tests/testthat/test-DataDiscoveryRetrieval.R
In USEPA/TADA: EPA TADA (Tools for Automated Data Analysis) R Package
test_that("TADA_DataRetrieval", {
randomday <- TADA_RandomTestingData(number_of_days = 2, choose_random_state = TRUE)
# you could just pick the important columns:
expect_true(all(c(
"OrganizationIdentifier",
"OrganizationFormalName",
"ActivityIdentifier",
"ActivityTypeCode",
"ActivityMediaName",
"TADA.ActivityMediaName",
"ActivityMediaSubdivisionName",
"ActivityStartDate",
"ActivityStartTime.Time",
"ActivityStartTime.TimeZoneCode",
"ActivityEndDate",
"ActivityEndTime.Time",
"ActivityEndTime.TimeZoneCode",
"ActivityRelativeDepthName",
"ActivityDepthHeightMeasure.MeasureValue",
"ActivityDepthHeightMeasure.MeasureUnitCode",
"ActivityDepthAltitudeReferencePointText",
"ActivityTopDepthHeightMeasure.MeasureValue",
"ActivityTopDepthHeightMeasure.MeasureUnitCode",
"ActivityBottomDepthHeightMeasure.MeasureValue",
"ActivityBottomDepthHeightMeasure.MeasureUnitCode",
"ProjectIdentifier",
"ProjectName",
"ActivityConductingOrganizationText",
"MonitoringLocationIdentifier",
"MonitoringLocationName",
"ActivityCommentText",
"SampleAquifer",
"HydrologicCondition",
"HydrologicEvent",
"SampleCollectionMethod.MethodIdentifier",
"SampleCollectionMethod.MethodIdentifierContext",
"SampleCollectionMethod.MethodName",
"SampleCollectionEquipmentName",
"ActivityLocation.LatitudeMeasure",
"ActivityLocation.LongitudeMeasure",
"ResultDetectionConditionText",
"MethodSpeciationName",
"CharacteristicName",
"TADA.CharacteristicName",
"ResultSampleFractionText",
"ResultMeasureValue",
"TADA.ResultMeasureValue",
"TADA.ResultMeasureValueDataTypes.Flag",
"ResultMeasure.MeasureUnitCode",
"TADA.ResultMeasure.MeasureUnitCode",
"MeasureQualifierCode",
"ResultStatusIdentifier",
"StatisticalBaseCode",
"ResultValueTypeName",
"ResultWeightBasisText",
"ResultTimeBasisText",
"ResultTemperatureBasisText",
"ResultParticleSizeBasisText",
"DataQuality.PrecisionValue",
"DataQuality.BiasValue",
"DataQuality.ConfidenceIntervalValue",
"DataQuality.UpperConfidenceLimitValue",
"DataQuality.LowerConfidenceLimitValue",
"ResultCommentText",
"USGSPCode",
"ResultDepthHeightMeasure.MeasureValue",
"ResultDepthHeightMeasure.MeasureUnitCode",
"ResultDepthAltitudeReferencePointText",
"SubjectTaxonomicName",
"SampleTissueAnatomyName",
"BinaryObjectFileName",
"BinaryObjectFileTypeCode",
"ResultFileUrl",
"ResultAnalyticalMethod.MethodIdentifier",
"ResultAnalyticalMethod.MethodIdentifierContext",
"ResultAnalyticalMethod.MethodName",
"ResultAnalyticalMethod.MethodUrl",
"ResultAnalyticalMethod.MethodDescriptionText",
"LaboratoryName",
"AnalysisStartDate",
"ResultLaboratoryCommentText",
"ResultDetectionQuantitationLimitUrl",
"DetectionQuantitationLimitTypeName",
"DetectionQuantitationLimitMeasure.MeasureValue",
"TADA.DetectionQuantitationLimitMeasure.MeasureValue",
"TADA.DetectionQuantitationLimitMeasure.MeasureValueDataTypes.Flag",
"DetectionQuantitationLimitMeasure.MeasureUnitCode",
"LabSamplePreparationUrl",
"LastUpdated",
"ProviderName",
"ActivityStartDateTime",
"MonitoringLocationTypeName",
"MonitoringLocationDescriptionText",
"HUCEightDigitCode",
"DrainageAreaMeasure.MeasureValue",
"DrainageAreaMeasure.MeasureUnitCode",
"ContributingDrainageAreaMeasure.MeasureValue",
"ContributingDrainageAreaMeasure.MeasureUnitCode",
"LatitudeMeasure",
"TADA.LatitudeMeasure",
"LongitudeMeasure",
"TADA.LongitudeMeasure",
"SourceMapScaleNumeric",
"HorizontalAccuracyMeasure.MeasureValue",
"HorizontalAccuracyMeasure.MeasureUnitCode",
"HorizontalCollectionMethodName",
"HorizontalCoordinateReferenceSystemDatumName",
"VerticalMeasure.MeasureValue",
"VerticalMeasure.MeasureUnitCode",
"VerticalAccuracyMeasure.MeasureValue",
"VerticalAccuracyMeasure.MeasureUnitCode",
"VerticalCollectionMethodName",
"VerticalCoordinateReferenceSystemDatumName",
"CountryCode",
"StateCode",
"CountyCode",
"AquiferName",
"LocalAqfrName",
"FormationTypeText",
"AquiferTypeName",
"ConstructionDateText",
"WellDepthMeasure.MeasureValue",
"WellDepthMeasure.MeasureUnitCode",
"WellHoleDepthMeasure.MeasureValue",
"WellHoleDepthMeasure.MeasureUnitCode",
"MethodSpeciationName"
) %in% names(randomday)))
})
test_that("TADA_DataRetrieval", {
randomstate <- TADA_RandomTestingData(number_of_days = 2, choose_random_state = TRUE)
# you could just pick the important columns:
expect_true(all(c(
