USEPA · cristinamullin · May 24, 2024 · Jan 9, 2024 · Jan 10, 2024 · Jan 10, 2024
diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,7 @@
 # RStudio files
 TADA.Rproj
 .Rproj.user
+test_function.R
 
 # History files
 .Rhistory

diff --git a/NAMESPACE b/NAMESPACE
@@ -8,12 +8,14 @@ export(TADA_AutoFilter)
 export(TADA_BigDataRetrieval)
 export(TADA_Boxplot)
 export(TADA_CalculateTotalNP)
+export(TADA_ColorPalette)
 export(TADA_ConvertDepthUnits)
 export(TADA_ConvertResultUnits)
 export(TADA_ConvertSpecialChars)
 export(TADA_CreateComparableID)
 export(TADA_CreateUnitRef)
 export(TADA_DataRetrieval)
+export(TADA_DepthProfilePlot)
 export(TADA_FieldCounts)
 export(TADA_FieldValuesPie)
 export(TADA_FieldValuesTable)
@@ -27,6 +29,7 @@ export(TADA_FlagAboveThreshold)
 export(TADA_FlagBelowThreshold)
 export(TADA_FlagContinuousData)
 export(TADA_FlagCoordinates)
+export(TADA_FlagDepthCategory)
 export(TADA_FlagFraction)
 export(TADA_FlagMeasureQualifierCode)
 export(TADA_FlagMethod)
@@ -48,6 +51,7 @@ export(TADA_GetWQXCharValRef)
 export(TADA_HarmonizeSynonyms)
 export(TADA_Histogram)
 export(TADA_IDCensoredData)
+export(TADA_IDDepthProfiles)
 export(TADA_InsertBreaks)
 export(TADA_JoinWQPProfiles)
 export(TADA_MakeSpatial)
@@ -66,6 +70,7 @@ export(TADA_SummarizeColumn)
 export(TADA_TwoCharacteristicScatterplot)
 export(TADA_UniqueCharUnitSpeciation)
 export(TADA_ViewATTAINS)
+export(TADA_ViewColorPalette)
 export(TADA_addPoints)
 export(TADA_addPolys)
 importFrom(magrittr,"%>%")
diff --git a/R/DepthProfile.R b/R/DepthProfile.R
diff --git a/R/Figures.R b/R/Figures.R
diff --git a/R/GeospatialFunctions.R b/R/GeospatialFunctions.R
@@ -534,11 +534,13 @@ TADA_ViewATTAINS <- function(.data) {
     # if data was spatial, remove for downstream leaflet dev:
     try(ATTAINS_table <- ATTAINS_table %>%
       sf::st_drop_geometry(), silent = TRUE)
+
+    tada.pal <- TADA_ColorPalette()
 
     colors <- data.frame(
       overallstatus = c("Not Supporting", "Fully Supporting", "Not Assessed"),
-      col = c("#DC851E", "#059FA4", "#A1A522"),
-      dark_col = c("#813B00", "#005258", "#4F5900"),
+      col = c(tada.pal[3], tada.pal[4], tada.pal[7]),
+      dark_col = c(tada.pal[12], tada.pal[6], tada.pal[11]),
       priority = c(1, 2, 3)
     )
 
@@ -605,7 +607,7 @@ TADA_ViewATTAINS <- function(.data) {
       leaflet.extras::addResetMapButton() %>%
       leaflet::addLegend(
         position = "bottomright",
-        colors = c("#DC851E", "#059FA4", "#A1A522", "black", NA),
+        colors = c(tada.pal[3], tada.pal[4], tada.pal[7], "black", NA),
         labels = c(
           "ATTAINS: Not Supporting", "ATTAINS: Supporting", "ATTAINS: Not Assessed", "Water Quality Observation(s)",
           "NHDPlus HR catchments containing water quality observations + ATTAINS feature are represented as clear polygons with black outlines."

diff --git a/R/RequiredCols.R b/R/RequiredCols.R
@@ -76,6 +76,11 @@ require.cols <- c(
   "TADA.CensoredMethod",
 
   # Result Depth
+  "TADA.ConsolidatedDepth",
+  "TADA.ConsolidatedDepth.Bottom",
+  "TADA.ConsolidatedDepth.Unit",
+  "TADA.DepthCategory.Flag",
+  "TADA.DepthProfileAggregation.Flag",
   "ResultDepthHeightMeasure.MeasureValue",
   "TADA.ResultDepthHeightMeasure.MeasureValue",
   "TADA.ResultDepthHeightMeasure.MeasureValueDataTypes.Flag",

diff --git a/R/ResultFlagsIndependent.R b/R/ResultFlagsIndependent.R
@@ -1403,4 +1403,4 @@ TADA_FindPotentialDuplicatesSingleOrg <- function(.data) {
 
