Account for new columns from WQX3 full phys chem profile

[cristinamullin]

Describe the bug

I noticed that the column ordering is not right now (current order below). The TADA Remove and Removal Reason columns should be last. I am updating EPATADA::TADA_OrderCols in the package to move these to the end. We also need to review and account for any new columns associated with the new full physical chemical profile. These should all be changed to the WQX2 legacy names unless they are completely new elements associated with WQX3. Need to review TADA_RenametoLegacy() to make sure it is all working as expected.

ResultIdentifier
ActivityTypeCode
TADA.ActivityType.Flag
ActivityMediaName
TADA.ActivityMediaName
ActivityMediaSubdivisionName
TADA.Media.Flag
CountryCode
StateCode
CountyCode
MonitoringLocationName
TADA.MonitoringLocationName
MonitoringLocationTypeName
TADA.MonitoringLocationTypeName
MonitoringLocationDescriptionText
LatitudeMeasure
TADA.LatitudeMeasure
LongitudeMeasure
TADA.LongitudeMeasure
HorizontalCoordinateReferenceSystemDatumName
TADA.SuspectCoordinates.Flag
HUCEightDigitCode
MonitoringLocationIdentifier
TADA.MonitoringLocationIdentifier
ResultSampleFractionText
TADA.ResultSampleFractionText
TADA.SampleFraction.Flag
CharacteristicName
TADA.CharacteristicName
SubjectTaxonomicName
SampleTissueAnatomyName
MethodSpeciationName
TADA.MethodSpeciationName
TADA.MethodSpeciation.Flag
TADA.ComparableDataIdentifier
ActivityStartDate
ActivityStartTime.Time
ActivityStartTime.TimeZoneCode
ActivityStartDateTime
ResultMeasureValue
ResultMeasure.MeasureUnitCode
TADA.ResultMeasureValue
TADA.ResultMeasure.MeasureUnitCode
TADA.WQXResultUnitConversion
TADA.ResultUnit.Flag
ResultValueTypeName
TADA.ResultMeasureValueDataTypes.Flag
TADA.ResultValueAboveUpperThreshold.Flag
TADA.ResultValueBelowLowerThreshold.Flag
ResultDetectionConditionText
DetectionQuantitationLimitTypeName
DetectionQuantitationLimitMeasure.MeasureValue
DetectionQuantitationLimitMeasure.MeasureUnitCode
TADA.DetectionQuantitationLimitMeasure.MeasureValue
TADA.DetectionQuantitationLimitMeasure.MeasureUnitCode
TADA.DetectionQuantitationLimitMeasure.MeasureValueDataTypes.Flag
TADA.CensoredData.Flag
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
TADA.ContinuousData.Flag
ResultAnalyticalMethod.MethodName
ResultAnalyticalMethod.MethodDescriptionText
ResultAnalyticalMethod.MethodIdentifier
ResultAnalyticalMethod.MethodIdentifierContext
ResultAnalyticalMethod.MethodUrl
TADA.AnalyticalMethod.Flag
SampleCollectionMethod.MethodIdentifier
SampleCollectionMethod.MethodIdentifierContext
SampleCollectionMethod.MethodName
SampleCollectionMethod.MethodDescriptionText
SampleCollectionEquipmentName
MeasureQualifierCode
ResultStatusIdentifier
TADA.MeasureQualifierCode.Flag
TADA.MeasureQualifierCode.Def
ResultCommentText
ActivityCommentText
HydrologicCondition
HydrologicEvent
DataQuality.PrecisionValue
DataQuality.BiasValue
DataQuality.ConfidenceIntervalValue
DataQuality.UpperConfidenceLimitValue
DataQuality.LowerConfidenceLimitValue
SamplingDesignTypeCode
LaboratoryName
ResultLaboratoryCommentText
ActivityIdentifier
OrganizationIdentifier
OrganizationFormalName
TADA.SingleOrgDupGroupID
TADA.SingleOrgDup.Flag
ProjectName
ProjectDescriptionText
ProjectIdentifier
ProjectFileUrl
QAPPApprovedIndicator
QAPPApprovalAgencyName
TADA.QAPPDocAvailable
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
ResultWeightBasisText
ResultTemperatureBasisText
ResultParticleSizeBasisText
USGSPCode
BinaryObjectFileName
BinaryObjectFileTypeCode