"OrganizationIdentifier",
"OrganizationFormalName",
"ActivityIdentifier",
"ActivityTypeCode",
"ActivityMediaName",
"TADA.ActivityMediaName",
"ActivityMediaSubdivisionName",
"ActivityStartDate",
"ActivityStartTime.Time",
"ActivityStartTime.TimeZoneCode",
"ActivityEndDate",
"ActivityEndTime.Time",
"ActivityEndTime.TimeZoneCode",
"ActivityRelativeDepthName",
"ActivityDepthHeightMeasure.MeasureValue",
"ActivityDepthHeightMeasure.MeasureUnitCode",
"ActivityDepthAltitudeReferencePointText",
"ActivityTopDepthHeightMeasure.MeasureValue",
"ActivityTopDepthHeightMeasure.MeasureUnitCode",
"ActivityBottomDepthHeightMeasure.MeasureValue",
"ActivityBottomDepthHeightMeasure.MeasureUnitCode",
"ProjectIdentifier",
"ProjectName",
"ActivityConductingOrganizationText",
"MonitoringLocationIdentifier",
"MonitoringLocationName",
"ActivityCommentText",
"SampleAquifer",
"HydrologicCondition",
"HydrologicEvent",
"SampleCollectionMethod.MethodIdentifier",
"SampleCollectionMethod.MethodIdentifierContext",
"SampleCollectionMethod.MethodName",
"SampleCollectionEquipmentName",
"ActivityLocation.LatitudeMeasure",
"ActivityLocation.LongitudeMeasure",
"ResultDetectionConditionText",
"MethodSpeciationName",
"CharacteristicName",
"TADA.CharacteristicName",
"ResultSampleFractionText",
"ResultMeasureValue",
"TADA.ResultMeasureValue",
"TADA.ResultMeasureValueDataTypes.Flag",
"ResultMeasure.MeasureUnitCode",
"TADA.ResultMeasure.MeasureUnitCode",
"MeasureQualifierCode",
"ResultStatusIdentifier",
"StatisticalBaseCode",
"ResultValueTypeName",
"ResultWeightBasisText",
"ResultTimeBasisText",
"ResultTemperatureBasisText",
"ResultParticleSizeBasisText",
"DataQuality.PrecisionValue",
"DataQuality.BiasValue",
"DataQuality.ConfidenceIntervalValue",
"DataQuality.UpperConfidenceLimitValue",
"DataQuality.LowerConfidenceLimitValue",
"ResultCommentText",
"USGSPCode",
"ResultDepthHeightMeasure.MeasureValue",
"ResultDepthHeightMeasure.MeasureUnitCode",
"ResultDepthAltitudeReferencePointText",
"SubjectTaxonomicName",
"SampleTissueAnatomyName",
"BinaryObjectFileName",
"BinaryObjectFileTypeCode",
"ResultFileUrl",
"ResultAnalyticalMethod.MethodIdentifier",
"ResultAnalyticalMethod.MethodIdentifierContext",
"ResultAnalyticalMethod.MethodName",
"ResultAnalyticalMethod.MethodUrl",
"ResultAnalyticalMethod.MethodDescriptionText",
"LaboratoryName",
"AnalysisStartDate",
"ResultLaboratoryCommentText",
"ResultDetectionQuantitationLimitUrl",
"DetectionQuantitationLimitTypeName",
"DetectionQuantitationLimitMeasure.MeasureValue",
"TADA.DetectionQuantitationLimitMeasure.MeasureValue",
"TADA.DetectionQuantitationLimitMeasure.MeasureValueDataTypes.Flag",
"DetectionQuantitationLimitMeasure.MeasureUnitCode",
"LabSamplePreparationUrl",
"LastUpdated",
"ProviderName",
"ActivityStartDateTime",
"MonitoringLocationTypeName",
"MonitoringLocationDescriptionText",
"HUCEightDigitCode",
"DrainageAreaMeasure.MeasureValue",
"DrainageAreaMeasure.MeasureUnitCode",
"ContributingDrainageAreaMeasure.MeasureValue",
"ContributingDrainageAreaMeasure.MeasureUnitCode",
"LatitudeMeasure",
"TADA.LatitudeMeasure",
"LongitudeMeasure",
"TADA.LongitudeMeasure",
"SourceMapScaleNumeric",
"HorizontalAccuracyMeasure.MeasureValue",
"HorizontalAccuracyMeasure.MeasureUnitCode",
"HorizontalCollectionMethodName",
"HorizontalCoordinateReferenceSystemDatumName",
"VerticalMeasure.MeasureValue",
"VerticalMeasure.MeasureUnitCode",
"VerticalAccuracyMeasure.MeasureValue",
"VerticalAccuracyMeasure.MeasureUnitCode",
"VerticalCollectionMethodName",
"VerticalCoordinateReferenceSystemDatumName",
"CountryCode",
"StateCode",
"CountyCode",
"AquiferName",
"LocalAqfrName",
"FormationTypeText",
"AquiferTypeName",
"ConstructionDateText",
"WellDepthMeasure.MeasureValue",
"WellDepthMeasure.MeasureUnitCode",
"WellHoleDepthMeasure.MeasureValue",
"WellHoleDepthMeasure.MeasureUnitCode",
"MethodSpeciationName"
) %in% names(randomstate)))
})
test_that("TADA_DataRetrieval", {
randomstate2 <- TADA_RandomTestingData(number_of_days = 2, choose_random_state = TRUE)
expect_true(all(
Filter(function(x) !any(grepl("TADA.", x)), require.cols) %in% names(randomstate2)
))
})
test_that("TADA_DataRetrieval", {
tada1 <- TADA_DataRetrieval(
siteid = c(
"USGS-054064785",
"USGS-430305089260600"
),
characteristicName = "Phosphorus",
ask = FALSE
)
# you could just pick the important columns:
expect_true(all(c(
"OrganizationIdentifier",
