diff --git a/R/Maintenance.R b/R/Maintenance.R index 378f204e..a6216d2c 100644 --- a/R/Maintenance.R +++ b/R/Maintenance.R @@ -56,7 +56,7 @@ TADA_UpdateExampleData <- function() { od_method = "as-is", od_multiplier = "null" ) - y <- dplyr::filter(y, TADA.ResultMeasureValueDataTypes.Flag != "Blank" & + y <- dplyr::filter(y, TADA.ResultMeasureValueDataTypes.Flag != "NA - Not Applicable" & TADA.ResultMeasureValueDataTypes.Flag != "Text" & TADA.ResultMeasureValueDataTypes.Flag != "Coerced to NA" & !is.na(TADA.ResultMeasureValue)) diff --git a/R/ResultFlagsDependent.R b/R/ResultFlagsDependent.R index f202f476..a4f89941 100644 --- a/R/ResultFlagsDependent.R +++ b/R/ResultFlagsDependent.R @@ -565,7 +565,7 @@ TADA_FindQCActivities <- function(.data, clean = FALSE, flaggedonly = FALSE) { #' prepare a dataframe for quantitative analyses. Ideally, this function should #' be run after other data cleaning, QA/QC, and harmonization steps are #' completed using other TADA package functions, or manually. Specifically, . -#' this function removes rows with "Text","Coerced to NA", and "Blank" +#' this function removes rows with "Text","Coerced to NA", and "NA - Not Applicable" #' in the TADA.ResultMeasureValueDataTypes.Flag column, or NA in the #' TADA.ResultMeasureValue column. #' @@ -593,7 +593,7 @@ TADA_AutoFilter <- function(.data) { "ActivityTypeCode" )) - autofilter <- dplyr::filter(.data, TADA.ResultMeasureValueDataTypes.Flag != "Blank" & + autofilter <- dplyr::filter(.data, TADA.ResultMeasureValueDataTypes.Flag != "NA - Not Applicable" & TADA.ResultMeasureValueDataTypes.Flag != "Text" & TADA.ResultMeasureValueDataTypes.Flag != "Coerced to NA" & !is.na(TADA.ResultMeasureValue)) # & @@ -651,6 +651,10 @@ TADA_AutoFilter <- function(.data) { #' #' # Remove all suspect samples: #' MeasureQualifierCode_clean <- TADA_FlagMeasureQualifierCode(Data_6Tribes_5y, clean = TRUE) +#' +#' # Remove all suspect samples and DO NOT include a new column with +#' # qualifier definitions (TADA.MeasureQualifierCode.Def): +#' MeasureQualifierCode_clean_nodefs <- TADA_FlagMeasureQualifierCode(Data_6Tribes_5y, clean = TRUE, define = FALSE) TADA_FlagMeasureQualifierCode <- function(.data, clean = FALSE, flaggedonly = FALSE, define = TRUE) { # check .data is data.frame TADA_CheckType(.data, "data.frame", "Input object") @@ -734,9 +738,9 @@ TADA_FlagMeasureQualifierCode <- function(.data, clean = FALSE, flaggedonly = FA missing_codes <- paste(missing_codes, collapse = ", ") print(paste0("MeasureQualifierCode column in dataset contains value(s) ", missing_codes, " which is/are not represented in the MeasureQualifierCode WQX domain table. These data records are placed under the TADA.MeasureQualifierCode.Flag: 'uncategorized'. Please contact TADA administrators to resolve.")) } - - # rename ResultMeasureQualifier NA values to Pass in TADA.MeasureQualifierCode.Flag column, not needed? - # flag.data["TADA.MeasureQualifierCode.Flag"][is.na(flag.data["MeasureQualifierCode"])] <- "Pass" + + # rename ResultMeasureQualifier NA values to Pass in TADA.MeasureQualifierCode.Flag column + flag.data["TADA.MeasureQualifierCode.Flag"][is.na(flag.data["MeasureQualifierCode"])] <- "NA - Not Applicable" # clean dataframe # if clean = FALSE, return full dataframe @@ -772,6 +776,7 @@ TADA_FlagMeasureQualifierCode <- function(.data, clean = FALSE, flaggedonly = FA } + final.data <- TADA_OrderCols(final.data) # return final dataframe return(final.data) } diff --git a/R/Utilities.R b/R/Utilities.R index 6e88073d..83e1585f 100644 --- a/R/Utilities.R +++ b/R/Utilities.R @@ -52,7 +52,7 @@ utils::globalVariables(c( "Target.Speciation", "TADA.NearbySiteGroups", "numres", "TADA.SingleOrgDupGroupID", "TADA.MeasureQualifierCode.Flag", "TADA.MeasureQualifierCode.Def", "MeasureQualifierCode", "value", "Flag_Column", "Data_NCTCShepherdstown_HUC12", "ActivityStartDateTime", "TADA.MultipleOrgDupGroupID", - "TADA.WQXVal.Flag" + "TADA.WQXVal.Flag", "Concat", ".", "MeasureQualifierCode.Split" )) @@ -150,7 +150,7 @@ TADA_AutoClean <- function(.data) { # Move detection limit value and unit to TADA Result Measure Value and Unit columns # Consider moving this to ID censored data in the future? - # this first row copies all over when result is blank but + # this first row copies all over when result is blank (NA) but # TADA.DetectionQuantitationLimitMeasure.MeasureValue is not and the # TADA.ResultMeasureValueDataTypes.Flag is not Text # Imp note: TADA result values are NA for text even though they are not NA in the original result value @@ -168,7 +168,7 @@ TADA_AutoClean <- function(.data) { .data$TADA.DetectionQuantitationLimitMeasure.MeasureUnitCode, .data$TADA.ResultMeasure.MeasureUnitCode) .data$TADA.ResultMeasureValueDataTypes.Flag <- ifelse( - .data$TADA.ResultMeasureValueDataTypes.Flag == "Blank" + .data$TADA.ResultMeasureValueDataTypes.Flag == "NA - Not Applicable" & !is.na(.data$TADA.DetectionQuantitationLimitMeasure.MeasureValue), "Result Value/Unit Copied from Detection Limit", .data$TADA.ResultMeasureValueDataTypes.Flag) @@ -384,7 +384,7 @@ TADA_ConvertSpecialChars <- function(.data, col) { if (is.numeric(chars.data$orig)) { clean.data <- chars.data %>% dplyr::mutate(flag = dplyr::case_when( - is.na(masked) ~ as.character("Blank"), + is.na(masked) ~ as.character("NA - Not Applicable"), TRUE ~ as.character("Numeric") )) } else { @@ -394,8 +394,8 @@ TADA_ConvertSpecialChars <- function(.data, col) { # of the specific type of character/data type clean.data <- chars.data %>% dplyr::mutate(flag = dplyr::case_when( - is.na(masked) ~ as.character("Blank"), - (masked == "ND") ~ as.character("Blank"), + is.na(masked) ~ as.character("NA - Not Applicable"), + (masked == "ND") ~ as.character("NA - Not Applicable"), (!is.na(suppressWarnings(as.numeric(masked)) == TRUE)) ~ as.character("Numeric"), (grepl("<", masked) == TRUE) ~ as.character("Less Than"), (grepl(">", masked) == TRUE) ~ as.character("Greater Than"), @@ -696,7 +696,7 @@ TADA_SubstituteDeprecatedChars <- function(.data) { # merge to dataset .data <- merge(.data, ref.table, all.x = TRUE) - # if CharacteristicName is deprecated and comparable name is not BLANK, use the provided Comparable.Name. Otherwise, keep TADA.CharacteristicName as-is. + # if CharacteristicName is deprecated and comparable name is not blank (NA), use the provided Comparable.Name. Otherwise, keep TADA.CharacteristicName as-is. .data$TADA.CharacteristicName <- ifelse(!is.na(.data$Char_Flag) & !.data$Comparable.Name %in% c(""), .data$Comparable.Name, .data$TADA.CharacteristicName) howmany <- length(.data$Char_Flag[!is.na(.data$Char_Flag)]) @@ -1221,7 +1221,7 @@ TADA_CheckRequiredFields <- function(.data) { #' prepare a dataframe for quantitative analyses. Ideally, this function should #' be run after other data cleaning, QA/QC, and harmonization steps are #' completed using other TADA package functions, or manually. Specifically, . -#' this function removes rows with "Text","Coerced to NA", and "Blank" +#' this function removes rows with "Text","Coerced to NA", and "NA - Not Applicable" #' in the TADA.ResultMeasureValueDataTypes.Flag column, or NA in the #' TADA.ResultMeasureValue column. #' @@ -1254,7 +1254,7 @@ TADA_AutoFilter <- function(.data) { start <- dim(.data)[1] # remove text, NAs and QC results - .data <- dplyr::filter(.data, TADA.ResultMeasureValueDataTypes.Flag != "Blank" & + .data <- dplyr::filter(.data, TADA.ResultMeasureValueDataTypes.Flag != "NA - Not Applicable" & TADA.ResultMeasureValueDataTypes.Flag != "Text" & TADA.ResultMeasureValueDataTypes.Flag != "Coerced to NA" & TADA.ActivityType.Flag == "Non_QC" & # filter out QA/QC ActivityTypeCode's diff --git a/data/Data_6Tribes_5y.rda b/data/Data_6Tribes_5y.rda index 3dc4039d..c7024590 100644 Binary files a/data/Data_6Tribes_5y.rda and b/data/Data_6Tribes_5y.rda differ diff --git a/data/Data_6Tribes_5y_Harmonized.rda b/data/Data_6Tribes_5y_Harmonized.rda index 050cffa7..cd271ad1 100644 Binary files a/data/Data_6Tribes_5y_Harmonized.rda and b/data/Data_6Tribes_5y_Harmonized.rda differ diff --git a/data/Data_NCTCShepherdstown_HUC12.rda b/data/Data_NCTCShepherdstown_HUC12.rda index 06d4b984..ab1b9636 100644 Binary files a/data/Data_NCTCShepherdstown_HUC12.rda and b/data/Data_NCTCShepherdstown_HUC12.rda differ diff --git a/data/Data_Nutrients_UT.rda b/data/Data_Nutrients_UT.rda index cbdda43e..d37a6465 100644 Binary files a/data/Data_Nutrients_UT.rda and b/data/Data_Nutrients_UT.rda differ diff --git a/inst/extdata/HarmonizationTemplate.csv b/inst/extdata/HarmonizationTemplate.csv index 0846a0f4..e38723e2 100644 --- a/inst/extdata/HarmonizationTemplate.csv +++ b/inst/extdata/HarmonizationTemplate.csv @@ -2,30 +2,30 @@ TADA.CharacteristicName,Target.TADA.CharacteristicName,TADA.CharacteristicNameAs AMMONIA,NA,NA,DISSOLVED,FILTERED,Assumes DISSOLVED and TOTAL SOLUBLE are equivalent to FILTERED. FILTERED is precise and preferred.,AS N,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen AMMONIA,NA,NA,DISSOLVED,FILTERED,Assumes DISSOLVED and TOTAL SOLUBLE are equivalent to FILTERED. FILTERED is precise and preferred.,AS NH3,AS N,Converts speciation and result values from AS NH3 to AS N,0.822,UG/L,MG/L,0.001,Nitrogen AMMONIA,NA,NA,DISSOLVED,FILTERED,Assumes DISSOLVED and TOTAL SOLUBLE are equivalent to FILTERED. FILTERED is precise and preferred.,AS NH4,AS N,Converts speciation and result values from AS NH4 to AS N,0.776,UG/L,MG/L,0.001,Nitrogen -AMMONIA,NA,NA,DISSOLVED,FILTERED,Assumes DISSOLVED and TOTAL SOLUBLE are equivalent to FILTERED. FILTERED is precise and preferred.,NA,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen +AMMONIA,NA,NA,DISSOLVED,FILTERED,Assumes DISSOLVED and TOTAL SOLUBLE are equivalent to FILTERED. FILTERED