AnalysisStartDate
ResultDetectionQuantitationLimitUrl
LabSamplePreparationUrl
ActivityStartTime.TimeZoneCode_offset
ActivityEndTime.TimeZoneCode_offset
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.Remove
TADA.RemovalReason
ProjectAttachment_FileName
ProjectAttachment_FileType
StateName
Location_CountryName
Location_CountyName
Location_HUCTwelveDigitCode
Location_TribalLandIndicator
Location_TribalLand
Location_LatitudeStandardized
Location_LongitudeStandardized
Location_HorzCoordStandardizedDatum
AlternateLocation_IdentifierCount
Activity_ActivityIdentifierUserSupplied
SamplingComponentName
AssemblageSampledName
ToxicityTestType
ActivityLocation.HorizontalCoordinateReferenceSystemDatumName
ActivityLocation_SourceMapScale
ActivityLocation_LatitudeStandardized
ActivityLocation_LongitudeStandardized
ActivityLocation_HorzCoordStandardizedDatum
ActivityLocation.HorizontalAccuracyMeasure.MeasureValue
ActivityLocation.HorizontalAccuracyMeasure.MeasureUnitCode
ActivityLocation.HorizontalCollectionMethodName
ActivityLocation_Description
SampleCollectionMethod.MethodQualifierTypeName
SampleCollectionMethod.SampleCollectionEquipmentCommentText
SamplePreparationMethod.MethodIdentifier
SamplePreparationMethod.MethodIdentifierContext
SamplePreparationMethod.MethodName
SamplePreparationMethod.MethodQualifierTypeName
SamplePrepMethod_Description
SamplePrepMethod_ContainerLabel
SampleContainerTypeName
SampleContainerColorName
ChemicalPreservativeUsedName
ThermalPreservativeUsedName
SampleTransportStorageDescription
ActivityAttachment_FileName
ActivityAttachment_FileType
ActivityFileUrl
Result_DataLoggerLine
Result_CharacteristicUserSupplied
Result_CASNumber
BiologicalIntentName
BiologicalIndividualIdentifier
ResultBiological_TaxonUserSupplied
ResultBiological_TaxonUserSuppliedReference
UnidentifiedSpeciesIdentifier
ResultBiological_GroupSummaryCount
GroupSummaryWeight_Measure
GroupSummaryWeight_MeasureUnit
ResultSamplingPointName
ResultDepthHeight_SamplingPointType
ResultDepthHeight_SamplingPointPlaceInSeries
ResultDepthHeight_SamplingPointComment
ResultDepthHeight_RecordIdentifierUserSupplied
Result_StatisticalNValue
DetectionLimit_CommentA
DetectionLimit_TypeB
DetectionLimit_MeasureB
DetectionLimit_MeasureUnitB
DetectionLimit_CommentB
LabInfo_LabSampleSplitRatio
LaboratoryAccreditationIndicator
LaboratoryAccreditationAuthorityName
TaxonomistAccreditationIndicator
TaxonomistAccreditationAuthorityName
ResultAnalyticalMethod.MethodQualifierTypeName
Result_ComparableMethodIdentifier
Result_ComparableMethodIdentifierContext
Result_ComparableMethodModification
AnalysisStartTime.Time
AnalysisStartTime.TimeZoneCode
AnalysisEndDate
AnalysisEndTime.Time
AnalysisEndTime.TimeZoneCode
LabSamplePreparationMethod.MethodIdentifier
LabSamplePreparationMethod.MethodIdentifierContext
LabSamplePreparationMethod.MethodName
LabSamplePreparationMethod.MethodQualifierTypeName
LabSamplePrepMethod_Description
PreparationStartDate
PreparationStartTime.Time
PreparationStartTime.TimeZoneCode
PreparationEndDate
LabSamplePrepMethod_EndTime
PreparationEndTime.Time
SubstitutionDilutionFactorNumeric
ResultAttachment_FileName
ResultAttachment_FileType
Result_CharacteristicComparable
Result_CharacteristicGroup
OrganizationType
LastChangeDate
Activity_StartTimeZone_offset
Activity_StartDateTime
Activity_EndTimeZone_offset
Activity_EndDateTime
LabInfo_AnalysisStartTimeZone_offset
LabInfo_AnalysisStartDateTime
LabSamplePrepMethod_StartTimeZone_offset
LabSamplePrepMethod_StartDateTime