"OrganizationFormalName",
"ActivityIdentifier",
"ActivityTypeCode",
"ActivityMediaName",
"TADA.ActivityMediaName",
"ActivityMediaSubdivisionName",
"ActivityStartDate",
"ActivityStartTime.Time",
"ActivityStartTime.TimeZoneCode",
"ActivityEndDate",
"ActivityEndTime.Time",
"ActivityEndTime.TimeZoneCode",
"ActivityRelativeDepthName",
"ActivityDepthHeightMeasure.MeasureValue",
"ActivityDepthHeightMeasure.MeasureUnitCode",
"ActivityDepthAltitudeReferencePointText",
"ActivityTopDepthHeightMeasure.MeasureValue",
"ActivityTopDepthHeightMeasure.MeasureUnitCode",
"ActivityBottomDepthHeightMeasure.MeasureValue",
"ActivityBottomDepthHeightMeasure.MeasureUnitCode",
"ProjectIdentifier",
"ProjectName",
"ActivityConductingOrganizationText",
"MonitoringLocationIdentifier",
"MonitoringLocationName",
"ActivityCommentText",
"SampleAquifer",
"HydrologicCondition",
"HydrologicEvent",
"SampleCollectionMethod.MethodIdentifier",
"SampleCollectionMethod.MethodIdentifierContext",
"SampleCollectionMethod.MethodName",
"SampleCollectionEquipmentName",
"ActivityLocation.LatitudeMeasure",
"ActivityLocation.LongitudeMeasure",
"ResultDetectionConditionText",
"MethodSpeciationName",
"CharacteristicName",
"TADA.CharacteristicName",
"ResultSampleFractionText",
"ResultMeasureValue",
"TADA.ResultMeasureValue",
"TADA.ResultMeasureValueDataTypes.Flag",
"ResultMeasure.MeasureUnitCode",
"TADA.ResultMeasure.MeasureUnitCode",
"MeasureQualifierCode",
"ResultStatusIdentifier",
"StatisticalBaseCode",
"ResultValueTypeName",
"ResultWeightBasisText",
"ResultTimeBasisText",
"ResultTemperatureBasisText",
"ResultParticleSizeBasisText",
"DataQuality.PrecisionValue",
"DataQuality.BiasValue",
"DataQuality.ConfidenceIntervalValue",
"DataQuality.UpperConfidenceLimitValue",
"DataQuality.LowerConfidenceLimitValue",
"ResultCommentText",
"USGSPCode",
"ResultDepthHeightMeasure.MeasureValue",
"ResultDepthHeightMeasure.MeasureUnitCode",
"ResultDepthAltitudeReferencePointText",
"SubjectTaxonomicName",
"SampleTissueAnatomyName",
"BinaryObjectFileName",
"BinaryObjectFileTypeCode",
"ResultFileUrl",
"ResultAnalyticalMethod.MethodIdentifier",
"ResultAnalyticalMethod.MethodIdentifierContext",
"ResultAnalyticalMethod.MethodName",
"ResultAnalyticalMethod.MethodUrl",
"ResultAnalyticalMethod.MethodDescriptionText",
"LaboratoryName",
"AnalysisStartDate",
"ResultLaboratoryCommentText",
"ResultDetectionQuantitationLimitUrl",
"DetectionQuantitationLimitTypeName",
"DetectionQuantitationLimitMeasure.MeasureValue",
"TADA.DetectionQuantitationLimitMeasure.MeasureValue",
"TADA.DetectionQuantitationLimitMeasure.MeasureValueDataTypes.Flag",
"DetectionQuantitationLimitMeasure.MeasureUnitCode",
"LabSamplePreparationUrl",
"LastUpdated",
"ProviderName",
"ActivityStartDateTime",
"MonitoringLocationTypeName",
"MonitoringLocationDescriptionText",
"HUCEightDigitCode",
"DrainageAreaMeasure.MeasureValue",
"DrainageAreaMeasure.MeasureUnitCode",
"ContributingDrainageAreaMeasure.MeasureValue",
"ContributingDrainageAreaMeasure.MeasureUnitCode",
"LatitudeMeasure",
"TADA.LatitudeMeasure",
"LongitudeMeasure",
"TADA.LongitudeMeasure",
"SourceMapScaleNumeric",
"HorizontalAccuracyMeasure.MeasureValue",
"HorizontalAccuracyMeasure.MeasureUnitCode",
"HorizontalCollectionMethodName",
"HorizontalCoordinateReferenceSystemDatumName",
"VerticalMeasure.MeasureValue",
"VerticalMeasure.MeasureUnitCode",
"VerticalAccuracyMeasure.MeasureValue",
"VerticalAccuracyMeasure.MeasureUnitCode",
"VerticalCollectionMethodName",
"VerticalCoordinateReferenceSystemDatumName",
"CountryCode",
"StateCode",
"CountyCode",
"AquiferName",
"LocalAqfrName",
"FormationTypeText",
"AquiferTypeName",
"ConstructionDateText",
"WellDepthMeasure.MeasureValue",
"WellDepthMeasure.MeasureUnitCode",
"WellHoleDepthMeasure.MeasureValue",
"WellHoleDepthMeasure.MeasureUnitCode",
"MethodSpeciationName"
) %in% names(tada1)))
})
# testing that NWIS USGS only domain value "meters" is successfully replaced with "m". This feature is part of the TADA_AutoClean function
# which runs automatically when TADA_DataRetrieval runs
test_that("TADA_DataRetrieval", {
check_autoclean_meters_works <- TADA_DataRetrieval(
statecode = "UT",
characteristicName = c("Ammonia", "Nitrate", "Nitrogen"),
startDate = "2021-01-01",
endDate = "2022-01-01",
ask = FALSE
)
expect_false("meters" %in% check_autoclean_meters_works$TADA.ResultMeasure.MeasureUnitCode)
})
