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USEPA / EPATADA

This R package can be used to compile and evaluate Water Quality Portal (WQP) data for samples collected from surface water monitoring sites on streams and lakes. It can be used to create applications that support water quality programs and help states, tribes, and other stakeholders efficiently analyze the data.
https://usepa.github.io/EPATADA/
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Address devtools check notes #478

Open cristinamullin opened 3 months ago

cristinamullin commented 3 months ago

Describe the issue

Address the following devtools::check() note regarding Rd line widths. To reproduce, run devtools::check() on TADA package.

If there is an easy bulk solution, add it to Maintenance.R and/or TADA Cheat Sheet so it can be easily replicated in the future if needed.


N  checking Rd line widths (916ms)
   Rd file 'TADA_AggregateMeasurements.Rd':
     \examples lines wider than 100 characters:
        # Select maximum value per day, site, comparable data identifier, result detection condition, and activity type code. Clean all non-max ... [TRUNCATED]
        Data_6Tribes_5y_agg <- TADA_AggregateMeasurements(Data_6Tribes_5y, grouping_cols = c("ActivityStartDate", "MonitoringLocationIdentifier ... [TRUNCATED]
        # Calculate a mean value per day, site, comparable data identifier, result detection condition, and activity type code. Keep all measur ... [TRUNCATED]
        Data_6Tribes_5y_agg <- TADA_AggregateMeasurements(Data_6Tribes_5y, grouping_cols = c("ActivityStartDate", "MonitoringLocationIdentifier ... [TRUNCATED]

   Rd file 'TADA_AnalysisDataFilter.Rd':
     \examples lines wider than 100 characters:
        Data_6Tribes_Assessment1 <- TADA_AnalysisDataFilter(Data_6Tribes_5y_Harmonized, clean = TRUE, surface_water = TRUE, ground_water = FALS ... [TRUNCATED]
        # Returns data frame with ONLY surface water results identified as usable and adds TADA.UseForAnalysis.Flag column.
        Data_6Tribes_Assessment2 <- TADA_AnalysisDataFilter(Data_6Tribes_5y_Harmonized, clean = FALSE, surface_water = TRUE, ground_water = FAL ... [TRUNCATED]

   Rd file 'TADA_AutoClean.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]
        TADAProfile <- TADA_JoinWQPProfiles(FullPhysChem = physchemProfile, Sites = stationProfile, Projects = projectProfile)

   Rd file 'TADA_BigDataRetrieval.Rd':
     \examples lines wider than 100 characters:
        tada1 <- TADA_BigDataRetrieval(startDate = "2019-01-01", endDate = "2021-12-31", characteristicName = "Temperature, water", statecode = ... [TRUNCATED]

   Rd file 'TADA_Boxplot.Rd':
     \examples lines wider than 100 characters:
        df <- dplyr::filter(Data_6Tribes_5y_Harmonized, TADA.ComparableDataIdentifier == "TOTAL PHOSPHORUS, MIXED FORMS_UNFILTERED_AS P_UG/L")
        Boxplots_TPbyOrg <- TADA_Boxplot(df, id_cols = c("TADA.ComparableDataIdentifier", "OrganizationIdentifier"))
        Boxplot_output <- TADA_Boxplot(Data_Nutrients_UT, id_cols = c("TADA.ComparableDataIdentifier", "MonitoringLocationTypeName"))

   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]
        TADAProfile <- TADA_JoinWQPProfiles(FullPhysChem = physchemProfile, Sites = stationProfile, Projects = projectProfile)

   Rd file 'TADA_ConvertDepthUnits.Rd':
     \examples lines wider than 100 characters:
        # are harmonized to "TADA.ActivityDepthHeightMeasure.MeasureUnitCode" and "TADA.ActivityDepthHeightMeasure.MeasureValue"

   Rd file 'TADA_ConvertResultUnits.Rd':
     \examples lines wider than 100 characters:
        # "TADA.WQXUnitConversionFactor", "TADA.WQXUnitConversionCoefficient", "TADA.WQXTargetUnit", and "TADA.SpeciationUnitConversion":

   Rd file 'TADA_ConvertSpecialChars.Rd':
     \examples lines wider than 100 characters:
        HandleSpecialChars_ResultMeasureValue <- TADA_ConvertSpecialChars(Data_Nutrients_UT, "ResultMeasureValue")
        HandleSpecialChars_DetLimMeasureValue <- TADA_ConvertSpecialChars(Data_Nutrients_UT, "TADA.DetectionQuantitationLimitMeasure.MeasureVal ... [TRUNCATED]
        unique(HandleSpecialChars_DetLimMeasureValue$TADA.DetectionQuantitationLimitMeasure.MeasureValueDataTypes.Flag)

   Rd file 'TADA_DataRetrieval.Rd':
     \examples lines wider than 100 characters:
        tada1 <- TADA_DataRetrieval(statecode = "WI", countycode = "Dane", characteristicName = "Phosphorus")
        tada2 <- TADA_DataRetrieval(statecode = "UT", characteristicName = c("Ammonia", "Nitrate", "Nitrogen"))

