* using log directory ‘/srv/hornik/tmp/CRAN_pretest/EPATADA.Rcheck’ * using R Under development (unstable) (2025-03-17 r87990) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘EPATADA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘EPATADA’ version ‘0.0.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [5s/69s] NOTE Maintainer: ‘Cristina Mullin ’ New submission Possibly misspelled words in DESCRIPTION: TADA (3:12) Unknown, possibly misspelled, fields in DESCRIPTION: ‘Remotes’ Size of tarball: 43293825 bytes * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘EPATADA’ can be installed ... [72s/72s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard file/directory found at top level: ‘dev’ * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [9s/9s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'TADA_AutoClean.Rd': \examples lines wider than 100 characters: # https://www.waterqualitydata.us/#statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType ... [TRUNCATED] stationProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Station/search?statecode=US%3A09&characteristicType=Nut ... [TRUNCATED] physchemProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Result/search?statecode=US%3A09&characteristicType=Nut ... [TRUNCATED] projectProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Project/search?statecode=US%3A09&characteristicType=Nut ... [TRUNCATED] Rd file 'TADA_CheckRequiredFields.Rd': \examples lines wider than 100 characters: # Example WQP URL: https://www.waterqualitydata.us/#statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11 ... [TRUNCATED] stationProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Station/search?statecode=US%3A09&characteristicType=Nut ... [TRUNCATED] physchemProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Result/search?statecode=US%3A09&characteristicType=Nut ... [TRUNCATED] projectProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Project/search?statecode=US%3A09&characteristicType=Nut ... [TRUNCATED] Rd file 'TADA_CreateDateTime.Rd': \examples lines wider than 100 characters: # Example WQP URL: https://www.waterqualitydata.us/#statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11 ... [TRUNCATED] stationProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Station/search?statecode=US%3A09&characteristicType=Nut ... [TRUNCATED] physchemProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Result/search?statecode=US%3A09&characteristicType=Nut ... [TRUNCATED] projectProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Project/search?statecode=US%3A09&characteristicType=Nut ... [TRUNCATED] Rd file 'TADA_JoinWQPProfiles.Rd': \examples lines wider than 100 characters: # WQP URL: https://www.waterqualitydata.us/#statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11-01-2023 ... [TRUNCATED] stationProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Station/search?statecode=US%3A09&characteristicType=Nut ... [TRUNCATED] physchemProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Result/search?statecode=US%3A09&characteristicType=Nut ... [TRUNCATED] projectProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Project/search?statecode=US%3A09&characteristicType=Nut ... [TRUNCATED] Rd file 'TADA_OrderCols.Rd': \examples lines wider than 100 characters: # Example WQP URL: https://www.waterqualitydata.us/#statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11 ... [TRUNCATED] stationProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Station/search?statecode=US%3A09&characteristicType=Nut ... [TRUNCATED] physchemProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Result/search?statecode=US%3A09&characteristicType=Nut ... [TRUNCATED] projectProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Project/search?statecode=US%3A09&characteristicType=Nut ... [TRUNCATED] Rd file 'TADA_ReadWQPWebServices.Rd': \examples lines wider than 100 characters: physchemresults1 <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Result/search?statecode=US%3A09&sampleMedia=water&sam ... [TRUNCATED] sites1 <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Station/search?statecode=US%3A09&sampleMedia=water&sampleMedia= ... [TRUNCATED] projects1 <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Project/search?statecode=US%3A09&sampleMedia=water&sampleMed ... [TRUNCATED] These lines will be truncated in the PDF manual. * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [20s/20s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [0m/30m] ERROR Running examples in ‘EPATADA-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: TADA_FindNearbySites > ### Title: Identify and group nearby monitoring locations (UNDER ACTIVE > ### DEVELOPMENT) > ### Aliases: TADA_FindNearbySites > > ### ** Examples > > GroupNearbySites_100m <- TADA_FindNearbySites(Data_Nutrients_UT) [1] "Transforming your data into a spatial object." [1] "Your WQP dataframe contains observations without a listed coordinate reference system (CRS). For these, we have assigned CRS 4326." Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed TADA_AggregateMeasurements 8.086 0.688 8.777 TADA_CreatePairRef 2.590 0.135 8.672 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [1m/13m] ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [1m/13m] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(EPATADA) > > test_check("EPATADA") Checking what data is available. This may take a moment. The number of sites and/or records matched by the query terms is large, so the download may take some time. [1] "Downloading data from sites with fewer than 350000 results by grouping them together." | | | 0% | |=============== | 22% | |======================================================================| 100% Checking what data is available. This may take a moment. [1] "Downloading WQP query results. This may take some time depending upon the query size." $statecode [1] "US:20" $startDate [1] "2021-01-01" $characteristicName [1] "Phosphorus" "Nitrate" $endDate [1] "2022-01-01" [1] "Data successfully downloaded. Running TADA_AutoClean function." [1] "TADA_Autoclean: creating TADA-specific columns." [1] "TADA_Autoclean: handling special characters and coverting TADA.ResultMeasureValue and TADA.DetectionQuantitationLimitMeasure.MeasureValue value fields to numeric." [1] "TADA_Autoclean: converting TADA.LatitudeMeasure and TADA.LongitudeMeasure fields to numeric." [1] "TADA_Autoclean: harmonizing synonymous unit names (m and meters) to m." [1] "TADA_Autoclean: updating deprecated (i.e. retired) characteristic names." [1] "No deprecated characteristic names found in dataset." [1] "TADA_Autoclean: harmonizing result and depth units." [1] "TADA_Autoclean: creating TADA.ComparableDataIdentifier field for use when generating visualizations and analyses." [1] "NOTE: This version of the TADA package is designed to work with numeric data with media name: 'WATER'. TADA_AutoClean does not currently remove (filter) data with non-water media types. If desired, the user must make this specification on their own outside of package functions. Example: dplyr::filter(.data, TADA.ActivityMediaName == 'WATER')" [1] "TADA_IDCensoredData: There are 22 results in your dataframe that are missing ResultDetectionConditionText. TADA requires BOTH ResultDetectionConditionText and DetectionQuantitationLimitTypeName fields to be populated in order to categorize censored data." [1] "TADA_IDCensoredData: DetectionQuantitationLimitTypeName column in dataframe contains value(s) NA which is/are not represented in the DetectionQuantitationLimitTypeName WQX domain table. These data records are placed under the TADA.CensoredData.Flag: Censored but not