[cristinamullin]

This subset were not in the TADA profile previously:

ProjectAttachment_FileName
ProjectAttachment_FileType
StateName
Location_CountryName
Location_CountyName
Location_HUCTwelveDigitCode
Location_TribalLandIndicator
Location_TribalLand
Location_LatitudeStandardized
Location_LongitudeStandardized
Location_HorzCoordStandardizedDatum
AlternateLocation_IdentifierCount
Activity_ActivityIdentifierUserSupplied
SamplingComponentName
AssemblageSampledName
ToxicityTestType
ActivityLocation.HorizontalCoordinateReferenceSystemDatumName
ActivityLocation_SourceMapScale
ActivityLocation_LatitudeStandardized
ActivityLocation_LongitudeStandardized
ActivityLocation_HorzCoordStandardizedDatum
ActivityLocation.HorizontalAccuracyMeasure.MeasureValue
ActivityLocation.HorizontalAccuracyMeasure.MeasureUnitCode
ActivityLocation.HorizontalCollectionMethodName
ActivityLocation_Description
SampleCollectionMethod.MethodQualifierTypeName
SampleCollectionMethod.SampleCollectionEquipmentCommentText
SamplePreparationMethod.MethodIdentifier
SamplePreparationMethod.MethodIdentifierContext
SamplePreparationMethod.MethodName
SamplePreparationMethod.MethodQualifierTypeName
SamplePrepMethod_Description
SamplePrepMethod_ContainerLabel
SampleContainerTypeName
SampleContainerColorName
ChemicalPreservativeUsedName
ThermalPreservativeUsedName
SampleTransportStorageDescription
ActivityAttachment_FileName
ActivityAttachment_FileType
ActivityFileUrl
Result_DataLoggerLine
Result_CharacteristicUserSupplied
Result_CASNumber
BiologicalIntentName
BiologicalIndividualIdentifier
ResultBiological_TaxonUserSupplied
ResultBiological_TaxonUserSuppliedReference
UnidentifiedSpeciesIdentifier
ResultBiological_GroupSummaryCount
GroupSummaryWeight_Measure
GroupSummaryWeight_MeasureUnit
ResultSamplingPointName
ResultDepthHeight_SamplingPointType
ResultDepthHeight_SamplingPointPlaceInSeries
ResultDepthHeight_SamplingPointComment
ResultDepthHeight_RecordIdentifierUserSupplied
Result_StatisticalNValue
DetectionLimit_CommentA
DetectionLimit_TypeB
DetectionLimit_MeasureB
DetectionLimit_MeasureUnitB
DetectionLimit_CommentB
LabInfo_LabSampleSplitRatio
LaboratoryAccreditationIndicator
LaboratoryAccreditationAuthorityName
TaxonomistAccreditationIndicator
TaxonomistAccreditationAuthorityName
ResultAnalyticalMethod.MethodQualifierTypeName
Result_ComparableMethodIdentifier
Result_ComparableMethodIdentifierContext
Result_ComparableMethodModification
AnalysisStartTime.Time
AnalysisStartTime.TimeZoneCode
AnalysisEndDate
AnalysisEndTime.Time
AnalysisEndTime.TimeZoneCode
LabSamplePreparationMethod.MethodIdentifier
LabSamplePreparationMethod.MethodIdentifierContext
LabSamplePreparationMethod.MethodName
LabSamplePreparationMethod.MethodQualifierTypeName
LabSamplePrepMethod_Description
PreparationStartDate
PreparationStartTime.Time
PreparationStartTime.TimeZoneCode
PreparationEndDate
LabSamplePrepMethod_EndTime
PreparationEndTime.Time
SubstitutionDilutionFactorNumeric
ResultAttachment_FileName
ResultAttachment_FileType
Result_CharacteristicComparable
Result_CharacteristicGroup
OrganizationType
LastChangeDate
Activity_StartTimeZone_offset
Activity_StartDateTime
Activity_EndTimeZone_offset
Activity_EndDateTime
LabInfo_AnalysisStartTimeZone_offset
LabInfo_AnalysisStartDateTime
LabSamplePrepMethod_StartTimeZone_offset
LabSamplePrepMethod_StartDateTime

[cristinamullin]

Here is some example code to test the different outputs:

EPA_WQX3_only <- 
  dataRetrieval::readWQPdata(statecode = "WI",
                             countycode = "Dane",
                             characteristicName = "Phosphorus",
                             startDate = "2023-05-01",
                             endDate = "2025-12-01",
                             service = "ResultWQX3",
                             dataProfile = "fullPhysChem",
                             ignore_attributes = TRUE,
                             providers = "STORET")

USGS_WQX3_only <- 
  dataRetrieval::read_waterdata_samples(stateFips = "US:55", #WI
                                        countyFips = "US:55:025", #Dane
                                        characteristic = "Phosphorus",
                                        activityStartDateLower = "2023-05-01",
                                        activityStartDateUpper = "2025-12-01", 
                                        dataProfile = "fullphyschem")

All_WQX3 <- dplyr::bind_rows(EPA_WQX3_only, USGS_WQX3_only)

All_WQX3_rename <- EPATADA::TADA_RenametoLegacy(All_WQX3)

All_WQX3_clean <- EPATADA::TADA_AutoClean(All_WQX3_rename)

All_WQX3_ordered <- EPATADA::TADA_OrderCols(All_WQX3_clean)

And this:

# legacy/production WQP, using only to verify counts, EPA WQX counts and data are the 
# same for legacy/production AND new WQX3 beta service
# only the USGS counts are different for legacy/production AND new WQP WQX3 beta service after March 2024
tada1 <- EPATADA::TADA_DataRetrieval(
  statecode = "WI", 
  countycode = "Dane",
  characteristicName = "Phosphorus",
  startDate = "2023-05-01",
  endDate = "2025-12-01",
  provider = "STORET", # only EPA WQX data = "STORET"
  ask = FALSE, 
  applyautoclean = FALSE
)