   Rd file 'TADA_DepthProfilePlot.Rd':
     \examples lines wider than 100 characters:
        # Create a depth profile figure with two parameters for a single monitoring location and date without displaying depth categories

   Rd file 'TADA_FieldCounts.Rd':
     \examples lines wider than 100 characters:
        fieldCountUTAmmonia <- TADA_FieldCounts(Data_Nutrients_UT, display = "most", characteristicName = "AMMONIA")

   Rd file 'TADA_FindPotentialDuplicatesMultipleOrgs.Rd':
     \examples lines wider than 100 characters:
        dat <- TADA_DataRetrieval(startDate = "2022-09-01", endDate = "2023-05-01", statecode = "PA", sampleMedia = "Water")
        dat1 <- TADA_FindPotentialDuplicatesMultipleOrgs(dat, dist_buffer = 100, org_hierarchy = c("21PA_WQX"))

   Rd file 'TADA_FlagAboveThreshold.Rd':
     \examples lines wider than 100 characters:
        WQXUpperThreshold_flagsonly <- TADA_FlagAboveThreshold(Data_Nutrients_UT, clean = FALSE, flaggedonly = TRUE)

   Rd file 'TADA_FlagBelowThreshold.Rd':
     \examples lines wider than 100 characters:
        WQXLowerThreshold_flagsonly <- TADA_FlagBelowThreshold(Data_Nutrients_UT, clean = FALSE, flaggedonly = TRUE)

   Rd file 'TADA_FlagContinuousData.Rd':
     \examples lines wider than 100 characters:
        all_data <- TADA_DataRetrieval(project = c("Continuous LC1", "MA_Continuous", "Anchorage Bacteria 20-21"))
        # Remove continuous data in dataframe (note that this dataframe will have 0 results because all are flagged in the example)
        Data_Nutrients_UT_flaggedonly <- TADA_FlagContinuousData(Data_Nutrients_UT, clean = FALSE, flaggedonly = TRUE)
        Data_R5_TADAPackageDemo_flaggedonly <- TADA_FlagContinuousData(Data_R5_TADAPackageDemo, clean = FALSE, flaggedonly = TRUE)

   Rd file 'TADA_FlagCoordinates.Rd':
     \examples lines wider than 100 characters:
        InvalidCoord_removed <- TADA_FlagCoordinates(Data_Nutrients_UT, clean_outsideUSA = "remove", clean_imprecise = TRUE)

   Rd file 'TADA_FlagDepthCategory.Rd':
     \examples lines wider than 100 characters:
        # assign TADA.DepthCategory.Flag and determine average values by depth category and returning only aggregate values
        Data_6Tribs_5y_Mean <- TADA_FlagDepthCategory(Data_6Tribes_5y, bycategory = "all", dailyagg = "avg", aggregatedonly = FALSE)

   Rd file 'TADA_FlagFraction.Rd':
     \examples lines wider than 100 characters:
        InvalidFraction_flaggedonly <- TADA_FlagFraction(Data_Nutrients_UT, clean = FALSE, flaggedonly = TRUE)

   Rd file 'TADA_FlagMeasureQualifierCode.Rd':
     \examples lines wider than 100 characters:
        MeasureQualifierCode_flags_only <- TADA_FlagMeasureQualifierCode(Data_6Tribes_5y, flaggedonly = TRUE)
        MeasureQualifierCode_clean_nodefs <- TADA_FlagMeasureQualifierCode(Data_6Tribes_5y, clean = TRUE, define = FALSE)

   Rd file 'TADA_FlagMethod.Rd':
     \examples lines wider than 100 characters:
        InvalidMethod_flaggedonly <- TADA_FlagMethod(Data_NCTCShepherdstown_HUC12, clean = FALSE, flaggedonly = TRUE)

   Rd file 'TADA_FlagResultUnit.Rd':
     \examples lines wider than 100 characters:
        InvalidUnit_flaggedonly <- TADA_FlagResultUnit(Data_Nutrients_UT, clean = "nonstandardized_only", flaggedonly = TRUE)
        NonstandardUnit_flaggedonly <- TADA_FlagResultUnit(Data_Nutrients_UT, clean = "invalid_only", flaggedonly = TRUE)

   Rd file 'TADA_FlagSpeciation.Rd':
     \examples lines wider than 100 characters:
        NonstandardSpeciation_clean <- TADA_FlagSpeciation(Data_Nutrients_UT, clean = "nonstandardized_only")
        InvalidSpeciation_flaggedonly <- TADA_FlagSpeciation(Data_Nutrients_UT, clean = "nonstandardized_only", flaggedonly = TRUE)
        NonstandardSpeciation_flaggedonly <- TADA_FlagSpeciation(Data_Nutrients_UT, clean = "invalid_only", flaggedonly = TRUE)

   Rd file 'TADA_HarmonizeSynonyms.Rd':
     \examples lines wider than 100 characters:
        Data_6Tribes_5yClean_Harmonized <- TADA_HarmonizeSynonyms(Data_6Tribes_5yClean, ref = CreateRefTable)