Categorized, and will not be used in censored data handling methods. Please contact TADA administrators to resolve." startDate endDate statecode "2020-06-10" "2020-06-11" "OR" Checking what data is available. This may take a moment. The number of sites and/or records matched by the query terms is large, so the download may take some time. [1] "Downloading data from sites with fewer than 350000 results by grouping them together." | | | 0% | |================================== | 49% | |======================================================================| 100% Checking what data is available. This may take a moment. The number of sites and/or records matched by the query terms is large, so the download may take some time. [1] "Downloading data from sites with fewer than 350000 results by grouping them together." | | | 0% | | | 1% | |= | 2% | |=== | 4% | |====== | 8% | |=========== | 16% | |=================== | 28% | |================================ | 46% | |======================================================== | 81% | |======================================================================| 100% startDate endDate statecode "2011-07-27" "2011-07-28" "DC" Checking what data is available. This may take a moment. [1] "Downloading WQP query results. This may take some time depending upon the query size." $statecode [1] "US:11" $startDate [1] "2011-07-27" $endDate [1] "2011-07-28" [1] "Returning empty results dataframe: Your WQP query returned no results (no data available). Try a different query. Removing some of your query filters OR broadening your search area may help." startDate endDate statecode "2016-04-19" "2016-04-20" "NV" Checking what data is available. This may take a moment. [1] "Downloading WQP query results. This may take some time depending upon the query size." $statecode [1] "US:32" $startDate [1] "2016-04-19" $endDate [1] "2016-04-20" [1] "Data successfully downloaded. Running TADA_AutoClean function." [1] "TADA_Autoclean: creating TADA-specific columns." [1] "TADA_Autoclean: handling special characters and coverting TADA.ResultMeasureValue and TADA.DetectionQuantitationLimitMeasure.MeasureValue value fields to numeric." [1] "TADA_Autoclean: converting TADA.LatitudeMeasure and TADA.LongitudeMeasure fields to numeric." [1] "TADA_Autoclean: harmonizing synonymous unit names (m and meters) to m." [1] "TADA_Autoclean: updating deprecated (i.e. retired) characteristic names." [1] "7 results in your dataset have one of the following deprecated characteristic names: Inorganic nitrogen (nitrate and nitrite); Inorganic nitrogen (nitrate and nitrite) ***retired***use Nitrate + Nitrite. These names have been substituted with the updated preferred names in the TADA.CharacteristicName field." [1] "TADA_Autoclean: harmonizing result and depth units." [1] "TADA_Autoclean: creating TADA.ComparableDataIdentifier field for use when generating visualizations and analyses." [1] "NOTE: This version of the TADA package is designed to work with numeric data with media name: 'WATER'. TADA_AutoClean does not currently remove (filter) data with non-water media types. If desired, the user must make this specification on their own outside of package functions. Example: dplyr::filter(.data, TADA.ActivityMediaName == 'WATER')" startDate endDate statecode "2016-06-08" "2016-06-10" "KY" Checking what data is available. This may take a moment. [1] "Downloading WQP query results. This may take some time depending upon the query size." $statecode [1] "US:21" $startDate [1] "2016-06-08" $endDate [1] "2016-06-10" [1] "Data successfully downloaded. Running TADA_AutoClean function." [1] "TADA_Autoclean: creating TADA-specific columns." [1] "TADA_Autoclean: harmonizing dissolved oxygen characterisic name to DISSOLVED OXYGEN SATURATION if unit is % or % SATURATN." [1] "TADA_Autoclean: handling special characters and coverting TADA.ResultMeasureValue and TADA.DetectionQuantitationLimitMeasure.MeasureValue value fields to numeric." [1] "TADA_Autoclean: converting TADA.LatitudeMeasure and TADA.LongitudeMeasure fields to numeric." [1] "TADA_Autoclean: harmonizing synonymous unit names (m and meters) to m." [1] "TADA_Autoclean: updating deprecated (i.e. retired) characteristic names." [1] "No deprecated characteristic names found in dataset." [1] "TADA_Autoclean: harmonizing result and depth units." [1] "TADA_Autoclean: creating TADA.ComparableDataIdentifier field for use when generating visualizations and analyses." [1] "NOTE: This version of the TADA package is designed to work with numeric data with media name: 'WATER'. TADA_AutoClean does not currently remove (filter) data with non-water media types. If desired, the user must make this specification on their own outside of package functions. Example: dplyr::filter(.data, TADA.ActivityMediaName == 'WATER')" startDate endDate statecode "2013-11-02" "2013-11-04" "ME" Checking what data is available. This may take a moment. [1] "Downloading WQP query results. This may take some time depending upon the query size." $statecode [1] "US:23" $startDate [1] "2013-11-02" $endDate [1] "2013-11-04" [1] "Data successfully downloaded. Running TADA_AutoClean function." [1] "TADA_Autoclean: creating TADA-specific columns." [1] "TADA_Autoclean: handling special characters and coverting TADA.ResultMeasureValue and TADA.DetectionQuantitationLimitMeasure.MeasureValue value fields to numeric." [1] "TADA_Autoclean: converting TADA.LatitudeMeasure and TADA.LongitudeMeasure fields to numeric." [1] "TADA_Autoclean: harmonizing synonymous unit names (m and meters) to m." [1] "TADA_Autoclean: updating deprecated (i.e. retired) characteristic names." [1] "No deprecated characteristic names found in dataset." [1] "TADA_Autoclean: harmonizing result and depth units." [1] "TADA_Autoclean: creating TADA.ComparableDataIdentifier field for use when generating visualizations and analyses." [1] "NOTE: This version of the TADA package is designed to work with numeric data with media name: 'WATER'. TADA_AutoClean does not currently remove (filter) data with non-water media types. If desired, the user must make this specification on their own outside of package functions. Example: dplyr::filter(.data, TADA.ActivityMediaName == 'WATER')" startDate endDate statecode "2010-07-07" "2010-07-09" "SD" Checking what data is available. This may take a moment. [1] "Downloading WQP query results. This may take some time depending upon the query size." $statecode [1] "US:46" $startDate [1] "2010-07-07" $endDate [1] "2010-07-09" [1] "Data successfully downloaded. Running TADA_AutoClean function." [1] "TADA_Autoclean: creating TADA-specific columns." [1] "TADA_Autoclean: harmonizing dissolved oxygen characterisic name to DISSOLVED OXYGEN SATURATION if unit is % or % SATURATN." [1] "TADA_Autoclean: handling special characters and coverting TADA.ResultMeasureValue and TADA.DetectionQuantitationLimitMeasure.MeasureValue value fields to numeric." [1] "TADA_Autoclean: converting TADA.LatitudeMeasure and TADA.LongitudeMeasure fields to numeric." [1] "TADA_Autoclean: harmonizing synonymous unit names (m and meters) to m." [1] "TADA_Autoclean: updating deprecated (i.e. retired) characteristic names." [1] "13 results in your dataset have one of the following deprecated characteristic names: Inorganic nitrogen (nitrate and nitrite) ***retired***use Nitrate + Nitrite. These names have been substituted with the updated preferred names in the TADA.CharacteristicName field." [1] "TADA_Autoclean: harmonizing result and depth units." [1] "TADA_Autoclean: creating TADA.ComparableDataIdentifier field for use when generating visualizations and analyses." [1] "NOTE: This version of the TADA package is designed to