# new stand alone USGS service for their samples data
# this data also gets delivered to the new WQP beta
# use this to get the USGS data only
tada2 <- dataRetrieval::read_waterdata_samples(stateFips = "US:55", #WI
                                               countyFips = "US:55:025", #Dane
                                               characteristic = "Phosphorus",
                                               activityStartDateLower = "2023-05-01",
                                               activityStartDateUpper = "2025-12-01", 
                                               dataProfile = "fullphyschem")

# new WQP WQX3 beta service, represents both EPA and USGS
# use to get the total expected counts for both USGS and EPA, regardless of dates
tada3 <- dataRetrieval::readWQPdata(statecode = "WI",
                                    countycode = "Dane", 
                                    characteristicName = "Phosphorus",   
                                    startDate = "2023-05-01",
                                    endDate = "2025-12-01",
                                    service = "ResultWQX3",
                                    dataProfile = "fullPhysChem",
                                    ignore_attributes = TRUE
                                    )

# new WQP WQX3 beta service, WQX only
tada4 <- dataRetrieval::readWQPdata(statecode = "WI",
                                    countycode = "Dane",
                                    characteristicName = "Phosphorus",
                                    startDate = "2023-05-01",
                                    endDate = "2025-12-01",
                                    service = "ResultWQX3",
                                    dataProfile = "fullPhysChem",
                                    ignore_attributes = TRUE,
                                    providers = "STORET"
)

# fail if the counts don't match
stopifnot(nrow(tada1) + nrow(tada2) == nrow(tada3))

# fail if the counts don't match, there is a bug so it will fail
stopifnot(nrow(tada1) == nrow(tada4))

# final to use in TADAShiny
# Add tada2 with tada4 (full join)

# 1) Ensure both have the exact same columns
stopifnot(setequal(names(tada4), names(tada2)))

# Align column order so names are identical and in the same sequence
tada2 <- tada2[, names(tada4)]

# Optional: sanity check types (will only warn; bind_rows can coerce)
classes_wqx <- sapply(tada4, function(x) paste(class(x), collapse = "+"))
classes_usgs <- sapply(tada2,  function(x) paste(class(x), collapse = "+"))
type_mismatch <- names(tada4)[classes_wqx != classes_usgs]
if (length(type_mismatch) > 0) {
  message("Warning: Type mismatches detected in columns: ",
          paste(type_mismatch, collapse = ", "))
  # If needed, harmonize types here before bind_rows (e.g., as.character, as.numeric, etc.)
}

# 2) Bind rows (stack records); no new columns should be introduced
tada_all <- dplyr::bind_rows(tada4, tada2)

# 3) Quick checks
stopifnot(ncol(tada_all) == ncol(tada4))
stopifnot(identical(names(tada_all), names(tada4)))
stopifnot(nrow(tada_all) == nrow(tada4) + nrow(tada2))

[cristinamullin]

@cefergus I added some example code here in case it is helpful for testing the changes.

[cristinamullin]

Beta output:

  [1] "Org_Identifier"                                         
  [2] "Org_FormalName"                                         
  [3] "Project_Identifier"                                     
  [4] "Project_Name"                                           
  [5] "Project_QAPPApproved"                                   
  [6] "Project_QAPPApprovalAgency"                             
  [7] "ProjectAttachment_FileName"                             
  [8] "ProjectAttachment_FileType"                             
  [9] "Location_Identifier"                                    
 [10] "Location_Name"                                          
 [11] "Location_Type"                                          
 [12] "Location_Description"                                   
 [13] "Location_State"                                         
 [14] "Location_CountryName"                                   
 [15] "Location_CountyName"                                    
 [16] "Location_CountryCode"                                   
 [17] "Location_StatePostalCode"                               
 [18] "Location_CountyCode"                                    
 [19] "Location_HUCEightDigitCode"                             
 [20] "Location_HUCTwelveDigitCode"                            
 [21] "Location_TribalLandIndicator"                           
 [22] "Location_TribalLand"                                    
 [23] "Location_Latitude"                                      
 [24] "Location_Longitude"                                     
 [25] "Location_HorzCoordReferenceSystemDatum"                 
 [26] "Location_LatitudeStandardized"                          
 [27] "Location_LongitudeStandardized"                         
 [28] "Location_HorzCoordStandardizedDatum"                    
 [29] "AlternateLocation_IdentifierCount"                      
 [30] "Activity_ActivityIdentifier"                            
 [31] "Activity_ActivityIdentifierUserSupplied"                
 [32] "Activity_TypeCode"                                      
 [33] "Activity_Media"                                         
 [34] "Activity_MediaSubdivision"                              
 [35] "Activity_BottomDepthSamplingComponent"                  
 [36] "ActivityBiological_AssemblageSampled"                   
 [37] "ActivityBiological_ToxicityTestType"                    
 [38] "Activity_ConductingOrganization"                        
 [39] "Activity_Comment"                                       
 [40] "ActivityLocation_Latitude"                              
 [41] "ActivityLocation_Longitude"                             
 [42] "ActivityLocation_HorzCoordReferenceSystemDatum"         
 [43] "ActivityLocation_SourceMapScale"                        
 [44] "ActivityLocation_LatitudeStandardized"                  
 [45] "ActivityLocation_LongitudeStandardized"                 
 [46] "ActivityLocation_HorzCoordStandardizedDatum"            
 [47] "ActivityLocation_HorzAccuracyMeasure"                   
 [48] "ActivityLocation_HorzAccuracyMeasureUnit"               
 [49] "ActivityLocation_HorizontalAccuracyHorzCollectionMethod"
 [50] "ActivityLocation_Description"                           
 [51] "Activity_StartDate"                                     
 [52] "Activity_StartTime"                                     
 [53] "Activity_StartTimeZone"                                 
 [54] "Activity_EndDate"                                       
 [55] "Activity_EndTime"                                       
 [56] "Activity_EndTimeZone"                                   
 [57] "Activity_DepthHeightMeasure"                            
 [58] "Activity_DepthHeightMeasureUnit"                        
 [59] "Activity_BottomDepthAltitudeReferencePoint"             
 [60] "Activity_ActivityRelativeDepth"                         
 [61] "Activity_TopDepthMeasure"                               
 [62] "Activity_TopDepthMeasureUnit"                           
 [63] "Activity_BottomDepthMeasure"                            
 [64] "Activity_BottomDepthMeasureUnit"                        
 [65] "SampleCollectionMethod_Identifier"                      
 [66] "SampleCollectionMethod_IdentifierContext"               
 [67] "SampleCollectionMethod_Name"                            
 [68] "SampleCollectionMethod_QualifierTypeName"               
 [69] "SampleCollectionMethod_Description"                     
 [70] "SampleCollectionMethod_EquipmentName"                   
 [71] "SampleCollectionMethod_EquipmentComment"                
 [72] "SamplePrepMethod_Identifier"                            
 [73] "SamplePrepMethod_IdentifierContext"                     
 [74] "SamplePrepMethod_Name"                                  
 [75] "SamplePrepMethod_QualifierType"                         
 [76] "SamplePrepMethod_Description"                           
 [77] "SamplePrepMethod_ContainerLabel"                        
 [78] "SamplePrepMethod_ContainerType"                         
 [79] "SamplePrepMethod_ContainerColor"                        
 [80] "SamplePrepMethod_ChemicalPreservativeUsed"              
 [81] "SamplePrepMethod_ThermalPreservativeUsed"               
 [82] "SamplePrepMethod_TransportStorageDescription"           
 [83] "Activity_HydrologicCondition"                           
 [84] "Activity_HydrologicEvent"                               
 [85] "ActivityAttachment_FileName"                            
 [86] "ActivityAttachment_FileType"                            
 [87] "ActivityAttachment_FileDownload"                        
 [88] "Result_DataLoggerLine"                                  
 [89] "Result_ResultDetectionCondition"                        
 [90] "Result_Characteristic"                                  
 [91] "Result_CharacteristicUserSupplied"                      
 [92] "Result_CASNumber"                                       
 [93] "Result_MethodSpeciation"                                