   Rd file 'TADA_Histogram.Rd':
     \examples lines wider than 100 characters:
        df <- dplyr::filter(Data_6Tribes_5y_Harmonized, TADA.ComparableDataIdentifier == "TOTAL PHOSPHORUS, MIXED FORMS_UNFILTERED_AS P_UG/L")
        Histogram_output <- TADA_Histogram(Data_Nutrients_UT, id_cols = c("TADA.ComparableDataIdentifier", "MonitoringLocationTypeName"))

   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]
        TADAProfile <- TADA_JoinWQPProfiles(FullPhysChem = physchemProfile, Sites = stationProfile, Projects = projectProfile)

   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]
        TADAProfile <- TADA_JoinWQPProfiles(FullPhysChem = physchemProfile, Sites = stationProfile, Projects = projectProfile)

   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]

   Rd file 'TADA_Scatterplot.Rd':
     \examples lines wider than 100 characters:
        df <- dplyr::filter(Data_6Tribes_5y_Harmonized, TADA.ComparableDataIdentifier == "TOTAL PHOSPHORUS, MIXED FORMS_UNFILTERED_AS P_UG/L")
        Scatterplot_output <- TADA_Scatterplot(Data_Nutrients_UT, id_cols = c("TADA.ComparableDataIdentifier", "MonitoringLocationTypeName"))

   Rd file 'TADA_SimpleCensoredMethods.Rd':
     \examples lines wider than 100 characters:
        Data_Nutrients_UT_CensoredFlag <- TADA_SimpleCensoredMethods(Data_Nutrients_UT, nd_method = "multiplier", nd_multiplier = 0.5, od_metho ... [TRUNCATED]
        # Check for agreement between detection condition and detection limit type, and in instances where the measurement is non-detect, set t ... [TRUNCATED]
        Data_Nutrients_UT_CensoredFlag <- TADA_SimpleCensoredMethods(Data_Nutrients_UT, nd_method = "randombelowlimit", nd_multiplier = "null", ... [TRUNCATED]

   Rd file 'TADA_SubstituteDeprecatedChars.Rd':
     \examples lines wider than 100 characters:
        df <- TADA_DataRetrieval(startDate = "2022-01-01", endDate = "2022-12-31", characteristicType = "Nutrient", statecode = "MT", applyauto ... [TRUNCATED]
        # deprecated and "Phosphate-phosphorus***retired***use Total Phosphorus, mixed forms" is a deprecated WQX
        df3 <- TADA_DataRetrieval(startDate = "2022-01-01", endDate = "2022-12-31", characteristicType = "Nutrient", statecode = "WY", applyaut ... [TRUNCATED]

   Rd file 'TADA_TwoCharacteristicScatterplot.Rd':
     \examples lines wider than 100 characters:
        TADA_TwoCharacteristicScatterplot(Data_Nutrients_UT, id_cols = "TADA.ComparableDataIdentifier", groups = c("AMMONIA_UNFILTERED_NA_MG/L" ... [TRUNCATED]
        df <- dplyr::filter(Data_6Tribes_5y_Harmonized, TADA.ComparableDataIdentifier == "TOTAL PHOSPHORUS, MIXED FORMS_UNFILTERED_AS P_UG/L")
        TADA_TwoCharacteristicScatterplot(df, id_cols = "MonitoringLocationName", groups = c("Upper Red Lake: West", "Upper Red Lake: West-Cent ... [TRUNCATED]

   Rd file 'TADA_addPoints.Rd':
     \examples lines wider than 100 characters:
        lmap <- TADA_addPoints(lmap, "extdata/VATribe.shp", "Tribes", "Virginia Federally Recognized Tribes")

   Rd file 'getBboxJson.Rd':
     \examples lines wider than 100 characters:
        bbox <- sf::st_bbox(c(xmin = min(Data_6Tribes_5y$TADA.LongitudeMeasure), ymin = min(Data_6Tribes_5y$TADA.LatitudeMeasure), xmax = max(D ... [TRUNCATED]

   Rd file 'getLayer.Rd':
     \examples lines wider than 100 characters:
        bbox <- sf::st_bbox(c(xmin = min(Data_6Tribes_5y_Harmonized$TADA.LongitudeMeasure), ymin = min(Data_6Tribes_5y_Harmonized$TADA.Latitude ... [TRUNCATED]
        # Get the American Indian Reservations feature layer, filtered by the bounding box for the Data_6Tribes_5y_Harmonized example dataset

   Rd file 'writeLayer.Rd':
     \examples lines wider than 100 characters:
        # Get the Oklahoma Tribal Statistical Areas feature layer and write local file to inst/extdata/OKTribe.shp

   These lines will be truncated in the PDF manual.
``'
hillarymarler commented 2 months ago

Quite a few of these are related to long urls. One way to fix them is to create shorter strings and paste them together to create the urls. I am not yet aware of other work arounds for this.