# Testing that regular and big data retrieval return the same number of rows on an identical query.
# cm edited to include start date on 2/27/23 because without this it takes too long to run
# these tests, and may time out
# test_that("Reg&BigdataRetrieval", {
# # big <- TADA_BigDataRetrieval(characteristicName = "Algae, substrate rock/bank cover (choice list)", sampleMedia = "Water", siteType = "Stream", startDate = "2020-01-01", applyautoclean = FALSE)
# reg <- TADA_DataRetrieval(characteristicName = "Algae, substrate rock/bank cover (choice list)", sampleMedia = "Water", siteType = "Stream", startDate = "2020-01-01", applyautoclean = FALSE, ask = FALSE)
#
# expect_equal(nrow(big), nrow(reg))
# })
# Testing that dates work correctly in queries in big data retrieval
# test_that("BigdataRetrieval_daterange", {
# startDate <- "2018-10-01"
# endDate <- "2021-09-30"
# # big <- TADA_BigDataRetrieval(startDate = startDate, endDate = endDate, huc = c("04030202", "04030201"), characteristicName = "Escherichia coli", siteType = "Stream")
# logic <- min(big$ActivityStartDate) >= as.Date(startDate, format = "%Y-%m-%d") & max(big$ActivityStartDate) <= as.Date(endDate, format = "%Y-%m-%d")
#
# expect_true(logic)
# })
# Testing that the TADA_JoinWQPProfiles() function in DataDiscoveryRetrieval.R
# has the expected number of columns after joining the full physical chemical
# profile and the sites profiles together. This function uses cyanobacteria
# full phys chem results and station metadata.
test_that("TADA_JoinWQPProfiles_works", {
# testthat::test_path() is automatically set to "tests/testthat". To get to the data files, you
# only need to add the additional pathway e.g., not the full path i.e.,
# "tests/testthat/testdata/Cyan_Stations.rds" but "testdata/Cyan_Results.rds"
physchemresults <- readRDS(testthat::test_path("testdata/Cyan_Results.rds"))
stations <- readRDS(testthat::test_path("testdata/Cyan_Stations.rds"))
add_sites_metadata <- TADA_JoinWQPProfiles(
Sites = stations,
FullPhysChem = physchemresults
)
expect_true(ncol(add_sites_metadata) == 113)
})
test_that("TADA_JoinWQPProfiles_columns", {
stationProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Station/search?statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType=csv&zip=yes&providers=NWIS&providers=STEWARDS&providers=STORET")
physchemProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Result/search?statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType=csv&zip=yes&dataProfile=resultPhysChem&providers=NWIS&providers=STEWARDS&providers=STORET")
projectProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Project/search?statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType=csv&zip=yes&providers=NWIS&providers=STEWARDS&providers=STORET")
# Join all three profiles using TADA_JoinWQPProfiles
join <- TADA_JoinWQPProfiles(
FullPhysChem = physchemProfile,
Sites = stationProfile,
Projects = projectProfile
)
# note that / ar replaced with . in dataRetrieval, so we also do the same in TADA_JoinWQPProfiles:
expect_true(all(c(
"OrganizationIdentifier",
"OrganizationFormalName",
"ActivityIdentifier",
"ActivityTypeCode",
"ActivityMediaName",
"ActivityMediaSubdivisionName",
"ActivityStartDate",
"ActivityStartTime.Time",
"VerticalAccuracyMeasure.MeasureValue",
"VerticalAccuracyMeasure.MeasureUnitCode",
"VerticalCollectionMethodName",
"VerticalCoordinateReferenceSystemDatumName",
"CountryCode",
"StateCode",
"CountyCode",
"AquiferName",
"LocalAqfrName",
"FormationTypeText",
"AquiferTypeName",
"ConstructionDateText",
"WellDepthMeasure.MeasureValue",
"WellDepthMeasure.MeasureUnitCode",
"WellHoleDepthMeasure.MeasureValue",
"WellHoleDepthMeasure.MeasureUnitCode",
"MethodSpeciationName"
) %in% names(join)))
})
USEPA/TADA documentation built on April 12, 2025, 1:47 p.m.