work with numeric data with media name: 'WATER'. TADA_AutoClean does not currently remove (filter) data with non-water media types. If desired, the user must make this specification on their own outside of package functions. Example: dplyr::filter(.data, TADA.ActivityMediaName == 'WATER')" Checking what data is available. This may take a moment. Checking what data is available. This may take a moment. The number of sites and/or records matched by the query terms is large, so the download may take some time. [1] "Downloading data from sites with fewer than 350000 results by grouping them together." | | | 0% | |======== | 12% | |======================================= | 56% | |======================================================================| 100% [1] "Transforming your data into a spatial object." [1] "Your WQP dataframe contains observations without a listed coordinate reference system (CRS). For these, we have assigned CRS 4326." [1] "Transforming your data into a spatial object." [1] "Your WQP dataframe contains observations without a listed coordinate reference system (CRS). For these, we have assigned CRS 4326." [1] "Transforming your data into a spatial object." [1] "Your WQP dataframe contains observations without a listed coordinate reference system (CRS). For these, we have assigned CRS 4269." [1] "Transforming your data into a spatial object." [1] "Your WQP dataframe contains observations without a listed coordinate reference system (CRS). For these, we have assigned CRS 4326." [1] "Transforming your data into a spatial object." [1] "Your WQP dataframe contains observations without a listed coordinate reference system (CRS). For these, we have assigned CRS 4326." [1] "Transforming your data into a spatial object." [1] "Your WQP dataframe contains observations without a listed coordinate reference system (CRS). For these, we have assigned CRS 4326." [1] "Transforming your data into a spatial object." [1] "Your WQP dataframe contains observations without a listed coordinate reference system (CRS). For these, we have assigned CRS 4326." 'data.frame': 418 obs. of 149 variables: $ ActivityTypeCode : chr "Sample-Routine" "Sample-Routine" "Sample-Routine" "Sample-Routine" ... $ ActivityMediaName : chr "Water" "Water" "Water" "Water" ... $ TADA.ActivityMediaName : chr "WATER" "WATER" "WATER" "WATER" ... $ ActivityMediaSubdivisionName : chr "Surface Water" "Surface Water" "Surface Water" "Surface Water" ... $ ResultSampleFractionText : chr "Total" "Total" "Dissolved" "Dissolved" ... $ TADA.ResultSampleFractionText : chr "TOTAL" "TOTAL" "DISSOLVED" "DISSOLVED" ... $ CharacteristicName : chr "pH" "pH" "pH" "pH" ... $ TADA.CharacteristicName : chr "PH" "PH" "PH" "PH" ... $ SubjectTaxonomicName : chr NA NA NA NA ... $ SampleTissueAnatomyName : chr NA NA NA NA ... $ MethodSpeciationName : chr NA NA NA NA ... $ TADA.MethodSpeciationName : chr NA NA NA NA ... $ TADA.ComparableDataIdentifier : chr "PH_TOTAL_NA_STD UNITS" "PH_TOTAL_NA_STD UNITS" "PH_DISSOLVED_NA_STD UNITS" "PH_DISSOLVED_NA_STD UNITS" ... $ ActivityStartDate : chr "2020-01-07" "2020-01-07" "2020-01-14" "2020-01-14" ... $ ActivityStartTime.Time : chr "10:45:00" "09:15:00" "14:00:00" "12:10:00" ... $ ActivityStartTime.TimeZoneCode : chr "MST" "MST" "MST" "MST" ... $ ActivityStartDateTime : chr "2020-01-07 17:45:00" "2020-01-07 16:15:00" "2020-01-14 21:00:00" "2020-01-14 19:10:00" ... $ ResultTimeBasisText : chr NA NA NA NA ... $ ResultMeasureValue : chr "8.1" "7.9" "7" "7" ... $ TADA.ResultMeasureValue : num 8.1 7.9 7 7 6.8 7 7.5 7.5 7.7 7.9 ... $ TADA.ResultMeasureValueDataTypes.Flag : chr "Numeric" "Numeric" "Numeric" "Numeric" ... $ ResultValueTypeName : chr "Actual" "Actual" "Actual" "Actual" ... $ ResultMeasure.MeasureUnitCode : chr "std units" "std units" "std units" "std units" ... $ TADA.ResultMeasure.MeasureUnitCode : chr "STD UNITS" "STD UNITS" "STD UNITS" "STD UNITS" ... $ TADA.WQXResultUnitConversion : chr "No Target Unit" "No Target Unit" "No Target Unit" "No Target Unit" ... $ ResultDetectionConditionText : chr NA NA NA NA ... $ DetectionQuantitationLimitTypeName : chr NA NA NA NA ... $ DetectionQuantitationLimitMeasure.MeasureValue : chr NA NA NA NA ... $ TADA.DetectionQuantitationLimitMeasure.MeasureValue : num NA NA NA NA NA NA 0.1 NA 0.1 NA ... $ TADA.DetectionQuantitationLimitMeasure.MeasureValueDataTypes.Flag: chr "NA - Not Available" "NA - Not Available" "NA - Not Available" "NA - Not Available" ... $ DetectionQuantitationLimitMeasure.MeasureUnitCode : chr NA NA NA NA ... $ TADA.DetectionQuantitationLimitMeasure.MeasureUnitCode : chr NA NA NA NA ... $ ResultDepthHeightMeasure.MeasureValue : chr NA NA NA NA ... $ TADA.ResultDepthHeightMeasure.MeasureValue : num NA NA NA NA NA NA NA NA NA NA ... $ TADA.ResultDepthHeightMeasure.MeasureValueDataTypes.Flag : chr "NA - Not Available" "NA - Not Available" "NA - Not Available" "NA - Not Available" ... $ ResultDepthHeightMeasure.MeasureUnitCode : chr NA NA NA NA ... $ TADA.ResultDepthHeightMeasure.MeasureUnitCode : chr NA NA NA NA ... $ ResultDepthAltitudeReferencePointText : chr NA NA NA NA ... $ ActivityRelativeDepthName : chr NA NA NA NA ... $ ActivityDepthHeightMeasure.MeasureValue : chr NA NA NA NA ... $ TADA.ActivityDepthHeightMeasure.MeasureValue : num NA NA NA NA NA NA NA NA NA NA ... $ TADA.ActivityDepthHeightMeasure.MeasureValueDataTypes.Flag : chr "NA - Not Available" "NA - Not Available" "NA - Not Available" "NA - Not Available" ... $ ActivityDepthHeightMeasure.MeasureUnitCode : chr NA NA NA NA ... $ TADA.ActivityDepthHeightMeasure.MeasureUnitCode : chr NA NA NA NA ... $ ActivityTopDepthHeightMeasure.MeasureValue : chr NA NA NA NA ... $ TADA.ActivityTopDepthHeightMeasure.MeasureValue : num NA NA NA NA NA NA NA NA NA NA ... $ TADA.ActivityTopDepthHeightMeasure.MeasureValueDataTypes.Flag : chr "NA - Not Available" "NA - Not Available" "NA - Not Available" "NA - Not Available" ... $ ActivityTopDepthHeightMeasure.MeasureUnitCode : chr NA NA NA NA ... $ TADA.ActivityTopDepthHeightMeasure.MeasureUnitCode : chr NA NA NA NA ... $ ActivityBottomDepthHeightMeasure.MeasureValue : chr NA NA NA NA ... $ TADA.ActivityBottomDepthHeightMeasure.MeasureValue : num NA NA NA NA NA NA NA NA NA NA ... $ TADA.ActivityBottomDepthHeightMeasure.MeasureValueDataTypes.Flag : chr "NA - Not Available" "NA - Not Available" "NA - Not Available" "NA - Not Available" ... $ ActivityBottomDepthHeightMeasure.MeasureUnitCode : chr NA NA NA NA ... $ TADA.ActivityBottomDepthHeightMeasure.MeasureUnitCode : chr NA NA NA NA ... $ StatisticalBaseCode : chr NA NA NA NA ... $ ResultFileUrl : chr NA NA NA NA ... $ ResultAnalyticalMethod.MethodName : chr "pH, field, electrometric" "pH, field, electrometric" "pH, from alkalinity instrument" "pH, from alkalinity instrument" ... $ ResultAnalyticalMethod.MethodDescriptionText : chr "USGS National Field Manual, Chapter A6.4" "USGS National Field Manual, Chapter A6.4" NA NA ... $ ResultAnalyticalMethod.MethodIdentifier : chr "PROBE" "PROBE" "EL017" "EL017" ... $ ResultAnalyticalMethod.MethodIdentifierContext : chr "USGS" "USGS" "USGS" "USGS" ... $ ResultAnalyticalMethod.MethodUrl : chr NA NA NA NA ... $ SampleCollectionMethod.MethodIdentifier : chr "40" "40" "70" "70" ... $ SampleCollectionMethod.MethodIdentifierContext : chr "USGS parameter code 82398" "USGS parameter code 82398" "USGS parameter code 82398" "USGS parameter code 82398" ... $ SampleCollectionMethod.MethodName : chr "Multiple verticals" "Multiple verticals" "Grab sample (dip)" "Grab sample (dip)" ... $ SampleCollectionMethod.MethodDescriptionText : chr NA NA NA NA ... $ SampleCollectionEquipmentName : chr "Other" "Other" "Grab sample" "Grab sample" ... $ MeasureQualifierCode : chr NA NA NA NA ... $ ResultCommentText : chr NA NA NA NA ... $ ActivityCommentText : chr NA NA NA NA ... $ HydrologicCondition : chr "Stable, normal stage" "Stable, normal stage" "Stable, normal stage" "Stable, normal stage" ... $ HydrologicEvent : chr "Routine sample" "Routine sample" "Routine sample" "Routine sample" ... $ DataQuality.PrecisionValue : chr NA NA NA NA ... $ DataQuality.BiasValue : chr NA NA NA NA ... $ DataQuality.ConfidenceIntervalValue : chr NA NA NA NA ... $ DataQuality.UpperConfidenceLimitValue : chr NA NA NA NA ... $ DataQuality.LowerConfidenceLimitValue : chr NA NA NA NA ... $ SamplingDesignTypeCode : chr NA NA NA NA ... $ LaboratoryName : chr "U.S. Geological Survey-Water Resources Discipline" "U.S. Geological Survey-Water Resources Discipline" "USGS CO WSC Water-Quality Research Lab, Denver" "USGS CO WSC Water-Quality Research Lab, Denver" ... $ ResultLaboratoryCommentText : chr NA "see result field comment" NA NA ... $ ResultIdentifier : chr "NWIS-118370288" "NWIS-118370337" "NWIS-118482581" "NWIS-118482615" ... $ ActivityIdentifier : chr "nwisco.01.02000515" "nwisco.01.02000516" "nwisco.01.02000577" "nwisco.01.02000575" ... $ OrganizationIdentifier : chr "USGS-CO" "USGS-CO" "USGS-CO" "USGS-CO" ... $ OrganizationFormalName : chr "USGS Colorado Water Science Center" "USGS Colorado Water Science Center" "USGS Colorado Water Science Center" "USGS Colorado Water Science Center" ... $ ProjectName : chr NA NA NA NA ... $ ProjectDescriptionText : chr NA NA NA NA ... $ ProjectIdentifier : chr NA NA NA NA ... $ ProjectFileUrl : chr NA NA NA NA ... $ QAPPApprovedIndicator : chr NA NA NA NA ... $ QAPPApprovalAgencyName : chr NA NA NA NA ... $ CountryCode : chr "US" "US" "US" "US" ... $ StateCode : chr "08" "08" "08" "08" ... $ CountyCode : chr "069" "069" "069" "069" ... $ MonitoringLocationName : chr NA NA NA NA ... $ MonitoringLocationTypeName : chr "Stream" "Stream" "Stream" "Spring" ... $ MonitoringLocationDescriptionText : chr NA NA NA NA ... $ LatitudeMeasure : chr "40.37873889000000" "40.38322778000000" "40.29090000000000" "40.29081794000000" ... $ TADA.LatitudeMeasure : num 40.4 40.4 40.3 40.3 40.3 ... $ LongitudeMeasure : chr "-105.0608167000000" "-105.0306972000000" "-105.6597000000000" "-105.6672272000000" ... $ TADA.LongitudeMeasure : num -105 -105 -106 -106 -106 ... [list output truncated] Classes 'sf' and 'data.frame': 418 obs. of 150 variables: $ ActivityTypeCode : chr "Sample-Routine" "Sample-Routine" "Sample-Routine" "Sample-Routine" ... $ ActivityMediaName : chr "Water" "Water" "Water" "Water" ... $ TADA.ActivityMediaName : chr "WATER" "WATER" "WATER" "WATER" ... $ ActivityMediaSubdivisionName : chr "Surface Water" "Surface Water" "Surface Water" "Surface Water" ... $ ResultSampleFractionText : chr "Total" "Total" "Dissolved" "Dissolved" ... $ TADA.ResultSampleFractionText : chr "TOTAL" "TOTAL" "DISSOLVED" "DISSOLVED" ... $ CharacteristicName : chr "pH" "pH" "pH" "pH" ... $ TADA.CharacteristicName : chr "PH" "PH" "PH" "PH" ... $ SubjectTaxonomicName : chr NA NA NA NA ... $ SampleTissueAnatomyName : chr NA NA NA NA ... $ MethodSpeciationName : chr NA NA NA NA ... $ TADA.MethodSpeciationName : chr NA NA NA NA ... $ TADA.ComparableDataIdentifier : chr "PH_TOTAL_NA_STD UNITS" "PH_TOTAL_NA_STD UNITS" "PH_DISSOLVED_NA_STD UNITS" "PH_DISSOLVED_NA_STD UNITS" ... $ ActivityStartDate : chr "2020-01-07" "2020-01-07" "2020-01-14" "2020-01-14" ... $ ActivityStartTime.Time : chr "10:45:00" "09:15:00" "14:00:00" "12:10:00" ... $ ActivityStartTime.TimeZoneCode : chr "MST" "MST" "MST" "MST" ... $ ActivityStartDateTime : chr "2020-01-07 17:45:00" "2020-01-07 16:15:00" "2020-01-14 21:00:00" "2020-01-14 19:10:00" ... $ ResultTimeBasisText : chr NA NA NA NA ... $ ResultMeasureValue : chr "8.1" "7.9" "7" "7" ... $ TADA.ResultMeasureValue : num 8.1 7.9 7 7 6.8 7 7.5 7.5 7.7 7.9 ... $ TADA.ResultMeasureValueDataTypes.Flag : chr "Numeric" "Numeric" "Numeric" "Numeric" ... $ ResultValueTypeName : chr "Actual" "Actual" "Actual" "Actual" ... $ ResultMeasure.MeasureUnitCode : chr "std units" "std units" "std units" "std units" ... $ TADA.ResultMeasure.MeasureUnitCode : chr "STD UNITS" "STD UNITS" "STD UNITS" "STD UNITS" ... $ TADA.WQXResultUnitConversion : chr "No Target Unit" "No Target Unit" "No Target Unit" "No Target Unit" ... $ ResultDetectionConditionText : chr NA NA NA NA ... $ DetectionQuantitationLimitTypeName : chr NA NA NA NA ... $ DetectionQuantitationLimitMeasure.MeasureValue : chr NA NA NA NA ... $ TADA.DetectionQuantitationLimitMeasure.MeasureValue : num NA NA NA NA NA NA 0.1 NA 0.1 NA ... $ TADA.DetectionQuantitationLimitMeasure.MeasureValueDataTypes.Flag: chr "NA - Not Available" "NA - Not Available" "NA - Not Available" "NA - Not Available" ... $ DetectionQuantitationLimitMeasure.MeasureUnitCode : chr NA NA NA NA ... $ TADA.DetectionQuantitationLimitMeasure.MeasureUnitCode : chr NA NA NA NA ... $ ResultDepthHeightMeasure.MeasureValue : chr NA NA NA NA ... $ TADA.ResultDepthHeightMeasure.MeasureValue : num NA NA NA NA NA NA NA NA NA NA ... $ TADA.ResultDepthHeightMeasure.MeasureValueDataTypes.Flag : chr "NA - Not Available" "NA - Not Available" "NA - Not Available" "NA - Not Available" ... $ ResultDepthHeightMeasure.MeasureUnitCode : chr NA NA NA NA ... $ TADA.ResultDepthHeightMeasure.MeasureUnitCode : chr NA NA NA NA ... $ ResultDepthAltitudeReferencePointText : chr NA NA NA NA ... $ ActivityRelativeDepthName : chr NA NA NA NA ... $ ActivityDepthHeightMeasure.MeasureValue : chr NA NA NA NA ... $ TADA.ActivityDepthHeightMeasure.MeasureValue : num NA NA NA NA NA NA NA NA NA NA ... $ TADA.ActivityDepthHeightMeasure.MeasureValueDataTypes.Flag : chr "NA - Not Available" "NA - Not Available" "NA - Not Available" "NA - Not Available" ... $ ActivityDepthHeightMeasure.MeasureUnitCode : chr NA NA NA NA ... $ TADA.ActivityDepthHeightMeasure.MeasureUnitCode : chr NA NA NA NA ... $ ActivityTopDepthHeightMeasure.MeasureValue : chr NA NA NA NA ... $ TADA.ActivityTopDepthHeightMeasure.MeasureValue : num NA NA NA NA NA NA NA NA NA NA ... $ TADA.ActivityTopDepthHeightMeasure.MeasureValueDataTypes.Flag : chr "NA - Not Available" "NA - Not Available" "NA - Not Available" "NA - Not Available" ... $ ActivityTopDepthHeightMeasure.MeasureUnitCode : chr NA NA NA NA ... $ TADA.ActivityTopDepthHeightMeasure.MeasureUnitCode : chr NA NA NA NA ... $ ActivityBottomDepthHeightMeasure.MeasureValue : chr NA NA NA NA ... $ TADA.ActivityBottomDepthHeightMeasure.MeasureValue : num NA NA NA NA NA NA NA NA NA NA ... $ TADA.ActivityBottomDepthHeightMeasure.MeasureValueDataTypes.Flag : chr "NA - Not Available" "NA - Not Available" "NA - Not Available" "NA - Not Available" ... $ ActivityBottomDepthHeightMeasure.MeasureUnitCode : chr NA NA NA NA ... $ TADA.ActivityBottomDepthHeightMeasure.MeasureUnitCode : chr NA NA NA NA ... $ StatisticalBaseCode : chr NA NA NA NA ... $ ResultFileUrl : chr NA NA NA NA ... $ ResultAnalyticalMethod.MethodName : chr "pH, field, electrometric" "pH, field, electrometric" "pH, from alkalinity instrument" "pH, from alkalinity instrument" ... $ ResultAnalyticalMethod.MethodDescriptionText : chr "USGS National Field Manual, Chapter A6.4" "USGS National Field Manual, Chapter A6.4" NA NA ... $ ResultAnalyticalMethod.MethodIdentifier : chr "PROBE" "PROBE" "EL017" "EL017" ... $ ResultAnalyticalMethod.MethodIdentifierContext : chr "USGS" "USGS" "USGS" "USGS" ... $ ResultAnalyticalMethod.MethodUrl : chr NA NA NA NA ... $ SampleCollectionMethod.MethodIdentifier : chr "40" "40" "70" "70" ... $ SampleCollectionMethod.MethodIdentifierContext : chr "USGS parameter code 82398" "USGS parameter code 82398" "USGS parameter code 82398" "USGS parameter code 82398" ... $ SampleCollectionMethod.MethodName : chr "Multiple verticals" "Multiple verticals" "Grab sample (dip)" "Grab sample (dip)" ... $ SampleCollectionMethod.MethodDescriptionText : chr NA NA NA NA ... $ SampleCollectionEquipmentName : chr "Other" "Other" "Grab sample" "Grab sample" ... $ MeasureQualifierCode : chr NA NA NA NA ... $ ResultCommentText : chr NA NA NA NA ... $ ActivityCommentText : chr NA NA NA NA ... $ HydrologicCondition : chr "Stable, normal stage" "Stable, normal stage" "Stable, normal stage" "Stable, normal stage" ... $ HydrologicEvent : chr "Routine sample" "Routine sample" "Routine sample" "Routine sample" ... $ DataQuality.PrecisionValue : chr NA NA NA NA ... $ DataQuality.BiasValue : chr NA NA NA NA ... $ DataQuality.ConfidenceIntervalValue : chr NA NA NA NA ... $ DataQuality.UpperConfidenceLimitValue : chr NA NA NA NA ... $ DataQuality.LowerConfidenceLimitValue : chr NA NA NA NA ... $ SamplingDesignTypeCode : chr NA NA NA NA ... $ LaboratoryName : chr "U.S. Geological Survey-Water Resources Discipline" "U.S. Geological Survey-Water Resources Discipline" "USGS CO WSC Water-Quality Research Lab, Denver" "USGS CO WSC Water-Quality Research Lab, Denver" ... $ ResultLaboratoryCommentText : chr NA "see result field comment" NA NA ... $ ResultIdentifier : chr "NWIS-118370288" "NWIS-118370337" "NWIS-118482581" "NWIS-118482615" ... $ ActivityIdentifier : chr "nwisco.01.02000515" "nwisco.01.02000516" "nwisco.01.02000577" "nwisco.01.02000575" ... $ OrganizationIdentifier : chr "USGS-CO" "USGS-CO" "USGS-CO" "USGS-CO" ... $ OrganizationFormalName : chr "USGS Colorado Water Science Center" "USGS Colorado Water Science Center" "USGS Colorado Water Science Center" "USGS Colorado Water Science Center" ... $ ProjectName : chr NA NA NA NA ... $ ProjectDescriptionText : chr NA NA NA NA ... $ ProjectIdentifier : chr NA NA NA NA ... $ ProjectFileUrl : chr NA NA NA NA ... $ QAPPApprovedIndicator : chr NA NA NA NA ... $ QAPPApprovalAgencyName : chr NA NA NA NA ... $ CountryCode : chr "US" "US" "US" "US" ... $ StateCode : chr "08" "08" "08" "08" ... $ CountyCode : chr "069" "069" "069" "069" ... $ MonitoringLocationName : chr NA NA NA NA ... $ MonitoringLocationTypeName : chr "Stream" "Stream" "Stream" "Spring" ... $ MonitoringLocationDescriptionText : chr NA NA NA NA ... $ LatitudeMeasure : chr "40.37873889000000" "40.38322778000000" "40.29090000000000" "40.29081794000000" ... $ TADA.LatitudeMeasure : num 40.4 40.4 40.3 40.3 40.3 ... $ LongitudeMeasure : chr "-105.0608167000000" "-105.0306972000000" "-105.6597000000000" "-105.6672272000000" ... $ TADA.LongitudeMeasure : num -105 -105 -106 -106 -106 ... [list output truncated] - attr(*, "sf_column")= chr "geometry" - attr(*, "agr")= Factor w/ 3 levels "constant","aggregate",..: NA NA NA NA NA NA NA NA NA NA ... ..- attr(*, "names")= chr [1:149] "ActivityTypeCode" "ActivityMediaName" "TADA.ActivityMediaName" "ActivityMediaSubdivisionName" ... [1] "Transforming your data into a spatial object." [1] "Your WQP dataframe contains observations without a listed coordinate reference system (CRS). For these, we have assigned CRS 4326." Spherical geometry (s2) switched off [1] "Depending on your data's observation count and its spatial range, the ATTAINS pull may take a while." Linking to GEOS 3.13.1, GDAL 3.10.2, PROJ 9.5.1; sf_use_s2() is FALSE [1] "There are no ATTAINS features associated with your area of interest." [1] "Depending on your data's observation count and its spatial range, the ATTAINS pull may take a while." [1] "No NHD HR features associated with your area of interest." [1] "Transforming your data into a spatial object." [1] "Your WQP dataframe contains observations without a listed coordinate reference system (CRS). For these, we have assigned CRS 4326." [1] "Depending on your data's observation count and its spatial range, the ATTAINS pull may take a while." [1] "There are no ATTAINS catchments associated with these WQP observations. Returning an empty dataframe for `TADA_with_ATTAINS`." [1] "Transforming your data into a spatial object." [1] "Your WQP dataframe contains observations without a listed coordinate reference system (CRS). For these, we have assigned CRS 4326." [1] "Depending on your data's observation count and its spatial range, the ATTAINS pull may take a while." [1] "Depending on your data's observation count and its spatial range, the ATTAINS pull may take a while." [1] "Transforming your data into a spatial object." [1] "Your WQP dataframe contains observations without a listed coordinate reference system (CRS). For these, we have assigned CRS 4326." [1] "Depending on your data's observation count and its spatial range, the ATTAINS pull may take a while." [1] "Depending on your data's observation count and its spatial range, the ATTAINS pull may take a while." [1] "Your Water Quality Portal dataframe has no observations. Returning an empty dataframe with empty ATTAINS features." Checking what data is available. This may take a moment. The number of sites and/or records matched by the query terms is large, so the download may take some time. [1] "Downloading data from sites with fewer than 350000 results by grouping them together." | | | 0% | |=================== | 27% | |======================================================================| 100% startDate endDate statecode "2009-07-06" "2009-07-07" "RI" Checking what data is available. This may take a moment. [1] "Downloading WQP query results. This may take some time depending upon the query size." $statecode [1] "US:44" $startDate [1] "2009-07-06" $endDate [1] "2009-07-07" [1] "Data successfully downloaded. Running TADA_AutoClean function." [1] "TADA_Autoclean: creating TADA-specific columns." [1] "TADA_Autoclean: handling special characters and coverting TADA.ResultMeasureValue and TADA.DetectionQuantitationLimitMeasure.MeasureValue value fields to numeric." [1] "TADA_Autoclean: converting TADA.LatitudeMeasure and TADA.LongitudeMeasure fields to numeric." [1] "TADA_Autoclean: harmonizing synonymous unit names (m and meters) to m." [1] "TADA_Autoclean: updating deprecated (i.e. retired) characteristic names." [1] "No deprecated characteristic names found in dataset." [1] "TADA_Autoclean: harmonizing result and depth units." [1] "TADA_Autoclean: creating TADA.ComparableDataIdentifier field for use when generating visualizations and analyses." [1] "NOTE: This version of the TADA package is designed to work with numeric data with media name: 'WATER'. TADA_AutoClean does not currently remove (filter) data with non-water media types. If desired, the user must make this specification on their own outside of package functions. Example: dplyr::filter(.data, TADA.ActivityMediaName == 'WATER')" [1] "No Suspect method/characteristic combinations in your dataframe. Returning the input dataframe with TADA.AnalyticalMethod.Flag column for tracking." [1] "Quality control samples have been removed or were not present in the input dataframe. Returning dataframe with TADA.ActivityType.Flag column for tracking." [1] "No data below the WQX Lower Threshold were found in your dataframe. Returning the input dataframe with TADA.ResultValueBelowLowerThreshold.Flag column for tracking." [1] "No QAPP document url data found in your dataframe. Returning input dataframe with TADA.QAPPDocAvailable column for tracking." startDate endDate statecode "2024-08-27" "2024-08-28" "VT" Checking what data is available. This may take a moment. [1] "Downloading WQP query results. This may take some time depending upon the query size." $statecode [1] "US:50" $startDate [1] "2024-08-27" $endDate [1] "2024-08-28" [1] "Data successfully downloaded. Running TADA_AutoClean