diff --git a/R/Figures.R b/R/Figures.R
index e94f637a..5359d920 100644
--- 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, "
",
"Activity Start Date Time:", plot.data$ActivityStartDateTime, "
",
"Monitoring Location Name:", plot.data$MonitoringLocationName, "
",
+ "Media:", plot.data$TADA.ActivityMediaName, "
",
+ "Media Subdivision:", plot.data$ActivityMediaSubdivisionName, "
",
"Result Depth:", paste0(
plot.data$TADA.ResultDepthHeightMeasure.MeasureValue, " ",
plot.data$TADA.ResultDepthHeightMeasure.MeasureUnitCode
), "
",
- "Activity Relative Depth Name:", plot.data$ActivityRelativeDepthName, "
",
+ "Activity Relative Depth:", plot.data$ActivityRelativeDepthName, "
",
"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$ActivityStartDate, "
",
"Activity Start Date Time:", param1$ActivityStartDateTime, "
",
"Monitoring Location Name:", param1$MonitoringLocationName, "
",
+ "Media:", param1$TADA.ActivityMediaName, "
",
+ "Media Subdivision:", param1$ActivityMediaSubdivisionName, "
",
"Result Depth:", paste0(
param1$TADA.ResultDepthHeightMeasure.MeasureValue, " ",
param1$TADA.ResultDepthHeightMeasure.MeasureUnitCode
@@ -811,6 +809,8 @@ TADA_TwoCharacteristicScatterplot <- function(.data, id_cols = "TADA.ComparableD
"Activity Start Date:", param2$ActivityStartDate, "
",
"Activity Start Date Time:", param2$ActivityStartDateTime, "
",
"Monitoring Location Name:", param2$MonitoringLocationName, "
",
+ "Media:", param2$TADA.ActivityMediaName, "
",
+ "Media Subdivision:", param2$ActivityMediaSubdivisionName, "
",
"Result Depth:", paste0(
param2$TADA.ResultDepthHeightMeasure.MeasureValue, " ",
param2$TADA.ResultDepthHeightMeasure.MeasureUnitCode
diff --git a/R/Tables.R b/R/Tables.R
index 9f661b7c..609cc6bb 100644
--- 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
index d6ae4579..ed4269de 100644
--- 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)