Merge pull request #348 from USEPA/plotfix2

Fixes plotting issues
USEPA · Oct 26, 2023 · 65b6bc3 · 65b6bc3
2 parents 7c84058 + 0ed1fa6
commit 65b6bc3
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Showing 3 changed files with 25 additions and 23 deletions.
diff --git a/R/Figures.R b/R/Figures.R
@@ -67,7 +67,8 @@ TADA_Boxplot <- function(.data, id_cols = c("TADA.ComparableDataIdentifier")) {
   TADA_CheckColumns(.data, id_cols)
 
   # check .data has required columns
-  TADA_CheckColumns(.data, c("TADA.ResultMeasureValue", "TADA.ResultMeasure.MeasureUnitCode"))
+  TADA_CheckColumns(.data, c("TADA.ResultMeasureValue", 
+                             "TADA.ResultMeasure.MeasureUnitCode"))
 
   start <- dim(.data)[1]
 
@@ -232,21 +233,13 @@ TADA_Histogram <- function(.data, id_cols = c("TADA.ComparableDataIdentifier"))
     warning("TADA.ComparableDataIdentifier not found in id_cols argument and is highly recommended: plotting without it may produce errors in the plot.")
   }
 
-  req_cols <- c(
-    "TADA.ComparableDataIdentifier", 
-    "TADA.CharacteristicName",
-    "TADA.ResultSampleFractionText",
-    "TADA.MethodSpecificationName",
-    "TADA.ResultMeasure.MeasureUnitCode",
-    "TADA.ResultMeasureValue",
-    "ActivityStartDate",
-    "MonitoringLocationIdentifier",
-    "ActivityTypeCode"
-  )
+  # check .data has required columns
+  TADA_CheckColumns(.data, id_cols)
 
   # check .data has required columns
-  TADA_CheckColumns(.data, expected_cols = req_cols)
-
+  TADA_CheckColumns(.data, c("TADA.ResultMeasureValue", 
+                             "TADA.ResultMeasure.MeasureUnitCode"))
+
   start <- dim(.data)[1]
 
   .data <- subset(.data, !is.na(.data$TADA.ResultMeasureValue))
@@ -549,11 +542,13 @@ TADA_Scatterplot <- function(.data, id_cols = c("TADA.ComparableDataIdentifier")
     warning("TADA.ComparableDataIdentifier not found in id_cols argument and is highly recommended: plotting without it may produce errors in the plot.")
   }
 
+  # check .data has required columns
+  TADA_CheckColumns(.data, id_cols)
+
   # check .data has required columns
   TADA_CheckColumns(.data, c("ActivityStartDate",
                              "TADA.ResultMeasureValue",
-                             "TADA.ResultMeasure.MeasureUnitCode",
-                             "TADA.ComparableDataIdentifier"))
+                             "TADA.ResultMeasure.MeasureUnitCode"))
 
   .data <- .data %>%
     dplyr::group_by(dplyr::across(dplyr::all_of(id_cols))) %>%
@@ -590,11 +585,13 @@ TADA_Scatterplot <- function(.data, id_cols = c("TADA.ComparableDataIdentifier")
         "Activity Start Date:", plot.data$ActivityStartDate, "<br>",
         "Activity Start Date Time:", plot.data$ActivityStartDateTime, "<br>", 
         "Monitoring Location Name:", plot.data$MonitoringLocationName, "<br>", 
+        "Media:", plot.data$TADA.ActivityMediaName, "<br>",
+        "Media Subdivision:", plot.data$ActivityMediaSubdivisionName, "<br>",
         "Result Depth:", paste0(
           plot.data$TADA.ResultDepthHeightMeasure.MeasureValue, " ",
           plot.data$TADA.ResultDepthHeightMeasure.MeasureUnitCode
         ), "<br>",
-        "Activity Relative Depth Name:", plot.data$ActivityRelativeDepthName, "<br>",
+        "Activity Relative Depth:", plot.data$ActivityRelativeDepthName, "<br>",
         "Activity Depth:", paste0(
           plot.data$TADA.ActivityDepthHeightMeasure.MeasureValue, " ",
           plot.data$TADA.ActivityDepthHeightMeasure.MeasureUnitCode
@@ -697,13 +694,12 @@ TADA_TwoCharacteristicScatterplot <- function(.data, id_cols = "TADA.ComparableD
   TADA_CheckType(.data, "data.frame", "Input object")
 