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test_that("TADA_DataRetrieval", {
randomday <- TADA_RandomTestingData(number_of_days = 2, choose_random_state = TRUE)
# you could just pick the important columns:
expect_true(all(c(
"OrganizationIdentifier",
"OrganizationFormalName",
"ActivityIdentifier",
"ActivityTypeCode",
"ActivityMediaName",
"TADA.ActivityMediaName",
"ActivityMediaSubdivisionName",
"ActivityStartDate",
"ActivityStartTime.Time",
"ActivityStartTime.TimeZoneCode",
"ActivityEndDate",
"ActivityEndTime.Time",
"ActivityEndTime.TimeZoneCode",
"ActivityRelativeDepthName",
"ActivityDepthHeightMeasure.MeasureValue",
"ActivityDepthHeightMeasure.MeasureUnitCode",
"ActivityDepthAltitudeReferencePointText",
"ActivityTopDepthHeightMeasure.MeasureValue",
"ActivityTopDepthHeightMeasure.MeasureUnitCode",
"ActivityBottomDepthHeightMeasure.MeasureValue",
"ActivityBottomDepthHeightMeasure.MeasureUnitCode",
"ProjectIdentifier",
"ProjectName",
"ActivityConductingOrganizationText",
"MonitoringLocationIdentifier",
"MonitoringLocationName",
"ActivityCommentText",
"SampleAquifer",
"HydrologicCondition",
"HydrologicEvent",
"SampleCollectionMethod.MethodIdentifier",
"SampleCollectionMethod.MethodIdentifierContext",
"SampleCollectionMethod.MethodName",
"SampleCollectionEquipmentName",
"ActivityLocation.LatitudeMeasure",
"ActivityLocation.LongitudeMeasure",
"ResultDetectionConditionText",
"MethodSpeciationName",
"CharacteristicName",
"TADA.CharacteristicName",
"ResultSampleFractionText",
"ResultMeasureValue",
"TADA.ResultMeasureValue",
"TADA.ResultMeasureValueDataTypes.Flag",
"ResultMeasure.MeasureUnitCode",
"TADA.ResultMeasure.MeasureUnitCode",
"MeasureQualifierCode",
"ResultStatusIdentifier",
"StatisticalBaseCode",
"ResultValueTypeName",
"ResultWeightBasisText",
"ResultTimeBasisText",
"ResultTemperatureBasisText",
"ResultParticleSizeBasisText",
"DataQuality.PrecisionValue",
"DataQuality.BiasValue",
"DataQuality.ConfidenceIntervalValue",
"DataQuality.UpperConfidenceLimitValue",
"DataQuality.LowerConfidenceLimitValue",
"ResultCommentText",
"USGSPCode",
"ResultDepthHeightMeasure.MeasureValue",
"ResultDepthHeightMeasure.MeasureUnitCode",
"ResultDepthAltitudeReferencePointText",
"SubjectTaxonomicName",
"SampleTissueAnatomyName",
"BinaryObjectFileName",
"BinaryObjectFileTypeCode",
"ResultFileUrl",
"ResultAnalyticalMethod.MethodIdentifier",
"ResultAnalyticalMethod.MethodIdentifierContext",
"ResultAnalyticalMethod.MethodName",
"ResultAnalyticalMethod.MethodUrl",
"ResultAnalyticalMethod.MethodDescriptionText",
"LaboratoryName",
"AnalysisStartDate",
"ResultLaboratoryCommentText",
"ResultDetectionQuantitationLimitUrl",
"DetectionQuantitationLimitTypeName",
"DetectionQuantitationLimitMeasure.MeasureValue",
"TADA.DetectionQuantitationLimitMeasure.MeasureValue",
"TADA.DetectionQuantitationLimitMeasure.MeasureValueDataTypes.Flag",
"DetectionQuantitationLimitMeasure.MeasureUnitCode",
"LabSamplePreparationUrl",
"LastUpdated",
"ProviderName",
"ActivityStartDateTime",
"MonitoringLocationTypeName",
"MonitoringLocationDescriptionText",
"HUCEightDigitCode",
"DrainageAreaMeasure.MeasureValue",
"DrainageAreaMeasure.MeasureUnitCode",
"ContributingDrainageAreaMeasure.MeasureValue",
"ContributingDrainageAreaMeasure.MeasureUnitCode",
"LatitudeMeasure",
"TADA.LatitudeMeasure",
"LongitudeMeasure",
"TADA.LongitudeMeasure",
"SourceMapScaleNumeric",
"HorizontalAccuracyMeasure.MeasureValue",
"HorizontalAccuracyMeasure.MeasureUnitCode",
"HorizontalCollectionMethodName",
"HorizontalCoordinateReferenceSystemDatumName",
"VerticalMeasure.MeasureValue",
"VerticalMeasure.MeasureUnitCode",
"VerticalAccuracyMeasure.MeasureValue",
"VerticalAccuracyMeasure.MeasureUnitCode",
"VerticalCollectionMethodName",
"VerticalCoordinateReferenceSystemDatumName",
"CountryCode",
"StateCode",
"CountyCode",
"AquiferName",
"LocalAqfrName",
"FormationTypeText",
"AquiferTypeName",
"ConstructionDateText",
"WellDepthMeasure.MeasureValue",
"WellDepthMeasure.MeasureUnitCode",
"WellHoleDepthMeasure.MeasureValue",
"WellHoleDepthMeasure.MeasureUnitCode",
"MethodSpeciationName"
) %in% names(randomday)))
})
test_that("TADA_DataRetrieval", {
randomstate <- TADA_RandomTestingData(number_of_days = 2, choose_random_state = TRUE)
# you could just pick the important columns:
expect_true(all(c(
"OrganizationIdentifier",
"OrganizationFormalName",