function." [1] "TADA_Autoclean: creating TADA-specific columns." [1] "TADA_Autoclean: handling special characters and coverting TADA.ResultMeasureValue and TADA.DetectionQuantitationLimitMeasure.MeasureValue value fields to numeric." [1] "TADA_Autoclean: converting TADA.LatitudeMeasure and TADA.LongitudeMeasure fields to numeric." [1] "TADA_Autoclean: harmonizing synonymous unit names (m and meters) to m." [1] "TADA_Autoclean: updating deprecated (i.e. retired) characteristic names." [1] "No deprecated characteristic names found in dataset." [1] "TADA_Autoclean: harmonizing result and depth units." [1] "TADA_Autoclean: creating TADA.ComparableDataIdentifier field for use when generating visualizations and analyses." [1] "NOTE: This version of the TADA package is designed to work with numeric data with media name: 'WATER'. TADA_AutoClean does not currently remove (filter) data with non-water media types. If desired, the user must make this specification on their own outside of package functions. Example: dplyr::filter(.data, TADA.ActivityMediaName == 'WATER')" [1] "No data above the WQX Upper Threshold was found in your dataframe. Returning the input dataframe with TADA.ResultValueAboveUpperThreshold.Flag column for tracking." [1] "No data above the WQX Upper Threshold was found in your dataframe. Returning the input dataframe with TADA.ResultValueAboveUpperThreshold.Flag column for tracking." [1] "No data above the WQX Upper Threshold was found in your dataframe. Returning the input dataframe with TADA.ResultValueAboveUpperThreshold.Flag column for tracking." [1] "No data above the WQX Upper Threshold was found in your dataframe. Returning the input dataframe with TADA.ResultValueAboveUpperThreshold.Flag column for tracking." [1] "No data below the WQX Lower Threshold were found in your dataframe. Returning the input dataframe with TADA.ResultValueBelowLowerThreshold.Flag column for tracking." [1] "No data below the WQX Lower Threshold were found in your dataframe. Returning the input dataframe with TADA.ResultValueBelowLowerThreshold.Flag column for tracking." [1] "No data below the WQX Lower Threshold were found in your dataframe. Returning the input dataframe with TADA.ResultValueBelowLowerThreshold.Flag column for tracking." [1] "No data below the WQX Lower Threshold were found in your dataframe. Returning the input dataframe with TADA.ResultValueBelowLowerThreshold.Flag column for tracking." startDate endDate statecode "2011-03-04" "2011-03-05" "NM" Checking what data is available. This may take a moment. [1] "Downloading WQP query results. This may take some time depending upon the query size." $statecode [1] "US:35" $startDate [1] "2011-03-04" $endDate [1] "2011-03-05" [1] "Data successfully downloaded. Running TADA_AutoClean function." [1] "TADA_Autoclean: creating TADA-specific columns." [1] "TADA_Autoclean: harmonizing dissolved oxygen characterisic name to DISSOLVED OXYGEN SATURATION if unit is % or % SATURATN." [1] "TADA_Autoclean: handling special characters and coverting TADA.ResultMeasureValue and TADA.DetectionQuantitationLimitMeasure.MeasureValue value fields to numeric." [1] "TADA_Autoclean: converting TADA.LatitudeMeasure and TADA.LongitudeMeasure fields to numeric." [1] "TADA_Autoclean: harmonizing synonymous unit names (m and meters) to m." [1] "TADA_Autoclean: updating deprecated (i.e. retired) characteristic names." [1] "No deprecated characteristic names found in dataset." [1] "TADA_Autoclean: harmonizing result and depth units." [1] "TADA_Autoclean: creating TADA.ComparableDataIdentifier field for use when generating visualizations and analyses." [1] "NOTE: This version of the TADA package is designed to work with numeric data with media name: 'WATER'. TADA_AutoClean does not currently remove (filter) data with non-water media types. If desired, the user must make this specification on their own outside of package functions. Example: dplyr::filter(.data, TADA.ActivityMediaName == 'WATER')" [1] "Quality control samples have been removed or were not present in the input dataframe. Returning dataframe with TADA.ActivityType.Flag column for tracking." Checking what data is available. This may take a moment. [1] "Downloading WQP query results. This may take some time depending upon the query size." $statecode [1] "US:20" $startDate [1] "2021-01-01" $characteristicName [1] "Phosphorus" "Nitrate" $endDate [1] "2022-01-01" [1] "Data successfully downloaded. Running TADA_AutoClean function." [1] "TADA_Autoclean: creating TADA-specific columns." [1] "TADA_Autoclean: handling special characters and coverting TADA.ResultMeasureValue and TADA.DetectionQuantitationLimitMeasure.MeasureValue value fields to numeric." [1] "TADA_Autoclean: converting TADA.LatitudeMeasure and TADA.LongitudeMeasure fields to numeric." [1] "TADA_Autoclean: harmonizing synonymous unit names (m and meters) to m." [1] "TADA_Autoclean: updating deprecated (i.e. retired) characteristic names." [1] "No deprecated characteristic names found in dataset." [1] "TADA_Autoclean: harmonizing result and depth units." [1] "TADA_Autoclean: creating TADA.ComparableDataIdentifier field for use when generating visualizations and analyses." [1] "NOTE: This version of the TADA package is designed to work with numeric data with media name: 'WATER'. TADA_AutoClean does not currently remove (filter) data with non-water media types. If desired, the user must make this specification on their own outside of package functions. Example: dplyr::filter(.data, TADA.ActivityMediaName == 'WATER')" [1] "Dataset contains 87 results missing both a TADA result value and a detection limit. These values will not be represented in the stats summary table. Suggest removing or handling." [1] "TADA_IDCensoredData: There are 22 results in your dataframe that are missing ResultDetectionConditionText. TADA requires BOTH ResultDetectionConditionText and DetectionQuantitationLimitTypeName fields to be populated in order to categorize censored data." [1] "TADA_IDCensoredData: DetectionQuantitationLimitTypeName column in dataframe contains value(s) NA which is/are not represented in the DetectionQuantitationLimitTypeName WQX domain table. These data records are placed under the TADA.CensoredData.Flag: Censored but not Categorized, and will not be used in censored data handling methods. Please contact TADA administrators to resolve." startDate endDate statecode "2012-12-16" "2012-12-17" "MD" Checking what data is available. This may take a moment. [1] "Downloading WQP query results. This may take some time depending upon the query size." $statecode [1] "US:24" $startDate [1] "2012-12-16" $endDate [1] "2012-12-17" [1] "Data successfully downloaded. Running TADA_AutoClean function." [1] "TADA_Autoclean: creating TADA-specific columns." [1] "TADA_Autoclean: harmonizing dissolved oxygen characterisic name to DISSOLVED OXYGEN SATURATION if unit is % or % SATURATN." [1] "TADA_Autoclean: handling special characters and coverting TADA.ResultMeasureValue and TADA.DetectionQuantitationLimitMeasure.MeasureValue value fields to numeric." [1] "TADA_Autoclean: converting TADA.LatitudeMeasure and TADA.LongitudeMeasure fields to numeric." [1] "TADA_Autoclean: harmonizing synonymous unit names (m and meters) to m." [1] "TADA_Autoclean: updating deprecated (i.e. retired) characteristic names." [1] "20 results in your dataset have one of the following deprecated characteristic names: Inorganic nitrogen (nitrate and nitrite) ***retired***use Nitrate + Nitrite. These names have been substituted with the updated preferred names in the TADA.CharacteristicName field." [1] "TADA_Autoclean: harmonizing result and depth units." [1] "TADA_Autoclean: creating