   # check .data has required columns
+  TADA_CheckColumns(.data, id_cols)
 
+  # check .data has required columns
   reqcols <- c("TADA.ResultMeasureValue", 
                "TADA.ResultMeasure.MeasureUnitCode", 
-               "ActivityStartDate", 
-               "ActivityStartDateTime",
-               "TADA.ComparableDataIdentifier",
-               "MonitoringLocationName")
+               "ActivityStartDate")
 
   # check .data has required columns
   TADA_CheckColumns(.data, reqcols)
@@ -784,6 +780,8 @@ TADA_TwoCharacteristicScatterplot <- function(.data, id_cols = "TADA.ComparableD
         "Activity Start Date:", param1$ActivityStartDate, "<br>",
         "Activity Start Date Time:", param1$ActivityStartDateTime, "<br>", 
         "Monitoring Location Name:", param1$MonitoringLocationName, "<br>", 
+        "Media:", param1$TADA.ActivityMediaName, "<br>",
+        "Media Subdivision:", param1$ActivityMediaSubdivisionName, "<br>",
         "Result Depth:", paste0(
           param1$TADA.ResultDepthHeightMeasure.MeasureValue, " ",
           param1$TADA.ResultDepthHeightMeasure.MeasureUnitCode
@@ -811,6 +809,8 @@ TADA_TwoCharacteristicScatterplot <- function(.data, id_cols = "TADA.ComparableD
         "Activity Start Date:", param2$ActivityStartDate, "<br>",
         "Activity Start Date Time:", param2$ActivityStartDateTime, "<br>", 
         "Monitoring Location Name:", param2$MonitoringLocationName, "<br>", 
+        "Media:", param2$TADA.ActivityMediaName, "<br>",
+        "Media Subdivision:", param2$ActivityMediaSubdivisionName, "<br>",
         "Result Depth:", paste0(
           param2$TADA.ResultDepthHeightMeasure.MeasureValue, " ",
           param2$TADA.ResultDepthHeightMeasure.MeasureUnitCode

diff --git a/R/Tables.R b/R/Tables.R
@@ -75,7 +75,7 @@ TADA_SummarizeColumn <- function(.data, col = "TADA.CharacteristicName") {
 TADA_Stats <- function(.data, group_cols = c("TADA.ComparableDataIdentifier")) {
   if (any(is.na(.data$TADA.ResultMeasureValue))) {
     sumNAs <- length(.data$TADA.ResultMeasureValue[is.na(.data$TADA.ResultMeasureValue)])
-    warning(paste0("Dataset contains ", sumNAs, " results missing both a TADA result value and a detection limit. These values will not be represented in the summary table. Suggest removing or handling."))
+    print(paste0("Dataset contains ", sumNAs, " results missing both a TADA result value and a detection limit. These values will not be represented in the stats summary table. Suggest removing or handling."))
   }
 
   if (!"TADA.CensoredData.Flag" %in% names(.data)) {

diff --git a/R/Transformations.R b/R/Transformations.R
@@ -408,12 +408,14 @@ TADA_CalculateTotalNP <- function(.data, sum_ref, daily_agg = c("max", "min", "m
   depths <- names(.data)[grepl("DepthHeightMeasure", names(.data))]
   depths <- depths[grepl("TADA.", depths)]
   grpcols <- c("ActivityStartDate", 
-               "ActivityStartDateTime",
+               #"ActivityStartDateTime", #does not make sense to include for daily agg
                "ActivityRelativeDepthName",
                "MonitoringLocationIdentifier",
+               "MonitoringLocationName",
                "TADA.LongitudeMeasure",
                "TADA.LatitudeMeasure",
                "ActivityMediaSubdivisionName",
+               "TADA.ActivityMediaName",
                "TADA.ComparableDataIdentifier",
                "TADA.ResultMeasure.MeasureUnitCode",
                depths)