"ActivityIdentifier",
"ActivityTypeCode",
"ActivityMediaName",
"TADA.ActivityMediaName",
"ActivityMediaSubdivisionName",
"ActivityStartDate",
"ActivityStartTime.Time",
"ActivityStartTime.TimeZoneCode",
"ActivityEndDate",
"ActivityEndTime.Time",
"ActivityEndTime.TimeZoneCode",
"ActivityRelativeDepthName",
"ActivityDepthHeightMeasure.MeasureValue",
"ActivityDepthHeightMeasure.MeasureUnitCode",
"ActivityDepthAltitudeReferencePointText",
"ActivityTopDepthHeightMeasure.MeasureValue",
"ActivityTopDepthHeightMeasure.MeasureUnitCode",
"ActivityBottomDepthHeightMeasure.MeasureValue",
"ActivityBottomDepthHeightMeasure.MeasureUnitCode",
"ProjectIdentifier",
"ProjectName",
"ActivityConductingOrganizationText",
"MonitoringLocationIdentifier",
"MonitoringLocationName",
"ActivityCommentText",
"SampleAquifer",
"HydrologicCondition",
"HydrologicEvent",
"SampleCollectionMethod.MethodIdentifier",
"SampleCollectionMethod.MethodIdentifierContext",
"SampleCollectionMethod.MethodName",
"SampleCollectionEquipmentName",
"ActivityLocation.LatitudeMeasure",
"ActivityLocation.LongitudeMeasure",
"ResultDetectionConditionText",
"MethodSpeciationName",
"CharacteristicName",
"TADA.CharacteristicName",
"ResultSampleFractionText",
"ResultMeasureValue",
"TADA.ResultMeasureValue",
"TADA.ResultMeasureValueDataTypes.Flag",
"ResultMeasure.MeasureUnitCode",
"TADA.ResultMeasure.MeasureUnitCode",
"MeasureQualifierCode",
"ResultStatusIdentifier",
"StatisticalBaseCode",
"ResultValueTypeName",
"ResultWeightBasisText",
"ResultTimeBasisText",
"ResultTemperatureBasisText",
"ResultParticleSizeBasisText",
"DataQuality.PrecisionValue",
"DataQuality.BiasValue",
"DataQuality.ConfidenceIntervalValue",
"DataQuality.UpperConfidenceLimitValue",
"DataQuality.LowerConfidenceLimitValue",
"ResultCommentText",
"USGSPCode",
"ResultDepthHeightMeasure.MeasureValue",
"ResultDepthHeightMeasure.MeasureUnitCode",
"ResultDepthAltitudeReferencePointText",
"SubjectTaxonomicName",
"SampleTissueAnatomyName",
"BinaryObjectFileName",
"BinaryObjectFileTypeCode",
"ResultFileUrl",
"ResultAnalyticalMethod.MethodIdentifier",
"ResultAnalyticalMethod.MethodIdentifierContext",
"ResultAnalyticalMethod.MethodName",
"ResultAnalyticalMethod.MethodUrl",
"ResultAnalyticalMethod.MethodDescriptionText",
"LaboratoryName",
"AnalysisStartDate",
"ResultLaboratoryCommentText",
"ResultDetectionQuantitationLimitUrl",
"DetectionQuantitationLimitTypeName",
"DetectionQuantitationLimitMeasure.MeasureValue",
"TADA.DetectionQuantitationLimitMeasure.MeasureValue",
"TADA.DetectionQuantitationLimitMeasure.MeasureValueDataTypes.Flag",
"DetectionQuantitationLimitMeasure.MeasureUnitCode",
"LabSamplePreparationUrl",
"LastUpdated",
"ProviderName",
"ActivityStartDateTime",
"MonitoringLocationTypeName",
"MonitoringLocationDescriptionText",
"HUCEightDigitCode",
"DrainageAreaMeasure.MeasureValue",
"DrainageAreaMeasure.MeasureUnitCode",
"ContributingDrainageAreaMeasure.MeasureValue",
"ContributingDrainageAreaMeasure.MeasureUnitCode",
"LatitudeMeasure",
"TADA.LatitudeMeasure",
"LongitudeMeasure",
"TADA.LongitudeMeasure",
"SourceMapScaleNumeric",
"HorizontalAccuracyMeasure.MeasureValue",
"HorizontalAccuracyMeasure.MeasureUnitCode",
"HorizontalCollectionMethodName",
"HorizontalCoordinateReferenceSystemDatumName",
"VerticalMeasure.MeasureValue",
"VerticalMeasure.MeasureUnitCode",
"VerticalAccuracyMeasure.MeasureValue",
"VerticalAccuracyMeasure.MeasureUnitCode",
"VerticalCollectionMethodName",
"VerticalCoordinateReferenceSystemDatumName",
"CountryCode",
"StateCode",
"CountyCode",
"AquiferName",
"LocalAqfrName",
"FormationTypeText",
"AquiferTypeName",
"ConstructionDateText",
"WellDepthMeasure.MeasureValue",
"WellDepthMeasure.MeasureUnitCode",
"WellHoleDepthMeasure.MeasureValue",
"WellHoleDepthMeasure.MeasureUnitCode",
"MethodSpeciationName"
) %in% names(randomstate)))
})
test_that("TADA_DataRetrieval", {
randomstate2 <- TADA_RandomTestingData(number_of_days = 2, choose_random_state = TRUE)
expect_true(all(
Filter(function(x) !any(grepl("TADA.", x)), require.cols) %in% names(randomstate2)
))
})
test_that("TADA_DataRetrieval", {
tada1 <- TADA_DataRetrieval(
siteid = c(
"USGS-054064785",
"USGS-430305089260600"
),
characteristicName = "Phosphorus",
ask = FALSE
)
# you could just pick the important columns:
expect_true(all(c(
"OrganizationIdentifier",
"OrganizationFormalName",