   .data <- TADA_OrderCols(.data)
   return(.data)
-}
+}
diff --git a/R/Utilities.R b/R/Utilities.R
@@ -72,7 +72,17 @@ utils::globalVariables(c(
   "ResultMeasure.MeasureUnitCode", "TADA.DetectionQuantitationLimitMeasure.MeasureUnitCode",
   "DetectionQuantitationLimitMeasure.MeasureUnitCode", "NCode",
   "ATTAINS.assessmentunitidentifier", "ATTAINS_AU", "TOTALAREA_MI", "TOTALAREA_KM",
-  "ATTAINS_AUs"
+  "ATTAINS_AUs",  "ARD_Category", "ActivityRelativeDepthName", "DepthsByGroup",
+  "DepthsPerGroup","MeanResults", "MonitoringLocationTypeName", "N", "SecchiConversion",
+  "TADA.ActivityBottomDepthHeightMeasure.MeasureValue", 
+  "TADA.ActivityDepthHeightMeasure.MeasureUnitCode", "TADA.ActivityDepthHeightMeasure.MeasureValue",
+  "TADA.CharacteristicsForDepthProfile TADA.ConsolidatedDepth", 
+  "TADA.ConsolidatedDepth.Bottom TADA.ConsolidatedDepth.Unit", "TADA.DepthCategory.Flag",
+  "TADA.DepthProfileAggregation.Flag", "TADA.NResults", 
+  "TADA.ResultDepthHeightMeasure.MeasureUnitCode", "TADA.ResultDepthHeightMeasure.MeasureValue",
+  "YAxis.DepthUnit", "TADA.CharacteristicsForDepthProfile", "TADA.ConsolidatedDepth",
+  "TADA.ConsolidatedDepth.Bottom", "TADA.ConsolidatedDepth.Unit", "col2rgb",
+  "palette.colors", "rect", "rgb", "text"
 ))
 
 # global variables for tribal feature layers used in TADA_OverviewMap in Utilities.R
@@ -1386,3 +1396,67 @@ TADA_UniqueCharUnitSpeciation <- function(.data) {
     dplyr::select(-NCode)
 }
 