 [94] "Result_SampleFraction"                                  
 [95] "ResultBiological_Intent"                                
 [96] "ResultBiological_IndividualIdentifier"                  
 [97] "ResultBiological_Taxon"                                 
 [98] "ResultBiological_TaxonUserSupplied"                     
 [99] "ResultBiological_TaxonUserSuppliedReference"            
[100] "ResultBiological_UnidentifiedSpeciesIdentifier"         
[101] "ResultBiological_SampleTissueAnatomy"                   
[102] "ResultBiological_GroupSummaryCount"                     
[103] "GroupSummaryWeight_Measure"                             
[104] "GroupSummaryWeight_MeasureUnit"                         
[105] "ResultDepthHeight_Measure"                              
[106] "ResultDepthHeight_MeasureUnit"                          
[107] "ResultDepthHeight_AltitudeReferencePoint"               
[108] "ResultDepthHeight_SamplingPointName"                    
[109] "ResultDepthHeight_SamplingPointType"                    
[110] "ResultDepthHeight_SamplingPointPlaceInSeries"           
[111] "ResultDepthHeight_SamplingPointComment"                 
[112] "ResultDepthHeight_RecordIdentifierUserSupplied"         
[113] "Result_MeasureIdentifier"                               
[114] "Result_Measure"                                         
[115] "Result_MeasureUnit"                                     
[116] "Result_MeasureQualifierCode"                            
[117] "Result_MeasureStatusIdentifier"                         
[118] "Result_StatisticalBase"                                 
[119] "Result_StatisticalNValue"                               
[120] "Result_MeasureType"                                     
[121] "Result_WeightBasis"                                     
[122] "Result_TimeBasis"                                       
[123] "Result_MeasureTemperatureBasis"                         
[124] "Result_MeasureParticleSizeBasis"                        
[125] "DataQuality_PrecisionValue"                             
[126] "DataQuality_BiasValue"                                  
[127] "DataQuality_ConfidenceIntervalValue"                    
[128] "DataQuality_UpperConfidenceLimitValue"                  
[129] "DataQuality_LowerConfidenceLimitValue"                  
[130] "DataQuality_ResultComment"                              
[131] "DetectionLimit_TypeA"                                   
[132] "DetectionLimit_MeasureA"                                
[133] "DetectionLimit_MeasureUnitA"                            
[134] "DetectionLimit_CommentA"                                
[135] "DetectionLimit_TypeB"                                   
[136] "DetectionLimit_MeasureB"                                
[137] "DetectionLimit_MeasureUnitB"                            
[138] "DetectionLimit_CommentB"                                
[139] "LabInfo_LabSampleSplitRatio"                            
[140] "LabInfo_LabAccreditationIndicator"                      
[141] "LabInfo_LabAccreditationAuthority"                      
[142] "LabInfo_TaxonAccreditationIndicator"                    
[143] "LabInfo_TaxonAccreditationAuthority"                    
[144] "ResultAnalyticalMethod_Identifier"                      
[145] "ResultAnalyticalMethod_IdentifierContext"               
[146] "ResultAnalyticalMethod_Name"                            
[147] "ResultAnalyticalMethod_QualifierType"                   
[148] "ResultAnalyticalMethod_Description"                     
[149] "Result_ComparableMethodIdentifier"                      
[150] "Result_ComparableMethodIdentifierContext"               
[151] "Result_ComparableMethodModification"                    
[152] "LabInfo_Name"                                           
[153] "LabInfo_AnalysisStartDate"                              
[154] "LabInfo_AnalysisStartTime"                              
[155] "LabInfo_AnalysisStartTimeZone"                          
[156] "LabInfo_AnalysisEndDate"                                
[157] "LabInfo_AnalysisEndTime"                                
[158] "LabInfo_AnalysisEndTimeZone"                            
[159] "LabInfo_LaboratoryComment"                              
[160] "LabSamplePrepMethod_Identifier"                         
[161] "LabSamplePrepMethod_IdentifierContext"                  
[162] "LabSamplePrepMethod_Name"                               
[163] "LabSamplePrepMethod_QualifierType"                      
[164] "LabSamplePrepMethod_Description"                        
[165] "LabSamplePrepMethod_StartDate"                          
[166] "LabSamplePrepMethod_StartTime"                          
[167] "LabSamplePrepMethod_StartTimeZone"                      
[168] "LabSamplePrepMethod_EndDate"                            
[169] "LabSamplePrepMethod_EndTime"                            
[170] "LabSamplePrepMethod_EndTimeZone"                        
[171] "LabSamplePrepMethod_DilutionFactor"                     
[172] "ResultAttachment_FileName"                              
[173] "ResultAttachment_FileType"                              
[174] "ResultAttachment_FileDownload"                          
[175] "ProviderName"                                           
[176] "Result_CharacteristicComparable"                        
[177] "Result_CharacteristicGroup"                             
[178] "Org_Type"                                               
[179] "LastChangeDate"                                         
[180] "USGSpcode"                                              
[181] "USGSSampleAquifer"                                      
[182] "Activity_StartTimeZone_offset"                          
[183] "Activity_StartDateTime"                                 
[184] "Activity_EndTimeZone_offset"                            
[185] "Activity_EndDateTime"                                   
[186] "LabInfo_AnalysisStartTimeZone_offset"                   
[187] "LabInfo_AnalysisStartDateTime" 