"ActivityIdentifier",
"ActivityTypeCode",
"ActivityMediaName",
"TADA.ActivityMediaName",
"ActivityMediaSubdivisionName",
"ActivityStartDate",
"ActivityStartTime.Time",
"ActivityStartTime.TimeZoneCode",
"ActivityEndDate",
"ActivityEndTime.Time",
"ActivityEndTime.TimeZoneCode",
"ActivityRelativeDepthName",
"ActivityDepthHeightMeasure.MeasureValue",
"ActivityDepthHeightMeasure.MeasureUnitCode",
"ActivityDepthAltitudeReferencePointText",
"ActivityTopDepthHeightMeasure.MeasureValue",
"ActivityTopDepthHeightMeasure.MeasureUnitCode",
"ActivityBottomDepthHeightMeasure.MeasureValue",
"ActivityBottomDepthHeightMeasure.MeasureUnitCode",
"ProjectIdentifier",
"ProjectName",
"ActivityConductingOrganizationText",
"MonitoringLocationIdentifier",
"MonitoringLocationName",
"ActivityCommentText",
"SampleAquifer",
"HydrologicCondition",
"HydrologicEvent",
"SampleCollectionMethod.MethodIdentifier",
"SampleCollectionMethod.MethodIdentifierContext",
"SampleCollectionMethod.MethodName",
"SampleCollectionEquipmentName",
"ActivityLocation.LatitudeMeasure",
"ActivityLocation.LongitudeMeasure",
"ResultDetectionConditionText",
"MethodSpeciationName",
"CharacteristicName",
"TADA.CharacteristicName",
"ResultSampleFractionText",
"ResultMeasureValue",
"TADA.ResultMeasureValue",
"TADA.ResultMeasureValueDataTypes.Flag",
"ResultMeasure.MeasureUnitCode",
"TADA.ResultMeasure.MeasureUnitCode",
"MeasureQualifierCode",
"ResultStatusIdentifier",
"StatisticalBaseCode",
"ResultValueTypeName",
"ResultWeightBasisText",
"ResultTimeBasisText",
"ResultTemperatureBasisText",
"ResultParticleSizeBasisText",
"DataQuality.PrecisionValue",
"DataQuality.BiasValue",
"DataQuality.ConfidenceIntervalValue",
"DataQuality.UpperConfidenceLimitValue",
"DataQuality.LowerConfidenceLimitValue",
"ResultCommentText",
"USGSPCode",
"ResultDepthHeightMeasure.MeasureValue",
"ResultDepthHeightMeasure.MeasureUnitCode",
"ResultDepthAltitudeReferencePointText",
"SubjectTaxonomicName",
"SampleTissueAnatomyName",
"BinaryObjectFileName",
"BinaryObjectFileTypeCode",
"ResultFileUrl",
"ResultAnalyticalMethod.MethodIdentifier",
"ResultAnalyticalMethod.MethodIdentifierContext",
"ResultAnalyticalMethod.MethodName",
"ResultAnalyticalMethod.MethodUrl",
"ResultAnalyticalMethod.MethodDescriptionText",
"LaboratoryName",
"AnalysisStartDate",
"ResultLaboratoryCommentText",
"ResultDetectionQuantitationLimitUrl",
"DetectionQuantitationLimitTypeName",
"DetectionQuantitationLimitMeasure.MeasureValue",
"TADA.DetectionQuantitationLimitMeasure.MeasureValue",
"TADA.DetectionQuantitationLimitMeasure.MeasureValueDataTypes.Flag",
"DetectionQuantitationLimitMeasure.MeasureUnitCode",
"LabSamplePreparationUrl",
"LastUpdated",
"ProviderName",
"ActivityStartDateTime",
"MonitoringLocationTypeName",
"MonitoringLocationDescriptionText",
"HUCEightDigitCode",
"DrainageAreaMeasure.MeasureValue",
"DrainageAreaMeasure.MeasureUnitCode",
"ContributingDrainageAreaMeasure.MeasureValue",
"ContributingDrainageAreaMeasure.MeasureUnitCode",
"LatitudeMeasure",
"TADA.LatitudeMeasure",
"LongitudeMeasure",
"TADA.LongitudeMeasure",
"SourceMapScaleNumeric",
"HorizontalAccuracyMeasure.MeasureValue",
"HorizontalAccuracyMeasure.MeasureUnitCode",
"HorizontalCollectionMethodName",
"HorizontalCoordinateReferenceSystemDatumName",
"VerticalMeasure.MeasureValue",
"VerticalMeasure.MeasureUnitCode",
"VerticalAccuracyMeasure.MeasureValue",
"VerticalAccuracyMeasure.MeasureUnitCode",
"VerticalCollectionMethodName",
"VerticalCoordinateReferenceSystemDatumName",
"CountryCode",
"StateCode",
"CountyCode",
"AquiferName",
"LocalAqfrName",
"FormationTypeText",
"AquiferTypeName",
"ConstructionDateText",
"WellDepthMeasure.MeasureValue",
"WellDepthMeasure.MeasureUnitCode",
"WellHoleDepthMeasure.MeasureValue",
"WellHoleDepthMeasure.MeasureUnitCode",
"MethodSpeciationName"
) %in% names(tada1)))
})
# testing that NWIS USGS only domain value "meters" is successfully replaced with "m". This feature is part of the TADA_AutoClean function
# which runs automatically when TADA_DataRetrieval runs
test_that("TADA_DataRetrieval", {
check_autoclean_meters_works <- TADA_DataRetrieval(
statecode = "UT",
characteristicName = c("Ammonia", "Nitrate", "Nitrogen"),
startDate = "2021-01-01",
endDate = "2022-01-01",
ask = FALSE
)
expect_false("meters" %in% check_autoclean_meters_works$TADA.ResultMeasure.MeasureUnitCode)
})