TADA.ComparableDataIdentifier field for use when generating visualizations and analyses." [1] "NOTE: This version of the TADA package is designed to work with numeric data with media name: 'WATER'. TADA_AutoClean does not currently remove (filter) data with non-water media types. If desired, the user must make this specification on their own outside of package functions. Example: dplyr::filter(.data, TADA.ActivityMediaName == 'WATER')" [1] "No Suspect method/characteristic combinations in your dataframe. Returning the input dataframe with TADA.AnalyticalMethod.Flag column for tracking." Checking what data is available. This may take a moment. [1] "Downloading WQP query results. This may take some time depending upon the query size." $statecode [1] "US:49" $startDate [1] "2023-01-01" $characteristicName [1] "Ammonia" "Nitrate" "Nitrogen" $organization [1] "USGS-UT" $endDate [1] "2023-03-01" [1] "Data successfully downloaded. Running TADA_AutoClean function." [1] "TADA_Autoclean: creating TADA-specific columns." [1] "TADA_Autoclean: handling special characters and coverting TADA.ResultMeasureValue and TADA.DetectionQuantitationLimitMeasure.MeasureValue value fields to numeric." [1] "TADA_Autoclean: converting TADA.LatitudeMeasure and TADA.LongitudeMeasure fields to numeric." [1] "TADA_Autoclean: harmonizing synonymous unit names (m and meters) to m." [1] "TADA_Autoclean: updating deprecated (i.e. retired) characteristic names." [1] "No deprecated characteristic names found in dataset." [1] "TADA_Autoclean: harmonizing result and depth units." [1] "TADA_Autoclean: creating TADA.ComparableDataIdentifier field for use when generating visualizations and analyses." [1] "NOTE: This version of the TADA package is designed to work with numeric data with media name: 'WATER'. TADA_AutoClean does not currently remove (filter) data with non-water media types. If desired, the user must make this specification on their own outside of package functions. Example: dplyr::filter(.data, TADA.ActivityMediaName == 'WATER')" startDate endDate statecode "2010-02-11" "2010-02-14" "VA" Checking what data is available. This may take a moment. [1] "Downloading WQP query results. This may take some time depending upon the query size." $statecode [1] "US:51" $startDate [1] "2010-02-11" $endDate [1] "2010-02-14" [1] "Data successfully downloaded. Running TADA_AutoClean function." [1] "TADA_Autoclean: creating TADA-specific columns." [1] "TADA_Autoclean: harmonizing dissolved oxygen characterisic name to DISSOLVED OXYGEN SATURATION if unit is % or % SATURATN." [1] "TADA_Autoclean: handling special characters and coverting TADA.ResultMeasureValue and TADA.DetectionQuantitationLimitMeasure.MeasureValue value fields to numeric." [1] "TADA_Autoclean: converting TADA.LatitudeMeasure and TADA.LongitudeMeasure fields to numeric." [1] "TADA_Autoclean: harmonizing synonymous unit names (m and meters) to m." [1] "TADA_Autoclean: updating deprecated (i.e. retired) characteristic names." [1] "33 results in your dataset have one of the following deprecated characteristic names: Inorganic nitrogen (nitrate and nitrite) ***retired***use Nitrate + Nitrite. These names have been substituted with the updated preferred names in the TADA.CharacteristicName field." [1] "TADA_Autoclean: harmonizing result and depth units." [1] "TADA_Autoclean: creating TADA.ComparableDataIdentifier field for use when generating visualizations and analyses." [1] "NOTE: This version of the TADA package is designed to work with numeric data with media name: 'WATER'. TADA_AutoClean does not currently remove (filter) data with non-water media types. If desired, the user must make this specification on their own outside of package functions. Example: dplyr::filter(.data, TADA.ActivityMediaName == 'WATER')" [1] "TADA.CreateUnitRef: The following characteristics have more than one listed target unit: NITROGEN (MG/L and G); NITRATE (MG/L and MEQ/L); DEPTH (M and NONE); AMMONIUM (MG/L and MEQ/L); PHOSPHORUS (UG/L and G); PHEOPHYTIN RATIO (% and UG/L); SILICA (MMOL/L and UG/L); SULFATE (MEQ/L and UG/L); CHLORIDE (MEQ/L and UG/L) and CARBON (UG/L and G). This may be due to units of different types that cannot be converted to match each other. You may wish to review the output of TADA.CreateUnitRef and edit it." Joining with `by = join_by(TADA.CharacteristicName, ResultMeasure.MeasureUnitCode)` startDate endDate statecode "2006-04-25" "2006-04-30" "DC" Checking what data is available. This may take a moment. [1] "Downloading WQP query results. This may take some time depending upon the query size." $statecode [1] "US:11" $startDate [1] "2006-04-25" $endDate [1] "2006-04-30" [1] "Returning empty results dataframe: Your WQP query returned no results (no data available). Try a different query. Removing some of your query filters OR broadening your search area may help." startDate endDate statecode "2017-11-19" "2017-11-24" "NH" Checking what data is available. This may take a moment. [1] "Downloading WQP query results. This may take some time depending upon the query size." $statecode [1] "US:33" $startDate [1] "2017-11-19" $endDate [1] "2017-11-24" [1] "Returning empty results dataframe: Your WQP query returned no results (no data available). Try a different query. Removing some of your query filters OR broadening your search area may help." startDate endDate statecode "2017-01-28" "2017-02-02" "TX" Checking what data is available. This may take a moment. [1] "Downloading WQP query results. This may take some time depending upon the query size." $statecode [1] "US:48" $startDate [1] "2017-01-28" $endDate [1] "2017-02-02" [1] "TADA_Autoclean: creating TADA-specific columns." [1] "TADA_Autoclean: handling special characters and coverting TADA.ResultMeasureValue and TADA.DetectionQuantitationLimitMeasure.MeasureValue value fields to numeric." [1] "TADA_Autoclean: converting TADA.LatitudeMeasure and TADA.LongitudeMeasure fields to numeric." [1] "TADA_Autoclean: harmonizing synonymous unit names (m and meters) to m." [1] "TADA_Autoclean: updating deprecated (i.e. retired) characteristic names." [1] "78 results in your dataset have one of the following deprecated characteristic names: Desisopropyl atrazine; Inorganic nitrogen (nitrate and nitrite); Inorganic nitrogen (nitrate and nitrite) ***retired***use Nitrate + Nitrite. These names have been substituted with the updated preferred names in the TADA.CharacteristicName field." [1] "TADA_Autoclean: harmonizing result and depth units." [1] "TADA_Autoclean: creating TADA.ComparableDataIdentifier field for use when generating visualizations and analyses." [1] "NOTE: This version of the TADA package is designed to work with numeric data with media name: 'WATER'. TADA_AutoClean does not currently remove (filter) data with non-water media types. If desired, the user must make this specification on their own outside of package functions. Example: dplyr::filter(.data, TADA.ActivityMediaName == 'WATER')" [ FAIL 6 | WARN 1 | SKIP 0 | PASS 69 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-CensoredDataSuite.R:2:3'): TADA_IDCensoredData orphans ───────── Error in `httr2::req_perform(obs_url)`: HTTP 413 Payload Too Large. Backtrace: ▆ 1. └─EPATADA::TADA_DataRetrieval(...) at test-CensoredDataSuite.R:2:3 2. └─purrr (local) quiet_whatWQPsites(siteid = unique(results.DR$MonitoringLocationIdentifier)) 3. ├─purrr:::capture_output(.f(...)) 4. │ └─base::withCallingHandlers(code, warning = wHandler, message = mHandler) 5. └─dataRetrieval (local) .f(...) 6. └─dataRetrieval::importWQP(baseURL, convertType = convertType) 7. └─dataRetrieval::getWebServiceData(obs_url) 8. └─httr2::req_perform(obs_url) 9. └─httr2:::handle_resp(req, resp, error_call = error_call) 10. └─httr2:::resp_failure_cnd(req, resp, error_call = error_call) 11. ├─rlang::catch_cnd(...) 