectionQuantitationLimitMeasure.MeasureUnitCode)
+    & .data$ResultMeasureValue == "BPQL" |
+      .data$ResultMeasureValue == "BDL" |
+      .data$ResultMeasureValue == "ND" , 
+    .data$TADA.DetectionQuantitationLimitMeasure.MeasureUnitCode, 
+    .data$TADA.ResultMeasure.MeasureUnitCode)
+
   # Identify detection limit data
   print("TADA_Autoclean: identifying detection limit data.")
   .data <- TADA_IDCensoredData(.data)