My thoughts so far:

...new columns generated by some of the depth functions are appended to the end of the dataframe (TADA.ConsolidatedDpeth.Bottom, TADA.DepthCategory.Flag, TADA.DepthProfileAggregation.Flag & there may be more). Can you add any new columns that are created to the require.cols list at the top of RequiredCols.R.

Yes I will add those to require.cols in RequiredCols.R

"adding some additional colors to the palette in TADA_ColorPalette and then only using color ramp if a really large number of colors is needed". Do you want to create a separate issue for that or include in this PR?

This is not difficult technically, but I will do that separately as I will need seem time to figure out which colors to add so that the palette remains colorblind accessible

• The orange outline for sites in the TADA_OverviewMap is a bit faint/hard to see. Should we use the same dark blue outline for the sites that is used for TADA_Scatterplot point outlines

Yes, I'll change this

• In TADA_TwoCharacteristicScatterplot the second char points are orange with a blue outline. Could these have a darker orange outline instead? So the inside would be Created TADA_AutoClean.R #2 in the TADA palette and outline would be [7]

Yes, I'll change this

• TADA_FieldValuesPie. For figures like this that use a lot of colors, I am wondering if the TADA_ColorPalette could specify by default which colors to use first and in which order? For example, if we always want to use blue first followed by orange) can that specification be included in TADA_ColorPalette?

I have noticed that the order of the colors in the palette does not seem to determine which colors are selected first in TAD_FieldValuesPie. I think we should specify the order we want the colors used in, but it may need to happen within the plotly functions used to create the figure. I think there is a way to tell it to use the colors in order from the palette or specify the order within the function. I'll take a look at this and figure out the best place to do it.

@hillarymarler I tried running TADA_DepthProfilePlot with the surfacevalue and bottomvalue null which currently produces as error message. Recommendation: update this so that when these inputs are null, the function returns the figure without the black horizontal lines and text on the figure marking surface, middle, and bottom.