+
+#' Create Color Palette For Use in Graphs and Maps
+#' 
+#' Creates a consistent color palette for use in TADA visualizations. Currently,
+#' the palette is utilizing the "Okabe-Ito" palette from base R via the palette.colors
+#' function. The palette includes 9 colors by default. However, additional colors 
+#' can be added to the palette as needed as more complex visualization functions 
+#' are added to the TADA package. 
+#' 
+#' @return A color palette based on the "Okabe-Ito" palette, extended to 15 colors,
+#'  with modifications for use in mapping and graphing functions
+#' 
+#' @export
+#' 
+#' @examples
+#' TestColorPalette <- TADA_ColorPalette()
+#' 
+ TADA_ColorPalette <- function() {
+
+   pal <- c("#000000", "#835A00", "#DC851E", "#059FA4", "#56B4E9",
+            "#005258",  "#A1A522", "#F0E442", "#66A281", "#1E6F98",
+            "#4F5900", "#813B00", "#CD758F", "#B686A1", "#999999")
+
+     return(pal)
+ }
+
+
+ #' View TADA Color Palette
+ #' 
+ #' View a swatch of the colors in the TADA Color palette labeled by color and
+ #' index number. TADA developers can reference this function when deciding which
+ #' colors to use in TADA visualizations. TADA users can also reference this 
+ #' palette function to create their own visually consistent figures.
+ #' 
+ #' @return A color swatch figure based on the TADA color palette.
+ #' 
+ #' @export
+ #' 
+ #' @examples 
+ #' TestViewPalette <- TADA_ViewColorPalette()
+ #' 
+ TADA_ViewColorPalette <- function() {
+
+   # call TADA color palette
+   pal <- TADA_ColorPalette()
+
+   # determine length of color palette
+   n <- length(pal)
+
+   # create list of label colors, first one needs to be white to show up clearly
+   label_colors <- rep("black", n)
+   label_colors[1] <- "white"
+
+   # create color swatch graphic
+   graphics::par(mar = c(5,0,5,0))
+   swatch <- graphics::plot(1, type = "n", xlab = "", ylab = "", xlim = c(0.5,n + 0.5), ylim = c(0,1), main = "TADA Palette", axes = FALSE)
+   rect(1:n - 0.5, 0, n + 0.5, 1, col = pal, border = NA)
+   text(x = 1:n, y = 0.5, labels = 1:n, pos = 3, col = label_colors)
+   text(x = 1:n, y = 0.5 - 0.2, labels = pal, pos = 1, col = label_colors, cex = 0.7, srt = 90)
+
+return(swatch)
+   }
+
+
diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -1,6 +1,7 @@
 ANDs
 ActivityBottomDepthHeightMeasure
 ActivityCommentText
+ActivityDate
 ActivityDepthHeightMeasure
 ActivityGroup
 ActivityMediaName
@@ -36,9 +37,11 @@ CharacteristicGroup
 CharacteristicName
 CharacteristicNameAssumptions
 CharacteristicNameUserSupplied
+CharacteristicsForDepthProfile
 CharactersticName
 Chilton
 ComparableDataIdentifier
+ConsolidatedDepth
 ConstructionDateText
 ContinuousData
 ConversionCoefficient
@@ -52,6 +55,9 @@ DataQuality
 DataRetreival
 DataRetrieval
 DataTypes
+DepthCategory
+DepthProfileAggregation
+DepthProfilePlot
 DetectionQuantitationLimiMeasure
 DetectionQuantitationLimitMeasure
 DetectionQuantitationLimitType
@@ -88,11 +94,13 @@ GetSynonymRef
 Github
 HUC
 HUCS
+HUCs
 HarmonizeSynonyms
 HorizontalCoordinateReferenceSystemDatumName
 HydrologicCondition
 HydrologicEvent
 IDCensoredData
+IDDepthProfiles
 InvalidCoordinates
 InvalidFraction
 InvalidResultUnit
@@ -116,6 +124,7 @@ MeasureUnit
 MeasureUnitCode
 MeasureValue
 MeasureValueDataTypes
+MeetsStandard
 MethodDescriptionText
 MethodIdentifier
 MethodIdentifierContext
@@ -124,6 +133,7 @@ MethodQualifierCodes
 MethodQualifierTypeName
 MethodSpeciation
 MethodSpeciationName
+MonitoringLocation
 MonitoringLocationIdentifier
 MonitoringLocationIdentifier's
 MonitoringLocationName
@@ -147,6 +157,7 @@ NutrientSummationEquation
 NutrientSummationGroup
 OA
 ORs
+Okabe
 OrganizationFormalName
 OrganizationIdentifier
 OutsideUSA
@@ -165,6 +176,7 @@ QAQC
 QAQC'd
 QAQCCharacteristicValidation
 QC'ing
+QCing
 README
 REDLAKE
 RMarkdown
@@ -178,6 +190,7 @@ Rancherias
 ReplicateSampleID
 Repo
 ResultAboveUpperThreshold
+ResultAggregation
 ResultAnalyticalMethod
 ResultCommentText
 ResultDepthHeightMeasure
@@ -221,7 +234,6 @@ SpeciationUnitConversion
 StateCode
 SubstituteDeprecatedChars
 SummarizeColumn
-TADA's
 TADADataRetrieval
 TADAGeospatialRefLayers
 TADAModule
@@ -238,11 +250,13 @@ USGS's
 Uncomment
 UncommonAnalyticalMethodID
 UniqueHarmonizationRef
+UnitCode
 UpdateTribalLayers
 UseForAnalysis
 VCS
 ViewATTAINS
 WGS
+WQC
 WQP
 WQX
 WQX's
@@ -259,13 +273,16 @@ WQXTargetUnit
 WQXUnitConversionFactor
 WQXcharValRef
 WQXunitRef
+Waterbody
+WaterbodyReport
 WellDepthMeasure
 WellHoleDepthMeasure
 Wikimedia
 YYYY
 addPoints
 addPolys
 agg
+aggregatedonly
 analytes
 applyautoclean
 arcgis
@@ -277,7 +294,9 @@ assmnt
 autoclean
 autocleaned
 bbox
+bottomvalue
 bplan
+bycategory
 catchmentareasqkm
 catchmentistribal
 catchmentresolution
@@ -292,9 +311,11 @@ countycode
 cristinamullin
 crs
 csv
+dailyagg
 dataProfile
 dataRetrieval
 datetimes
+depthcat
 devtools
 dimCheck
 dlist
@@ -307,7 +328,7 @@ endDate
 endDateHi
 english
 epa
-eval
+estimatiom
 extdata
 fabec
 fetchATTAINS
@@ -345,6 +366,7 @@ nhdplusid
 nondetections
 nonstandardized
 np
+nresults
 num
 od
 organizationid
@@ -354,6 +376,8 @@ orgtype
 ousideUSA
 outsideUSA
 overallstatus
+param
+params
 pch
 pchIcons
 pcodes
@@ -367,6 +391,7 @@ repo
 reportingcycle
 reproducibility
 sampleMedia
+secchi
 shp
 siteType
 siteid
@@ -379,6 +404,7 @@ startDateLo
 statecode
 sthda
 submissionid
+surfacevalue
 sysdata
 tada
 tas

diff --git a/man/TADA_ColorPalette.Rd b/man/TADA_ColorPalette.Rd
-Original file line number
+Diff line change
@@ Expand Up @@
       .data <- TADA_OrderCols(.data)
       return(.data)
-    }
+    }