is precise and preferred.,NA,AS N,Assumes original speciation for AMMONIA is AS NH3 and converts to AS N,0.822,UG/L,MG/L,0.001,Nitrogen AMMONIA,NA,NA,FILTERABLE,FILTERED,"Assumes FILTERED, LAB and FILTERED, FIELD are equivalent to FILTERABLE and FILTERED. FILTERED is precise and preferred.",AS N,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen AMMONIA,NA,NA,FILTERABLE,FILTERED,"Assumes FILTERED, LAB and FILTERED, FIELD are equivalent to FILTERABLE and FILTERED. FILTERED is precise and preferred.",AS NH3,AS N,Converts speciation and result values from AS NH3 to AS N,0.822,UG/L,MG/L,0.001,Nitrogen AMMONIA,NA,NA,FILTERED,NA,NA,AS N,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen -AMMONIA,NA,NA,FILTERED,NA,NA,NA,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen +AMMONIA,NA,NA,FILTERED,NA,NA,NA,AS N,Assumes original speciation for AMMONIA is AS NH3 and converts to AS N,0.822,UG/L,MG/L,0.001,Nitrogen AMMONIA,NA,NA,"FILTERED, FIELD",FILTERED,"Assumes FILTERED, LAB and FILTERED, FIELD are equivalent to FILTERABLE and FILTERED. FILTERED is precise and preferred.",AS N,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen AMMONIA,NA,NA,"FILTERED, LAB",FILTERED,"Assumes FILTERED, LAB and FILTERED, FIELD are equivalent to FILTERABLE and FILTERED. FILTERED is precise and preferred.",AS N,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen -AMMONIA,NA,NA,INORGANIC,NA,NA,AS N,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen +AMMONIA,NA,NA,INORGANIC,FILTERED,NA,AS N,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen AMMONIA,NA,NA,SUPERNATE,NA,NA,AS N,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen AMMONIA,NA,NA,TOTAL,UNFILTERED,"Assumes AMMONIA, TOTAL, AS N is synonymous to AMMONIA, UNFILTERED, AS N.",AS N,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen AMMONIA,NA,NA,TOTAL,UNFILTERED,"Assumes AMMONIA, TOTAL, AS NH3 is synonymous to AMMONIA, UNFILTERED, AS N after conversion.",AS NH3,AS N,Converts speciation and result values from AS NH3 to AS N,0.822,UG/L,MG/L,0.001,Nitrogen AMMONIA,NA,NA,TOTAL,UNFILTERED,"Assumes AMMONIA, TOTAL, AS NH4 is synonymous to AMMONIA, UNFILTERED, AS N after conversion.",AS NH4,AS N,Converts speciation and result values from AS NH4 to AS N,0.776,UG/L,MG/L,0.001,Nitrogen AMMONIA,NA,NA,TOTAL,UNFILTERED,"Assumes AMMONIA, TOTAL is synonymous to AMMONIA, UNFILTERED, AS N.",NA,AS N,Assumes AS N,NA,UG/L,MG/L,0.001,Nitrogen AMMONIA,NA,NA,TOTAL RECOVERABLE,UNFILTERED,"Assumes AMMONIA, TOTAL RECOVERABLE, AS N is synonymous to AMMONIA, UNFILTERED, AS N.",AS N,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen -AMMONIA,NA,NA,TOTAL SOLUBLE,FILTERED,Assumes DISSOLVED and TOTAL SOLUBLE are equivalent to FILTERED. FILTERED is precise and preferred.,NA,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen +AMMONIA,NA,NA,TOTAL SOLUBLE,FILTERED,Assumes DISSOLVED and TOTAL SOLUBLE are equivalent to FILTERED. FILTERED is precise and preferred.,NA,AS N,Assumes original speciation for AMMONIA is AS NH3 and converts to AS N,0.822,UG/L,MG/L,0.001,Nitrogen AMMONIA,NA,NA,UNFILTERED,NA,NA,AS N,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen AMMONIA,NA,NA,UNFILTERED,NA,NA,AS NH3,AS N,Converts speciation and result values from AS NH3 to AS N,0.822,UG/L,MG/L,0.001,Nitrogen -AMMONIA,NA,NA,UNFILTERED,NA,NA,NA,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen +AMMONIA,NA,NA,UNFILTERED,NA,NA,NA,AS N,Assumes original speciation for AMMONIA is AS NH3 and converts to AS N,0.822,UG/L,MG/L,0.001,Nitrogen AMMONIA,NA,NA,NA,NA,NA,AS N,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen AMMONIA,NA,NA,NA,NA,NA,AS NH3,AS N,Converts speciation and result values from AS NH3 to AS N,0.822,UG/L,MG/L,0.001,Nitrogen AMMONIA-NITROGEN,AMMONIA,Assumes AMMONIA-NITROGEN is synonymous to AMMONIA.,DISSOLVED,FILTERED,Assumes DISSOLVED and TOTAL SOLUBLE are equivalent to FILTERED. FILTERED is precise and preferred.,AS N,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen AMMONIA-NITROGEN,AMMONIA,Assumes AMMONIA-NITROGEN is synonymous to AMMONIA.,DISSOLVED,FILTERED,Assumes DISSOLVED and TOTAL SOLUBLE are equivalent to FILTERED. FILTERED is precise and preferred.,AS NH3,AS N,Converts speciation and result values from AS NH3 to AS N,0.822,UG/L,MG/L,0.001,Nitrogen AMMONIA-NITROGEN,AMMONIA,Assumes AMMONIA-NITROGEN is synonymous to AMMONIA.,DISSOLVED,FILTERED,Assumes DISSOLVED and TOTAL SOLUBLE are equivalent to FILTERED. FILTERED is precise and preferred.,AS NH4,AS N,Converts speciation and result values from AS NH4 to AS N,0.776,UG/L,MG/L,0.001,Nitrogen -AMMONIA-NITROGEN,AMMONIA,Assumes AMMONIA-NITROGEN is synonymous to AMMONIA.,DISSOLVED,FILTERED,Assumes DISSOLVED and TOTAL SOLUBLE are equivalent to FILTERED. FILTERED is precise and preferred.,NA,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen +AMMONIA-NITROGEN,AMMONIA,Assumes