After rename function:

> colnames(All_WQX3_rename)
  [1] "ResultIdentifier"                                             
  [2] "ActivityTypeCode"                                             
  [3] "ActivityMediaName"                                            
  [4] "ActivityMediaSubdivisionName"                                 
  [5] "CountryCode"                                                  
  [6] "StateCode"                                                    
  [7] "CountyCode"                                                   
  [8] "MonitoringLocationName"                                       
  [9] "MonitoringLocationTypeName"                                   
 [10] "MonitoringLocationDescriptionText"                            
 [11] "LatitudeMeasure"                                              
 [12] "LongitudeMeasure"                                             
 [13] "HorizontalCoordinateReferenceSystemDatumName"                 
 [14] "HUCEightDigitCode"                                            
 [15] "MonitoringLocationIdentifier"                                 
 [16] "ResultSampleFractionText"                                     
 [17] "CharacteristicName"                                           
 [18] "SubjectTaxonomicName"                                         
 [19] "SampleTissueAnatomyName"                                      
 [20] "MethodSpeciationName"                                         
 [21] "ActivityStartDate"                                            
 [22] "ActivityStartTime.Time"                                       
 [23] "ActivityStartTime.TimeZoneCode"                               
 [24] "ResultMeasureValue"                                           
 [25] "ResultMeasure.MeasureUnitCode"                                
 [26] "ResultValueTypeName"                                          
 [27] "ResultDetectionConditionText"                                 
 [28] "DetectionQuantitationLimitTypeName"                           
 [29] "DetectionQuantitationLimitMeasure.MeasureValue"               
 [30] "DetectionQuantitationLimitMeasure.MeasureUnitCode"            
 [31] "ResultDepthHeightMeasure.MeasureValue"                        
 [32] "ResultDepthHeightMeasure.MeasureUnitCode"                     
 [33] "ResultDepthAltitudeReferencePointText"                        
 [34] "ActivityRelativeDepthName"                                    
 [35] "ActivityDepthHeightMeasure.MeasureValue"                      
 [36] "ActivityDepthHeightMeasure.MeasureUnitCode"                   
 [37] "ActivityTopDepthHeightMeasure.MeasureValue"                   
 [38] "ActivityTopDepthHeightMeasure.MeasureUnitCode"                
 [39] "ActivityBottomDepthHeightMeasure.MeasureValue"                
 [40] "ActivityBottomDepthHeightMeasure.MeasureUnitCode"             
 [41] "ResultTimeBasisText"                                          
 [42] "StatisticalBaseCode"                                          
 [43] "ResultFileUrl"                                                
 [44] "ResultAnalyticalMethod.MethodName"                            
 [45] "ResultAnalyticalMethod.MethodDescriptionText"                 
 [46] "ResultAnalyticalMethod.MethodIdentifier"                      
 [47] "ResultAnalyticalMethod.MethodIdentifierContext"               
 [48] "SampleCollectionMethod.MethodIdentifier"                      
 [49] "SampleCollectionMethod.MethodIdentifierContext"               
 [50] "SampleCollectionMethod.MethodName"                            
 [51] "SampleCollectionMethod.MethodDescriptionText"                 
 [52] "SampleCollectionEquipmentName"                                
 [53] "MeasureQualifierCode"                                         
 [54] "ResultStatusIdentifier"                                       
 [55] "ResultCommentText"                                            
 [56] "ActivityCommentText"                                          
 [57] "HydrologicCondition"                                          
 [58] "HydrologicEvent"                                              
 [59] "DataQuality.PrecisionValue"                                   
 [60] "DataQuality.BiasValue"                                        
 [61] "DataQuality.ConfidenceIntervalValue"                          
 [62] "DataQuality.UpperConfidenceLimitValue"                        
 [63] "DataQuality.LowerConfidenceLimitValue"                        
 [64] "LaboratoryName"                                               
 [65] "ResultLaboratoryCommentText"                                  
 [66] "ActivityIdentifier"                                           
 [67] "OrganizationIdentifier"                                       
 [68] "OrganizationFormalName"                                       
 [69] "ProjectName"                                                  
 [70] "ProjectIdentifier"                                            
 [71] "QAPPApprovedIndicator"                                        
 [72] "QAPPApprovalAgencyName"                                       
 [73] "ActivityDepthAltitudeReferencePointText"                      
 [74] "ActivityEndDate"                                              
 [75] "ActivityEndTime.Time"                                         
 [76] "ActivityEndTime.TimeZoneCode"                                 
 [77] "ActivityConductingOrganizationText"                           
 [78] "SampleAquifer"                                                
 [79] "ActivityLocation.LatitudeMeasure"                             
 [80] "ActivityLocation.LongitudeMeasure"                            
 [81] "ResultWeightBasisText"                                        
 [82] "ResultTemperatureBasisText"                                   
 [83] "ResultParticleSizeBasisText"                                  
 [84] "USGSPCode"                                                    
 [85] "AnalysisStartDate"                                            
 [86] "ProviderName"                                                 
 [87] "ProjectAttachment_FileName"                                   
 [88] "ProjectAttachment_FileType"                                   
 [89] "StateName"                                                    
 [90] "Location_CountryName"                                         
 [91] "Location_CountyName"                                          
 [92] "Location_HUCTwelveDigitCode"                                  
 [93] "Location_TribalLandIndicator"                                 
 [94] "Location_TribalLand"                                          