> TADA_DepthProfilePlot(Data_6Tribes_5y_Harmonized,
+                       groups = c("TEMPERATURE_NA_NA_DEG C", "PH_NA_NA_NA", "DEPTH, SECCHI DISK DEPTH_NA_NA_M"),
+                       location = "REDLAKE_WQX-ANKE",
+                       activity_date = "2018-10-04", 
+                       surfacevalue = NULL,
+                       bottomvalue = NULL)
[1] "TADA_DepthProfilePlot: Running TADA_DepthCategoryFlag function to add required columns to data frame"
[1] "TADA_DepthCategory.Flag: checking data set for depth values. 69516 results have depth values available."
[1] "TADA_DepthCategory.Flag: assigning depth categories."
[1] "TADA_DepthCategory.Flag: Grouping results by MonitoringLocationIdentifier, OrganizationIdentifier, CharacteristicName, and ActivityStartDate for aggregation for entire water column."
[1] "TADA_DepthCategory.Flag: No aggregation performed."
[1] "TADA_DepthProfilePlot: Depth unit in data set matches depth unit specified by user for plot. No conversion necessary."
[1] "TADA_DepthProfilePlot: Identifying available depth profile data."
[1] "TADA_DepthProfilePlot: Any results for DEPTH, SECCHI DISK DEPTH, DEPTH, SECCHI DISK DEPTH (CHOICE LIST), DEPTH, SECCHI DISK DEPTH REAPPEARS, DEPTH, DATA-LOGGER (NON-PORTED), DEPTH, DATA-LOGGER (PORTED), RBP STREAM DEPTH - RIFFLE, RBP STREAM DEPTH - RUN, THALWEG DEPTH match the depth unit selected for the figure."
Joining with `by = join_by(ActivityTypeCode, TADA.ActivityType.Flag, ActivityMediaName, TADA.ActivityMediaName,
ActivityMediaSubdivisionName, ResultSampleFractionText, TADA.ResultSampleFractionText, TADA.SampleFraction.Flag,
TADA.FractionAssumptions, CharacteristicName, TADA.CharacteristicName, TADA.CharacteristicNameAssumptions, SubjectTaxonomicName,
SampleTissueAnatomyName, MethodSpeciationName, TADA.MethodSpeciationName, TADA.MethodSpeciation.Flag,
TADA.SpeciationAssumptions, TADA.ComparableDataIdentifier, TADA.Harmonized.Flag, ActivityStartDate, ActivityStartTime.Time,
ActivityStartTime.TimeZoneCode, ActivityStartDateTime, ResultMeasureValue, TADA.ResultMeasureValue,
TADA.ResultMeasureValueDataTypes.Flag, ResultValueTypeName, TADA.ResultValueAboveUpperThreshold.Flag,
TADA.ResultValueBelowLowerThreshold.Flag, ResultMeasure.MeasureUnitCode, TADA.ResultMeasure.MeasureUnitCode,
TADA.WQXResultUnitConversion, TADA.ResultUnit.Flag, ResultDetectionConditionText, DetectionQuantitationLimitTypeName,
DetectionQuantitationLimitMeasure.MeasureValue, TADA.DetectionQuantitationLimitMeasure.MeasureValue,
TADA.DetectionQuantitationLimitMeasure.MeasureValueDataTypes.Flag, DetectionQuantitationLimitMeasure.MeasureUnitCode,
TADA.DetectionQuantitationLimitMeasure.MeasureUnitCode, TADA.CensoredData.Flag, TADA.CensoredMethod, TADA.ConsolidatedDepth,
TADA.ConsolidatedDepth.Unit, ResultDepthHeightMeasure.MeasureValue, TADA.ResultDepthHeightMeasure.MeasureValue,
TADA.ResultDepthHeightMeasure.MeasureValueDataTypes.Flag, ResultDepthHeightMeasure.MeasureUnitCode,
TADA.ResultDepthHeightMeasure.MeasureUnitCode, ResultDepthAltitudeReferencePointText, ActivityRelativeDepthName,
ActivityDepthHeightMeasure.MeasureValue, TADA.ActivityDepthHeightMeasure.MeasureValue,
TADA.ActivityDepthHeightMeasure.MeasureValueDataTypes.Flag, ActivityDepthHeightMeasure.MeasureUnitCode,
TADA.ActivityDepthHeightMeasure.MeasureUnitCode, ActivityTopDepthHeightMeasure.MeasureValue,
TADA.ActivityTopDepthHeightMeasure.MeasureValue, TADA.ActivityTopDepthHeightMeasure.MeasureValueDataTypes.Flag,
ActivityTopDepthHeightMeasure.MeasureUnitCode, TADA.ActivityTopDepthHeightMeasure.MeasureUnitCode,
ActivityBottomDepthHeightMeasure.MeasureValue, TADA.ActivityBottomDepthHeightMeasure.MeasureValue,
TADA.ActivityBottomDepthHeightMeasure.MeasureValueDataTypes.Flag, ActivityBottomDepthHeightMeasure.MeasureUnitCode,
TADA.ActivityBottomDepthHeightMeasure.MeasureUnitCode, ResultTimeBasisText, StatisticalBaseCode, ResultFileUrl,
ResultAnalyticalMethod.MethodName, ResultAnalyticalMethod.MethodDescriptionText, ResultAnalyticalMethod.MethodIdentifier,
ResultAnalyticalMethod.MethodIdentifierContext, ResultAnalyticalMethod.MethodUrl, TADA.AnalyticalMethod.Flag,
SampleCollectionMethod.MethodIdentifier, SampleCollectionMethod.MethodIdentifierContext, SampleCollectionMethod.MethodName,
SampleCollectionMethod.MethodDescriptionText, SampleCollectionEquipmentName, MeasureQualifierCode,
TADA.MeasureQualifierCode.Flag, TADA.MeasureQualifierCode.Def, ResultCommentText, ActivityCommentText, HydrologicCondition,
HydrologicEvent, DataQuality.PrecisionValue, DataQuality.BiasValue, DataQuality.ConfidenceIntervalValue,
DataQuality.UpperConfidenceLimitValue, DataQuality.LowerConfidenceLimitValue, SamplingDesignTypeCode, LaboratoryName,
ResultLaboratoryCommentText, ResultIdentifier, ActivityIdentifier, OrganizationIdentifier, OrganizationFormalName,
TADA.MultipleOrgDuplicate, TADA.MultipleOrgDupGroupID, TADA.ResultSelectedMultipleOrgs, TADA.SingleOrgDupGroupID,
TADA.SingleOrgDup.Flag, ProjectName, ProjectDescriptionText, ProjectIdentifier, ProjectFileUrl, QAPPApprovedIndicator,
QAPPApprovalAgencyName, CountryCode, StateCode, CountyCode, MonitoringLocationName, MonitoringLocationTypeName,
MonitoringLocationDescriptionText, LatitudeMeasure, TADA.LatitudeMeasure, LongitudeMeasure, TADA.LongitudeMeasure,
HorizontalCoordinateReferenceSystemDatumName, HUCEightDigitCode, MonitoringLocationIdentifier, TADA.NearbySiteGroups,
AquiferName, AquiferTypeName, LocalAqfrName, ConstructionDateText, WellDepthMeasure.MeasureValue,
WellDepthMeasure.MeasureUnitCode, WellHoleDepthMeasure.MeasureValue, WellHoleDepthMeasure.MeasureUnitCode,
ActivityDepthAltitudeReferencePointText, ActivityEndDate, ActivityEndTime.Time, ActivityEndTime.TimeZoneCode,
ActivityEndDateTime, ActivityConductingOrganizationText, SampleAquifer, ActivityLocation.LatitudeMeasure,
ActivityLocation.LongitudeMeasure, ResultStatusIdentifier, ResultWeightBasisText, ResultTemperatureBasisText,
ResultParticleSizeBasisText, USGSPCode, BinaryObjectFileName, BinaryObjectFileTypeCode, AnalysisStartDate,
ResultDetectionQuantitationLimitUrl, LabSamplePreparationUrl, timeZoneStart, timeZoneEnd, SourceMapScaleNumeric,
HorizontalAccuracyMeasure.MeasureValue, HorizontalAccuracyMeasure.MeasureUnitCode, HorizontalCollectionMethodName,
VerticalMeasure.MeasureValue, VerticalMeasure.MeasureUnitCode, VerticalAccuracyMeasure.MeasureValue,
VerticalAccuracyMeasure.MeasureUnitCode, VerticalCollectionMethodName, VerticalCoordinateReferenceSystemDatumName,
FormationTypeText, ProjectMonitoringLocationWeightingUrl, DrainageAreaMeasure.MeasureValue, DrainageAreaMeasure.MeasureUnitCode,
ContributingDrainageAreaMeasure.MeasureValue, ContributingDrainageAreaMeasure.MeasureUnitCode, ProviderName, LastUpdated,
TADA.ConsolidatedDepth.Bottom, TADA.DepthCategory.Flag, TADA.DepthProfileAggregation.Flag)`
[1] "TADA_DepthProfilePlot: Adding surface delination to figure."
Error: Must supply `x` and `y` attributes

@cristinamullin should "null" be the default for surfacevalue and bottomvalue in this function?

@cristinamullin - ready for review