AMMONIA-NITROGEN is synonymous to AMMONIA.,DISSOLVED,FILTERED,Assumes DISSOLVED and TOTAL SOLUBLE are equivalent to FILTERED. FILTERED is precise and preferred.,NA,AS N,NA,NA,UG/L,MG/L,0.001,Nitrogen AMMONIA-NITROGEN,AMMONIA,Assumes AMMONIA-NITROGEN is synonymous to AMMONIA.,"FILTERED, LAB",FILTERED,"Assumes FILTERED, LAB and FILTERED are funtionally equivalent for data use.",AS N,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen AMMONIA-NITROGEN,AMMONIA,Assumes AMMONIA-NITROGEN is synonymous to AMMONIA.,SUPERNATE,NA,NA,AS N,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen AMMONIA-NITROGEN,AMMONIA,Assumes AMMONIA-NITROGEN is synonymous to AMMONIA.,TOTAL,UNFILTERED,"Assumes AMMONIA-NITROGEN, TOTAL is synonymous to AMMONIA, UNFILTERED",AS N,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen @@ -44,7 +44,7 @@ AMMONIUM,NA,NA,DISSOLVED,FILTERED,Assumes DISSOLVED and TOTAL SOLUBLE are equiva AMMONIUM,NA,NA,FILTERABLE,FILTERED,"Assumes FILTERED, LAB and FILTERED, FIELD are equivalent to FILTERABLE and FILTERED. FILTERED is precise and preferred.",AS NH4,AS N,Converts speciation and result values from AS NH4 to AS N,0.776,UG/L,MG/L,0.001,Nitrogen AMMONIUM,NA,NA,FILTERED,NA,NA,AS N,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen AMMONIUM,NA,NA,"FILTERED, LAB",FILTERED,"Assumes FILTERED, LAB and FILTERED, FIELD are equivalent to FILTERABLE and FILTERED. FILTERED is precise and preferred.",AS N,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen -AMMONIUM,NA,NA,TOTAL,UNFILTERED,"Assumes AMMONIA AND AMMONIUM, TOTAL is synonymous to AMMONIA AND AMMONIUM, UNFILTERED.",NA,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen +AMMONIUM,NA,NA,TOTAL,UNFILTERED,"Assumes AMMONIA AND AMMONIUM, TOTAL is synonymous to AMMONIA AND AMMONIUM, UNFILTERED.",NA,AS N,Assumes original speciation for AMMONIUM is AS NH4 and converts values to AS N,0.776,UG/L,MG/L,0.001,Nitrogen AMMONIUM,NA,NA,UNFILTERED,NA,NA,AS N,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen AMMONIUM ,NA,NA,FILTERABLE,FILTERED,"Assumes FILTERED, LAB and FILTERED, FIELD are equivalent to FILTERABLE and FILTERED. FILTERED is precise and preferred.",AS N,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen AMMONIUM ,NA,NA,FILTERED,NA,NA,AS N,NA,NA,NA,UG/L,MG/L,0.001,Nitrogen diff --git a/inst/extdata/WQXCharacteristicRef.csv b/inst/extdata/WQXCharacteristicRef.csv index 85481ed7..481d1aed 100644 --- a/inst/extdata/WQXCharacteristicRef.csv +++ b/inst/extdata/WQXCharacteristicRef.csv @@ -3620,6 +3620,9 @@ d","Deprecated","SULFLURAMID" "1H, 1H, 2H, 2H-[1,2-13C2]perfluorodecylphosphate","Accepted","" "1H, 1H, 2H, 2H-[1,2-13C2]perfluorodecylphosphate ion(1-)","Accepted","" "1H,10H-Perfluorodecane","Accepted","" +"1H,1H, 2H, 2H-Perfluorodecane sulfonic acid","Accepted","" +"1H,1H, 2H, 2H-Perfluorohexane sulfonic acid","Accepted","" +"1H,1H, 2H, 2H-Perfluorooctane sulfonic acid","Accepted","" "1H,1H,10H,10H-Perfluorodecane-1,10-diol","Accepted","" "1H,1H,11H,11H-Perfluorotetraethylene glycol","Accepted","" "1H,1H,1H,2H-Perfluoro-2-heptanol","Accepted","" @@ -4654,6 +4657,7 @@ d","Deprecated","SULFLURAMID" "2,3,3-Trifluoro-3-[perfluoro-3-(methoxy)propoxy]propanoic acid","Accepted","" "2,3,3-Trifluorobicyclo[2.2.1]hept-5-en-2-ol","Accepted","" "2,3,3-Trimethylpentane","Accepted","" +"2,3,3-trichloroprop-2-ene-1-SA","Accepted","" "2,3,3-tris(4-methoxyphenyl)-N,N-dimethylprop-2-en-1-amine","Accepted","" "2,3,3`,4,4`,5,5`,6-Octabromodiphenyl ether","Accepted","" "2,3,4',5,6-Pentachlorobiphenyl","Accepted","" @@ -5066,6 +5070,7 @@ d","Deprecated","SULFLURAMID" "2-(1-Ethenoxy-1,1,2,3,3,3-hexafluoropropan-2-yl)oxy-1,1,2,2-tetrafluoroethanesulfonyl fluoride","Accepted","" "2-(1-Ethoxy-1,2,2,3,3,4,4,4-octafluorobutyl)aniline","Accepted","" "2-(1-Hydroxyethyl)-6-methylaniline","Accepted","" +"2-(1-hydroxyethyl)-6-methylaniline (HEMA)","Accepted","" "2-(11-[Chloro(difluoro)methyl]perfluorododecyl)ethyl prop-2-enoate","Accepted","" "2-(2,2,3,3,3-Pentafluoropropanoyl)cyclohexan-1-one","Accepted","" "2-(2,2,3,3,3-Pentafluoropropoxy)ethan-1-ol","Accepted","" @@ -6556,6 +6561,7 @@ d","Deprecated","SULFLURAMID" "2?{Dimethyl[3? (3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13,14,14,15,15,16,16,16?nonacosafluorohexadecanesulfonamido)propyl]azaniumyl}acetate","Accepted","" "2?