12. │ ├─rlang::eval_bare(...) 13. │ ├─base::tryCatch(...) 14. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 15. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 16. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 17. │ └─base::force(expr) 18. └─rlang::abort(...) ── Error ('test-CensoredDataSuite.R:13:3'): TADA_IDCensoredData copies det lim values to result values if applicable ── Error in `httr2::req_perform(obs_url)`: HTTP 400 Bad Request. Backtrace: ▆ 1. └─EPATADA::TADA_RandomTestingData(choose_random_state = TRUE) at test-CensoredDataSuite.R:13:3 2. └─EPATADA (local) verify_random_data() 3. └─EPATADA (local) get_random_data() 4. └─EPATADA::TADA_DataRetrieval(...) 5. └─purrr (local) quiet_readWQPdata(...) 6. ├─purrr:::capture_output(.f(...)) 7. │ └─base::withCallingHandlers(code, warning = wHandler, message = mHandler) 8. └─dataRetrieval (local) .f(...) 9. └─dataRetrieval::importWQP(baseURL, tz = tz, convertType = convertType) 10. └─dataRetrieval::getWebServiceData(obs_url) 11. └─httr2::req_perform(obs_url) 12. └─httr2:::handle_resp(req, resp, error_call = error_call) 13. └─httr2:::resp_failure_cnd(req, resp, error_call = error_call) 14. ├─rlang::catch_cnd(...) 15. │ ├─rlang::eval_bare(...) 16. │ ├─base::tryCatch(...) 17. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 18. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 20. │ └─base::force(expr) 21. └─rlang::abort(...) ── Error ('test-CensoredDataSuite.R:42:3'): TADA_IDCensoredData correctly handles specific text values such as ND ── Error in `httr2::req_perform(obs_url)`: HTTP 494. Backtrace: ▆ 1. └─EPATADA::TADA_DataRetrieval(...) at test-CensoredDataSuite.R:42:3 2. └─purrr (local) quiet_whatWQPsites(siteid = unique(results.DR$MonitoringLocationIdentifier)) 3. ├─purrr:::capture_output(.f(...)) 4. │ └─base::withCallingHandlers(code, warning = wHandler, message = mHandler) 5. └─dataRetrieval (local) .f(...) 6. └─dataRetrieval::importWQP(baseURL, convertType = convertType) 7. └─dataRetrieval::getWebServiceData(obs_url) 8. └─httr2::req_perform(obs_url) 9. └─httr2:::handle_resp(req, resp, error_call = error_call) 10. └─httr2:::resp_failure_cnd(req, resp, error_call = error_call) 11. ├─rlang::catch_cnd(...) 12. │ ├─rlang::eval_bare(...) 13. │ ├─base::tryCatch(...) 14. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 15. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 16. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 17. │ └─base::force(expr) 18. └─rlang::abort(...) ── Error ('test-DataDiscoveryRetrieval.R:268:3'): TADA_DataRetrieval ─────────── Error in `.f(...)`: object 'baseURL' not found Backtrace: ▆ 1. └─EPATADA::TADA_DataRetrieval(...) at test-DataDiscoveryRetrieval.R:268:3 2. └─purrr (local) quiet_whatWQPdata(WQPquery) 3. ├─purrr:::capture_output(.f(...)) 4. │ └─base::withCallingHandlers(code, warning = wHandler, message = mHandler) 5. └─dataRetrieval (local) .f(...) 6. └─httr2::req_url_query(...) 7. └─httr2:::check_request(.req) 8. └─httr2:::is_request(req) ── Error ('test-DataDiscoveryRetrieval.R:406:3'): TADA_DataRetrieval ─────────── Error in `httr2::req_perform(obs_url)`: HTTP 413 Payload Too Large. Backtrace: ▆ 1. └─EPATADA::TADA_DataRetrieval(...) at test-DataDiscoveryRetrieval.R:406:3 2. └─purrr (local) quiet_whatWQPsites(siteid = unique(results.DR$MonitoringLocationIdentifier)) 3. ├─purrr:::capture_output(.f(...)) 4. │ └─base::withCallingHandlers(code, warning = wHandler, message = mHandler) 5. └─dataRetrieval (local) .f(...) 6. └─dataRetrieval::importWQP(baseURL, convertType = convertType) 7. └─dataRetrieval::getWebServiceData(obs_url) 8. └─httr2::req_perform(obs_url) 9. └─httr2:::handle_resp(req, resp, error_call = error_call) 10. └─httr2:::resp_failure_cnd(req, resp, error_call = error_call) 11. ├─rlang::catch_cnd(...) 12. │ ├─rlang::eval_bare(...) 13. │ ├─base::tryCatch(...) 14. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 15. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 16. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 17. │ └─base::force(expr) 18. └─rlang::abort(...) ── Error ('test-ResultFlagsDependent.R:4:3'): No NA's in dependent flag columns ── Error in `httr2::req_perform(obs_url)`: HTTP 413 Payload Too Large. Backtrace: ▆ 1. └─EPATADA::TADA_DataRetrieval(...) at test-ResultFlagsDependent.R:4:3 2. └─purrr (local) quiet_whatWQPsites(siteid = unique(results.DR$MonitoringLocationIdentifier)) 3. ├─purrr:::capture_output(.f(...)) 4. │ └─base::withCallingHandlers(code, warning = wHandler, message = mHandler) 5. └─dataRetrieval (local) .f(...) 6. └─dataRetrieval::importWQP(baseURL, convertType = convertType) 7. └─dataRetrieval::getWebServiceData(obs_url) 8. └─httr2::req_perform(obs_url) 9. └─httr2:::handle_resp(req, resp, error_call = error_call) 10. └─httr2:::resp_failure_cnd(req, resp, error_call = error_call) 11. ├─rlang::catch_cnd(...) 12. │ ├─rlang::eval_bare(...) 13. │ ├─base::tryCatch(...) 14. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 15. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 16. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 17. │ └─base::force(expr) 18. └─rlang::abort(...) [ FAIL 6 | WARN 1 | SKIP 0 | PASS 69 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘remotes’ 'library' or 'require' call not declared from: ‘remotes’ * checking package vignettes ... OK * checking re-building of vignette outputs ... [1m/19m] ERROR Error(s) in re-building vignettes: ... --- re-building ‘CONTRIBUTING.Rmd’ using rmarkdown --- finished re-building ‘CONTRIBUTING.Rmd’ --- re-building ‘TADAAssessmentUnitUseCase.Rmd’ using rmarkdown --- finished re-building ‘TADAAssessmentUnitUseCase.Rmd’ --- re-building ‘TADAModule1.Rmd’ using rmarkdown trying URL 'http://cran.us.r-project.org/src/contrib/remotes_2.5.0.tar.gz' Content type 'application/x-gzip' length 164496 bytes (160 KB) ================================================== downloaded 160 KB * installing *source* package ‘remotes’ ... ** this is package ‘remotes’ version ‘2.5.0’ ** package ‘remotes’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (remotes) The downloaded source packages are in '/tmp/RtmpgQfAcb/working_dir/Rtmp7uULBv/downloaded_packages' Quitting from TADAModule1.Rmd:233-235 [TADA_DataRetrieval] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'TADAModule1.Rmd' failed with diagnostics: HTTP 500 Internal Server Error. --- failed re-building ‘TADAModule1.Rmd’ --- re-building ‘TADAModule1_AdvancedTraining.Rmd’ using rmarkdown --- finished re-building ‘TADAModule1_AdvancedTraining.Rmd’ --- re-building ‘TADAModule1_BeginnerTraining.Rmd’ using rmarkdown --- finished re-building ‘TADAModule1_BeginnerTraining.Rmd’ --- re-building ‘TADAModule2.Rmd’ using rmarkdown --- finished re-building ‘TADAModule2.Rmd’ --- re-building ‘TADAModule3_PartA.Rmd’ using rmarkdown --- finished re-building ‘TADAModule3_PartA.Rmd’ --- re-building ‘TADAWaterSciConWorkshopDemo.Rmd’ using rmarkdown Quitting from TADAWaterSciConWorkshopDemo.Rmd:126-136 [TADA_DataRetrieval] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'TADAWaterSciConWorkshopDemo.Rmd' failed with diagnostics: HTTP 500 Internal Server Error. --- failed re-building ‘TADAWaterSciConWorkshopDemo.Rmd’ --- re-building ‘WQXValidationService.Rmd’ using rmarkdown --- finished re-building ‘WQXValidationService.Rmd’ SUMMARY: processing the following files failed: ‘TADAModule1.Rmd’ ‘TADAWaterSciConWorkshopDemo.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [4s/4s] OK * checking HTML version of manual ... [2s/2s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 3 ERRORs, 4 NOTEs