 [95] "Location_LatitudeStandardized"                                
 [96] "Location_LongitudeStandardized"                               
 [97] "Location_HorzCoordStandardizedDatum"                          
 [98] "AlternateLocation_IdentifierCount"                            
 [99] "Activity_ActivityIdentifierUserSupplied"                      
[100] "SamplingComponentName"                                        
[101] "AssemblageSampledName"                                        
[102] "ToxicityTestType"                                             
[103] "ActivityLocation.HorizontalCoordinateReferenceSystemDatumName"
[104] "ActivityLocation_SourceMapScale"                              
[105] "ActivityLocation_LatitudeStandardized"                        
[106] "ActivityLocation_LongitudeStandardized"                       
[107] "ActivityLocation_HorzCoordStandardizedDatum"                  
[108] "ActivityLocation.HorizontalAccuracyMeasure.MeasureValue"      
[109] "ActivityLocation.HorizontalAccuracyMeasure.MeasureUnitCode"   
[110] "ActivityLocation.HorizontalCollectionMethodName"              
[111] "ActivityLocation_Description"                                 
[112] "SampleCollectionMethod.MethodQualifierTypeName"               
[113] "SampleCollectionMethod.SampleCollectionEquipmentCommentText"  
[114] "SamplePreparationMethod.MethodIdentifier"                     
[115] "SamplePreparationMethod.MethodIdentifierContext"              
[116] "SamplePreparationMethod.MethodName"                           
[117] "SamplePreparationMethod.MethodQualifierTypeName"              
[118] "SamplePrepMethod_Description"                                 
[119] "SamplePrepMethod_ContainerLabel"                              
[120] "SampleContainerTypeName"                                      
[121] "SampleContainerColorName"                                     
[122] "ChemicalPreservativeUsedName"                                 
[123] "ThermalPreservativeUsedName"                                  
[124] "SampleTransportStorageDescription"                            
[125] "ActivityAttachment_FileName"                                  
[126] "ActivityAttachment_FileType"                                  
[127] "ActivityFileUrl"                                              
[128] "Result_DataLoggerLine"                                        
[129] "Result_CharacteristicUserSupplied"                            
[130] "Result_CASNumber"                                             
[131] "BiologicalIntentName"                                         
[132] "BiologicalIndividualIdentifier"                               
[133] "ResultBiological_TaxonUserSupplied"                           
[134] "ResultBiological_TaxonUserSuppliedReference"                  
[135] "UnidentifiedSpeciesIdentifier"                                
[136] "ResultBiological_GroupSummaryCount"                           
[137] "GroupSummaryWeight_Measure"                                   
[138] "GroupSummaryWeight_MeasureUnit"                               
[139] "ResultSamplingPointName"                                      
[140] "ResultDepthHeight_SamplingPointType"                          
[141] "ResultDepthHeight_SamplingPointPlaceInSeries"                 
[142] "ResultDepthHeight_SamplingPointComment"                       
[143] "ResultDepthHeight_RecordIdentifierUserSupplied"               
[144] "Result_StatisticalNValue"                                     
[145] "DetectionLimit_CommentA"                                      
[146] "DetectionLimit_TypeB"                                         
[147] "DetectionLimit_MeasureB"                                      
[148] "DetectionLimit_MeasureUnitB"                                  
[149] "DetectionLimit_CommentB"                                      
[150] "LabInfo_LabSampleSplitRatio"                                  
[151] "LaboratoryAccreditationIndicator"                             
[152] "LaboratoryAccreditationAuthorityName"                         
[153] "TaxonomistAccreditationIndicator"                             
[154] "TaxonomistAccreditationAuthorityName"                         
[155] "ResultAnalyticalMethod.MethodQualifierTypeName"               
[156] "Result_ComparableMethodIdentifier"                            
[157] "Result_ComparableMethodIdentifierContext"                     
[158] "Result_ComparableMethodModification"                          
[159] "AnalysisStartTime.Time"                                       
[160] "AnalysisStartTime.TimeZoneCode"                               
[161] "AnalysisEndDate"                                              
[162] "AnalysisEndTime.Time"                                         
[163] "AnalysisEndTime.TimeZoneCode"                                 
[164] "LabSamplePreparationMethod.MethodIdentifier"                  
[165] "LabSamplePreparationMethod.MethodIdentifierContext"           
[166] "LabSamplePreparationMethod.MethodName"                        
[167] "LabSamplePreparationMethod.MethodQualifierTypeName"           
[168] "LabSamplePrepMethod_Description"                              
[169] "PreparationStartDate"                                         
[170] "PreparationStartTime.Time"                                    
[171] "PreparationStartTime.TimeZoneCode"                            
[172] "PreparationEndDate"                                           
[173] "LabSamplePrepMethod_EndTime"                                  
[174] "PreparationEndTime.Time"                                      
[175] "SubstitutionDilutionFactorNumeric"                            
[176] "ResultAttachment_FileName"                                    
[177] "ResultAttachment_FileType"                                    
[178] "Result_CharacteristicComparable"                              
[179] "Result_CharacteristicGroup"                                   
[180] "OrganizationType"                                             
[181] "LastChangeDate"                                               
[182] "Activity_StartTimeZone_offset"                                
[183] "Activity_StartDateTime"                                       
[184] "Activity_EndTimeZone_offset"                                  
[185] "Activity_EndDateTime"                                         
[186] "LabInfo_AnalysisStartTimeZone_offset"                         
[187] "LabInfo_AnalysisStartDateTime" 

[cristinamullin]

We are going to only include a subset of columns for now - see #294. Keeping this issue open to remember to re-visit the re-name function in the future.