{Dimethyl[3? (3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13,14,14,15,15,16,16,17,17,18,18,18? tritriacontafluorooctadecanesulfonamido)propyl]azaniumyl}acetate","Accepted","" "2H,2H,3H,3H-Perfluorooctanoate","Accepted","" +"2H,2H,3H,3H-Perfluorooctanoic acid","Accepted","" "2H,6H-[1,2]Iodoxolo[4,5,1-hi][1,2]benziodoxole, 4-methyl-2,2,6,6-tetrakis(trifluoromethyl)-","Accepted","" "2H-1,3-Dioxole, 4-chloro-2,2-bis(trifluoromethyl)-","Accepted","" "2H-1,3-Dioxole, 4-fluoro-2,2-bis(trifluoromethyl)-","Accepted","" @@ -7400,8 +7406,10 @@ d","Deprecated","SULFLURAMID" "3-Pentene-2,2-diol,1,1,1,3,5,5,5-heptafluoro-4-(trifluoromethyl)-","Accepted","" "3-Pentyn-1-ol","Accepted","" "3-Perfluoroheptyl propanoate","Accepted","" +"3-Perfluoroheptyl propanoic acid","Accepted","" "3-Perfluorohexyl-2-hydroxypropyl acrylate","Accepted","" "3-Perfluoropropyl propanoate","Accepted","" +"3-Perfluoropropyl propanoic acid","Accepted","" "3-Phenoxybenzenemethanol","Accepted","" "3-Phenoxybenzoic acid","Accepted","" "3-Phenoxybenzoic acid-13C6","Accepted","" @@ -8117,6 +8125,7 @@ d","Deprecated","SULFLURAMID" "4-Chlorobenzenediazonium perfluorobutanoate perfluorobutanoic acid (1:1:1)","Accepted","" "4-Chlorobenzyl methyl sulfone","Accepted","" "4-Chlorobenzyl methyl sulfoxide","Accepted","" +"4-Chlorobenzylmethyl sulfoxide","Accepted","" "4-Chlorobenzylmethylsulfone","Accepted","" "4-Chlorobiphenyl","Accepted","" "4-Chlorobiphenyl-C13","Accepted","" @@ -8182,6 +8191,7 @@ d","Deprecated","SULFLURAMID" "4-Hydroxy-3-(hydroxyimino)-4-(nonafluorobutyl)-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-one","Accepted","" "4-Hydroxy-4-methyl-2-pentanone","Accepted","" "4-Hydroxy-chlorothalonil","Accepted","" +"4-Hydroxy-tert-fluometuron","Accepted","" "4-Hydroxybenzophenone","Accepted","" "4-Hydroxybenzotriazole","Accepted","" "4-Hydroxychlorothalonil","Accepted","" @@ -8912,6 +8922,7 @@ d","Deprecated","SULFLURAMID" "9-(Perfluoromethoxy)perfluorononane sulfonic acid","Accepted","" "9-Chloro-perfluorononanoic acid","Accepted","" "9-Chlorohexadecafluoro-3-oxanonane-1-sulfonate","Accepted","" +"9-Chlorohexadecafluoro-3-oxanonane-1-sulfonic acd","Accepted","" "9-Chlorohexadecafluoro-3-oxanonane-1-sulfonic acid","Accepted","" "9-Chlorohexadecafluoro-3-oxanonnane-1-sulfonate","Accepted","" "9-Diethoxyphosphoryl-1,1,1,2,2,3,3,4,4,5,5,6,6,7,7-pentadecafluoro-9-iodononane","Accepted","" @@ -9188,6 +9199,7 @@ d","Deprecated","SULFLURAMID" "Acetochlor ESA","Accepted","" "Acetochlor OA","Accepted","" "Acetochlor OXA","Accepted","" +"Acetochlor SAA","Accepted","" "Acetochlor oxanilic acid","Accepted","" "Acetochlor oxanilic acid-d5","Accepted","Acetochlor OA" "Acetochlor sulfinylacetic acid","Accepted","" @@ -9299,6 +9311,10 @@ d","Deprecated","SULFLURAMID" "Aeromonas hydrophila","Accepted","" "Aerosols, (nonflammable)","Accepted","" "Afidopyropen","Accepted","" +"Aflatoxin B1","Accepted","" +"Aflatoxin B2","Accepted","" +"Aflatoxin G1","Accepted","" +"Aflatoxin G2 ","Accepted","" "Aflatoxins","Accepted","" "Age","Accepted","" "Age, Otoliths (Fish)","Accepted","" @@ -9311,6 +9327,7 @@ d","Deprecated","SULFLURAMID" "Alachlor","Accepted","" "Alachlor ESA","Accepted","" "Alachlor OA","Accepted","" +"Alachlor SAA","Accepted","" "Alachlor oxanilic acid","Accepted","" "Alachlor sulfinylacetic acid","Accepted","" "Alachlor sulfynilacetic acid","Accepted","" @@ -9527,6 +9544,7 @@ d","Deprecated","SULFLURAMID" "Anabaenopeptins","Accepted","" "Anabasine","Accepted","" "Anatoxin","Accepted","" +"Anatoxin a","Accepted","" "Anatoxin-A","Accepted","" "Anatoxin-a equivalents","Accepted","" "Androstane","Accepted","" @@ -10201,6 +10219,7 @@ d","Deprecated","SULFLURAMID" "Benzene, 1,2-dibromo-4-(3-bromophenoxy)-***retired***use 3,3',4-TRBDE","Deprecated","3,3',4-TRBDE" "Benzene, 1,2-dibromo-4-(4-bromophenoxy)-***retired***use 3,4,4'-TRBDE","Deprecated","3,4,4'-TRBDE" "Benzene, 1,2-dibromo-4-phenoxy-***retired**use 3,4-DIBDE","Deprecated","3,4-DIBDE" +"Benzene, 1,2-dichloro-4-isocyanato-","Accepted","" "Benzene, 1,3,5-tribromo-2-(2,4,5-tribromophenoxy)-***retired***use BDE-154","Deprecated","BDE-154" "Benzene, 1,3,5-tribromo-2-(2,4,6-tribromophenoxy)-***retired***use BDE-155","Deprecated","BDE-155" "Benzene, 1,3,5-tribromo-2-(2,4-dibromophenoxy)-***retired***use BDE-100","Deprecated","BDE-100" @@ -11528,8 +11547,8 @@ d","Deprecated","SULFLURAMID" "Chlorophenol","Accepted","" "Chlorophyll","Accepted","" "Chlorophyll a","Accepted","" -"Chlorophyll a (probe relative fluorescence)","Accepted","" -"Chlorophyll a (probe)","Accepted","" +"Chlorophyll a (probe relative fluorescence)","Accepted","CHLOROPHYLL A" +"Chlorophyll a (probe)","Accepted","CHLOROPHYLL A" "Chlorophyll a (probe) concentration, Chlorophyte (green algae)","Accepted","" "Chlorophyll a (probe) concentration, Cryptophyta (cryptophytes)","Accepted","" "Chlorophyll a (probe) concentration, Cyanobacteria (bluegreen)","Accepted","" @@ -11998,8 +12017,10 @@ d","Deprecated","SULFLURAMID" "Cyclopentane, 1,1,2,2,3,3,4,4-octafluoro","Accepted","" "Cyclopentane, 1,1,2,2,3,3,4-heptafluoro-","Accepted","" "Cyclopentane, 1,1,2,2,3,3-hexafluoro-","Accepted","" +"Cyclopentane, 1,2,3-trimethyl-, (1.alpha.,2.alpha.,3.beta.)-","Accepted","" "Cyclopentane, 1,2,4-trimethyl-, (1.alpha.,2.alpha.,4.alpha.)