# Testing that regular and big data retrieval return the same number of rows on an identical query.
# cm edited to include start date on 2/27/23 because without this it takes too long to run
# these tests, and may time out
# test_that("Reg&BigdataRetrieval", {
# # big <- TADA_BigDataRetrieval(characteristicName = "Algae, substrate rock/bank cover (choice list)", sampleMedia = "Water", siteType = "Stream", startDate = "2020-01-01", applyautoclean = FALSE)
# reg <- TADA_DataRetrieval(characteristicName = "Algae, substrate rock/bank cover (choice list)", sampleMedia = "Water", siteType = "Stream", startDate = "2020-01-01", applyautoclean = FALSE, ask = FALSE)
#
# expect_equal(nrow(big), nrow(reg))
# })
# Testing that dates work correctly in queries in big data retrieval
# test_that("BigdataRetrieval_daterange", {
# startDate <- "2018-10-01"
# endDate <- "2021-09-30"
# # big <- TADA_BigDataRetrieval(startDate = startDate, endDate = endDate, huc = c("04030202", "04030201"), characteristicName = "Escherichia coli", siteType = "Stream")
# logic <- min(big$ActivityStartDate) >= as.Date(startDate, format = "%Y-%m-%d") & max(big$ActivityStartDate) <= as.Date(endDate, format = "%Y-%m-%d")
#
# expect_true(logic)
# })
# Testing that the TADA_JoinWQPProfiles() function in DataDiscoveryRetrieval.R
# has the expected number of columns after joining the full physical chemical
# profile and the sites profiles together. This function uses cyanobacteria
# full phys chem results and station metadata.
test_that("TADA_JoinWQPProfiles_works", {
# testthat::test_path() is automatically set to "tests/testthat". To get to the data files, you
# only need to add the additional pathway e.g., not the full path i.e.,
# "tests/testthat/testdata/Cyan_Stations.rds" but "testdata/Cyan_Results.rds"
physchemresults <- readRDS(testthat::test_path("testdata/Cyan_Results.rds"))
stations <- readRDS(testthat::test_path("testdata/Cyan_Stations.rds"))
add_sites_metadata <- TADA_JoinWQPProfiles(
Sites = stations,
FullPhysChem = physchemresults
)
expect_true(ncol(add_sites_metadata) == 113)
})
test_that("TADA_JoinWQPProfiles_columns", {
stationProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Station/search?statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType=csv&zip=yes&providers=NWIS&providers=STEWARDS&providers=STORET")
physchemProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Result/search?statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType=csv&zip=yes&dataProfile=resultPhysChem&providers=NWIS&providers=STEWARDS&providers=STORET")
projectProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Project/search?statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType=csv&zip=yes&providers=NWIS&providers=STEWARDS&providers=STORET")
# Join all three profiles using TADA_JoinWQPProfiles
join <- TADA_JoinWQPProfiles(
FullPhysChem = physchemProfile,
Sites = stationProfile,
Projects = projectProfile
)
# note that / ar replaced with . in dataRetrieval, so we also do the same in TADA_JoinWQPProfiles:
expect_true(all(c(
"OrganizationIdentifier",
"OrganizationFormalName",
"ActivityIdentifier",
"ActivityTypeCode",
"ActivityMediaName",
"ActivityMediaSubdivisionName",
"ActivityStartDate",
"ActivityStartTime.Time",
"VerticalAccuracyMeasure.MeasureValue",
"VerticalAccuracyMeasure.MeasureUnitCode",
"VerticalCollectionMethodName",
"VerticalCoordinateReferenceSystemDatumName",
"CountryCode",
"StateCode",
"CountyCode",
"AquiferName",
"LocalAqfrName",
"FormationTypeText",
"AquiferTypeName",
"ConstructionDateText",
"WellDepthMeasure.MeasureValue",
"WellDepthMeasure.MeasureUnitCode",
"WellHoleDepthMeasure.MeasureValue",
"WellHoleDepthMeasure.MeasureUnitCode",
"MethodSpeciationName"
) %in% names(join)))
})
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