-","Accepted","" "Cyclopentane, 1,2-dimethyl-, (1R,2R)-rel-","Accepted","" +"Cyclopentane, 1-ethyl-2-methyl-, cis-","Accepted","" "Cyclopentane, 1-ethyl-3-methyl-, (1R,3S)-rel-","Accepted","" "Cyclopentane, octafluoro(hexafluorocyclobutylidene)-","Accepted","" "Cyclopentane, octafluorobis(trifluoromethyl)-","Accepted","" @@ -12027,6 +12048,7 @@ d","Deprecated","SULFLURAMID" "Cyclopropane, (1,1,2,3,3,3-hexafluoropropyl)-","Accepted","" "Cyclopropane, 1,1,2,2,3,3-hexafluoro-","Accepted","" "Cyclopropane, 1,1,2,2-tetrafluoro-","Accepted","" +"Cyclopropane, 1,1,2-trimethyl-","Accepted","" "Cyclopropane, 1-(2-bromoethyl)-1,2,2,3,3-pentafluoro-","Accepted","" "Cyclopropane, ethyl-","Accepted","" "Cyclopropane, pentafluoro(1,1,2,2,3,3,3-heptafluoropropoxy)-","Accepted","" @@ -12251,6 +12273,7 @@ d","Deprecated","SULFLURAMID" "Demeclocycline","Accepted","" "Demethyl fluometuron","Accepted","" "Demethyl hexazinone B","Accepted","" +"Demethyl norflurazon","Accepted","" "Demethylfluometuron","Accepted","" "Demeton","Accepted","" "Demeton-O","Accepted","" @@ -12303,6 +12326,7 @@ d","Deprecated","SULFLURAMID" "Desethyl-desisopropyl Atrazine***retired***use 2-Chloro-4,6-diamino-s-triazine","Deprecated","2-CHLORO-4,6-DIAMINO-S-TRIAZINE" "Desethylatrazine (iso-propyl-D7)","Accepted","" "Desethylatrazine***retired***use 2-Chloro-4-isopropylamino-6-amino-s-triazine","Deprecated","2-CHLORO-4-ISOPROPYLAMINO-6-AMINO-S-TRIAZINE" +"Desiodo flubendiamide","Accepted","" "Desipramine","Accepted","" "Desisopropyl Atrazine-d5","Accepted","" "Desisopropyl atrazine***retired***use 2-Choro-6-ethylamino-4-amino-s-triazine","Deprecated","2-CHORO-6-ETHYLAMINO-4-AMINO-S-TRIAZINE" @@ -12602,6 +12626,7 @@ d","Deprecated","SULFLURAMID" "Diisopropanolamine","Accepted","" "Diisopropyl adipate","Accepted","" "Diisopropyl methylphosphonate","Accepted","" +"Diketonitrile isoxaflutole","Accepted","" "Dilantin","Accepted","" "Diltiazem","Accepted","" "Diltiazem hydrochloride","Accepted","" @@ -12613,6 +12638,7 @@ d","Deprecated","SULFLURAMID" "Dimethenamid","Accepted","" "Dimethenamid ESA","Accepted","" "Dimethenamid OA","Accepted","" +"Dimethenamid SAA","Accepted","" "Dimethenamid oxanilic acid","Accepted","" "Dimethenamid sulfinylacetic acid","Accepted","" "Dimethenamid-P","Accepted","" @@ -12859,6 +12885,7 @@ d","Deprecated","SULFLURAMID" "Dysprosium","Accepted","" "EDDP perchlorate","Accepted","" "EPT Index","Accepted","" +"EPTC R248722","Accepted","" "EPTC degradate R248722","Accepted","" "EPTC-d14","Accepted","" "EPTC-d14 (dipropyl-d14)","Accepted","" @@ -13432,6 +13459,7 @@ d","Deprecated","SULFLURAMID" "Famphur","Accepted","" "Farnesol","Accepted","" "Fast Riffle","Accepted","" +"Fathead minnow, larval growth and survival","Accepted","" "Fatty acids, C18-unsatd., dimers, 2-[methyl[(perfluoro-C4-8-alkyl)sulfonyl]amino]ethyl esters","Accepted","" "Fatty acids, C18-unsatd., dimers, diisocyanates, polymers with 2,3-bis(.gamma.-.omega.-perfluoro-C4-18-alkyl)-1,4-butanediol, 1,6-diisocyanato-2,2,4(or 2,4,4)-trimethylhexane and 2,2'-(methylimino)bis[ethanol]","Accepted","" "Fatty acids, C18-unsatd., trimers, 2-[[(1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,8-heptadecafluorooctyl)sulfonyl]methylamino]ethyl esters","Accepted","" @@ -13722,6 +13750,9 @@ d","Deprecated","SULFLURAMID" "Fulvestrant","Accepted","" "Fulvestrant 3-|A-D-Glucuronide","Accepted","" "Fulvestrant, 7beta-","Accepted","" +"Fumonisin B1","Accepted","" +"Fumonisin B2","Accepted","" +"Fumonisin B3","Accepted","" "Fungi","Accepted","" "Furan","Accepted","" "Furan, 2,2,3,3,4,4,5,5-octafluorotetrahydro-","Accepted","" @@ -13928,6 +13959,7 @@ d","Deprecated","SULFLURAMID" "HFE-347pcf2","Accepted","" "HFE-356mec3","Accepted","" "HFE-356mmz1","Accepted","" +"HT-2 toxin","Accepted","" "HUMM2 DNA Marker","Accepted","" "HUMM2 DNA Marker (purified)","Accepted","" "Habitat Cover Extent","Accepted","" @@ -14217,6 +14249,11 @@ d","Deprecated","SULFLURAMID" "Hexatriacontane","Accepted","" "Hexavalent chromium compounds","Accepted","" "Hexazinone","Accepted","" +"Hexazinone TP C","Accepted","" +"Hexazinone TP D","Accepted","" +"Hexazinone TP E","Accepted","" +"Hexazinone TP F","Accepted","" +"Hexazinone TP G","Accepted","" "Hexazinone Transformation Product C","Accepted","" "Hexazinone Transformation Product D","Accepted","" "Hexazinone Transformation Product E","Accepted","" @@ -14355,6 +14392,7 @@ d","Deprecated","SULFLURAMID" "Hydrothol 191","Accepted","" "Hydroxide","Accepted","" "Hydroxy didemethyl fluometuron","Accepted","" +"Hydroxy mono demethyl fluometuron","Accepted","" "Hydroxy monodemethyl fluometuron","Accepted","" "Hydroxy-amitriptyline, 10-","Accepted","" "Hydroxy-ibuprofen, 2-","Accepted","" @@ -14623,6 +14661,7 @@ d","Deprecated","SULFLURAMID" "Isovaleric acid","Accepted","" "Isoxaben","Accepted","" "Isoxaflutole","Accepted","" +"Isoxaflutole acid RPA 203328","Accepted","" "Isoxaflutole acid metabolite","Accepted","" "Isoxaflutole methylbenzoate","Accepted","" "Ivermectin","Accepted","" @@ -14853,6 +14892,7 @@ d","Deprecated","SULFLURAMID" "Light attenuation, depth at 10%","Accepted","" "Light attenuation, depth at 50%","Accepted","" "Light attenuation, depth at 99%","Accepted","" +"Light availability","Accepted","" "Light scatter","Accepted","" "Light transmissivity at measurement depth","Accepted","" "Light, (PAR at depth/PAR at surface) x 100","Accepted","" @@ -15413,6 +15453,7 @@ d","Deprecated","SULFLURAMID" "Methyl((nonafluorobutyl)sulfonyl)azanide","Accepted","" "Methyl(3,3,4,4,5,5,6,6,6-nonafluorohexyl)silane","Accepted","" "Methyl-(7,7,8,8,9,9,10,10,10-nonafluorodecyl)amine","Accepted","" +"Methyl-1H-benzotriazole","Accepted","" "Methyl-bis[(1,2,2,3,3,4,4,5,5,6,6-undecafluorocyclohexyl)oxy]silane","Accepted","" "Methylacenaphthene","Accepted","" "Methylamine","Accepted","" @@ -16259,7 +16300,9 @@ d","Deprecated","SULFLURAMID" "N-ethyl-d5-perfluoro-1-octanesulfonamidoacetic acid","Accepted","" "N-ethylperfluoro-1-octanesulfonamide***retired***use Sulfluramid","Deprecated","SULFLURAMID" "N-ethylsulfonylglycine, perfluoroalkyl (C5-10), potassium salt","Accepted","" +"N-methyl perfluorooctanesulfonamide","Accepted","" "N-methyl perfluorooctanesulfonamidoacetic acid","Accepted","" +"N-methyl perfluorooctanesulfonamidoethanol","Accepted","" "N-methyl-N-[(3-octadecyl-2-oxo-4-oxazolidinyl)methyl]perfluorooctanesulfonamide","Accepted","" "N-methyl-d3-perfluoro-1-octanesulfonamidoacetic acid","Accepted","" "N-methylperfluoro-1-octanesulfonamide","Accepted","" @@ -16468,6 +16511,7 @@ d","Deprecated","SULFLURAMID" "Nonafluoro(nitroso)cyclopentane","Accepted","" "Nonafluoro(trifluoromethoxy)cyclopentane","Accepted","" "Nonafluoro-3,6-dioxaheptanate","Accepted","" +"Nonafluoro-3,6-dioxaheptanoic acid","Accepted","" "Nonafluorobutan-1-amine","Accepted","" "Nonafluorobutane-1-sulfinic acid","Accepted","" "Nonafluorobutane-1-sulfonoperoxoic acid","Accepted","" @@ -16528,6 +16572,9 @@ d","Deprecated","SULFLURAMID" "Nonyl sulfate","Accepted","" "Nonylphenol","Accepted","" "Nonylphenol diethoxylate","Accepted","" +"Nonylphenol, diethoxy- (total, NPEO2)","Accepted","" +"Nonylphenol, diethoxylate- (total, NPEO2)","Accepted","" +"Nonylphenol, monoethoxy- (total NPEO1)","Accepted","" "Nonylphenoxyacetic acid","Accepted","" "Norbuprenorphine","Accepted","" "Norcarfentanil","Accepted","" @@ -16597,6 +16644,8 @@ d","Deprecated","SULFLURAMID" "O-Ethyl O-methyl S-propyl phosphorothioate","Accepted","" "O-Ethyl S-methyl S-propyl phosphorodithioate","Accepted","" "O-Ethyl S-propyl phosphorothioate","Accepted","" +"O-Ethyl-S-methyl-S-propyl phosphorodithioate","Accepted","" +"O-Ethyl-S-propyl phosphorothioate","Accepted","" "O-xylene & N-nonane","Accepted","" "Observed Recreational Use - Boating (Y/N) (choice list)","Accepted","" "Observed Recreational Use - Fishing (Y/N) (choice list)","Accepted","" @@ -16604,6 +16653,8 @@ d","Deprecated","SULFLURAMID" "Observed Recreational Use - Swimming (Y/N) (choice list)","Accepted","" "Observed flow (choice list)","Accepted","" "Obstructions (Y/N) (choice list)","Accepted","" +"Ochratoxin A","Accepted","" +"Ochratoxin B","Accepted","" "Octabromodiphenyl ether","Accepted","" "Octachlorobiphenyl","Accepted","" "Octachlorocyclopentene","Accepted","" @@ -16695,6 +16746,9 @@ d","Deprecated","SULFLURAMID" "Octylphenol","Accepted","" "Octylphenol diethoxylate","Accepted","" "Octylphenol monoethoxylate***retired***use 2-(4-Octylphenoxy)ethanol","Deprecated","2-(4-OCTYLPHENOXY)ETHANOL" +"Octylphenol, diethoxy- (OPEO2)","Accepted","" +"Octylphenol, diethoxylate- (OPEO2)","Accepted","" +"Octylphenol, monoethoxylate- (OPEO1)","Accepted","" "Ocytyl salicylate","Accepted","" "Odor (adverse or offensive) (Y/N) (choice list)","Accepted","" "Odor severity (choice list)","Accepted","" @@ -16843,7 +16897,7 @@ d","Deprecated","SULFLURAMID" "Oxydemeton-methyl","Accepted","" "Oxydisulfoton","Accepted","" "Oxyfluorfen","Accepted","" -"Oxygen","Accepted","" +"Oxygen","Accepted","OXYGEN" "Oxygen 18/oxygen 16 ratio in sulfate","Accepted","" "Oxygen Delta 18","Accepted","" "Oxygen plus argon","Accepted","" @@ -17514,6 +17568,7 @@ d","Deprecated","SULFLURAMID" "Perfluoro-1-butanesulfinic acid ammonium","Accepted","" "Perfluoro-1-butanesulfonyl chloride","Accepted","" "Perfluoro-1-decanesulfonamide","Accepted","" +"Perfluoro-1-decanesulfonic acid","Accepted","" "Perfluoro-1-decanol","Accepted","" "Perfluoro-1-decene","Accepted","" "Perfluoro-1-dodecanesulfonamide","Accepted","" @@ -17526,7 +17581,9 @@ d","Deprecated","SULFLURAMID" "Perfluoro-1-iodoalkane (C6-C8)","Accepted","" "Perfluoro-1-methyl-3-propylcyclohexane","Accepted","" "Perfluoro-1-nonanesulfonamide","Accepted","" +"Perfluoro-1-nonanesulfonic acid","Accepted","" "Perfluoro-1-octanesulfinic acid","Accepted","" +"Perfluoro-1-octanesulfonamide","Accepted","" "Perfluoro-1-octanesulfonyl chloride","Accepted","" "Perfluoro-1-propanesulfinic acid sodium","Accepted","" "Perfluoro-1-propanol","Accepted","" @@ -17997,6 +18054,7 @@ d","Deprecated","SULFLURAMID" "Perfluoropentane sulfonic anhydride","Accepted","" "Perfluoropentane-1-sulfinic acid","Accepted","" "Perfluoropentanesulfonate","Accepted","" +"Perfluoropentanesulfonic acid","Accepted","" "Perfluoropentanoate","Accepted","" "Perfluoropentanoate (anionic form)","Accepted","" "Perfluoropentanoic acid","Accepted","" @@ -18117,6 +18175,7 @@ d","Deprecated","SULFLURAMID" "Phenobarbital-D5","Accepted","" "Phenol","Accepted","" "Phenol dehydroabietylamine salt","Accepted","" +"Phenol, (1,1-dimethylethyl)-4-methoxy- (9CI)","Accepted","" "Phenol, 2,2'-[(1R,2R)-1,2-cyclohexanediylbis[(E)-nitrilomethylidyne]]bis[6-(1,1-dimethylethyl)-4-(heptadecafluorooctyl)-","Accepted","" "Phenol, 2,3-dichloro-6-methoxy-","Accepted","" "Phenol, 2,4-bis(1,1-dimethylethyl)-6-methyl-","Accepted","" @@ -18560,6 +18619,7 @@ d","Deprecated","SULFLURAMID" "Poly(oxy-1,2-ethanediyl), .alpha.-sulfo-.omega.-[2-[[(heptadecafluorooctyl)sulfonyl] propylamino]ethoxy]-","Accepted","" "Poly(oxy-1,2-ethanediyl), ?-[3,4,4,4-tetrafluoro-2-[1,2,2,2-tetrafluoro-1-(trifluoromethyl)ethyl]-1,3-bis(trifluoromethyl)-1-butenyl]-?-[[3,4,4,4-tetrafluoro-2-[1,2,2,2-tetrafluoro-1-(trifluoromethyl)ethyl]-1,3-bis(triSfluoromethyl)-1-butenyl]oxy]-","Accepted","" "Poly(oxy-1,2-ethanediyl), ?-methyl-?-[[3,4,4,4-tetrafluoro-2-[1,2,2,2-tetrafluoro-1-(trifluoromethyl)ethyl]-1,3-bis(trifluoromethyl)-1-butenyl]oxy]-","Accepted","" +"Poly(oxy-1,2-ethanediyl), a-(4-octylphenyl)-w-hydroxy- (9CI)","Accepted","" "Poly(oxy-1,2-ethanediyl),a-[5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,13,13,13-octadecafluoro-2-hydroxy-12-(trifluoromethyl)tridecyl]-w-hydroxy-","Accepted","" "Poly(propene-co-tetrafluoroethene-co-3,3,3-trifluoroprop-1-ene)","Accepted","" "Poly(propene/tetrafluoroethylene/3,3,3-trifluoropropene)","Accepted","" @@ -20675,10 +20735,12 @@ d","Deprecated","SULFLURAMID" "Tebuconazole-d6","Accepted","" "Tebufenozide","Accepted","" "Tebupirimfos","Accepted","" +"Tebupirimfos oxon","Accepted","" "Tebupirimphos oxon","Accepted","" "Tebuthiuron","Accepted","" "Tebuthiuron TP 104","Accepted","" "Tebuthiuron TP 106","Accepted","" +"Tebuthiuron TP 108","Accepted","" "Tebuthiuron TP 109 (OH)","Accepted","" "Tebuthiuron Transformation Product 108","Accepted","" "Tebuthiuron Transformation Product 109","Accepted","" @@ -20701,7 +20763,7 @@ d","Deprecated","SULFLURAMID" "Temephos","Accepted","" "Temephos sulfoxide","Accepted","" "Temoridae","Accepted","" -"Temperature","Accepted","" +"Temperature","Accepted","TEMPERATURE, WATER" "Temperature difference","Accepted","" "Temperature, air","Accepted","" "Temperature, dew point air","Accepted","" @@ -20710,9 +20772,10 @@ d","Deprecated","SULFLURAMID" "Temperature, sediment","Accepted","" "Temperature, soil","Accepted","" "Temperature, tissue","Accepted","" -"Temperature, water","Accepted","" +"Temperature, water","Accepted","TEMPERATURE, WATER" "Temperature, wet bulb","Accepted","" "Teniposide","Accepted","" +"Teratogenicity","Accepted","" "Terbacil","Accepted","" "Terbium","Accepted","" "Terbium, tris(6,6,7,7,8,8,8-heptafluoro-2,2-dimethyl-3,5-octanedionato-.kappa.O3,.kappa.O5)-","Accepted","" @@ -21657,6 +21720,7 @@ d","Deprecated","SULFLURAMID" "Volume Storage","Accepted","" "Volume settled","Accepted","" "Volume, total","Accepted","" +"Vomitoxin","Accepted","" "Vortioxetine","Accepted","" "Warfarin","Accepted","" "Warfarin-d5","Accepted","" @@ -22072,6 +22136,7 @@ d","Deprecated","SULFLURAMID" "hosphoric acid, methyl bis(2,2,3,3-tetrafluoropropyl) ester","Accepted","" "human-specific Bacteroides species","Accepted","" "hydrogen isotopes of water (d2H)","Accepted","" +"larval growth and survival","Accepted","" "m and p-Cresol","Accepted","" "m(and p)-Ethyltoluene","Accepted","" "m,p-Cresol","Accepted","" @@ -22240,8 +22305,10 @@ d","Deprecated","SULFLURAMID" "relative biovolume","Accepted","" "relative entity density","Accepted","" "sec-Acetochlor oxanilic acid","Accepted","" +"sec-Acetochlor-OA","Accepted","" "sec-Alachlor oxanilic acid","Accepted","" "sec-Alachlor sulfonic acid","Accepted","" +"sec-Alachlor-OA","Accepted","" "sec-Butylamine","Accepted","" "sec-Butylbenzene","Accepted","" "sec-Dichloropropane","Accepted","" @@ -22250,6 +22317,7 @@ d","Deprecated","SULFLURAMID" "syn-Dechlorane Plus","Accepted","" "syn-Dodecachloropentacyclooctadecadiene","Accepted","" "t-Stat","Accepted","" +"t-fluvalinate","Accepted","" "tert-Amyl ethyl ether","Accepted","" "tert-Amyl methyl ether","Accepted","" "tert-Amylbenzene","Accepted","" @@ -22372,3 +22440,4 @@ d","Deprecated","SULFLURAMID" "{[(Perfluorotridecyl)sulfonyl]amino}acetic acid","Accepted","" "{[(Perfluoroundecyl)sulfonyl]amino}-3-betaine","Accepted","" "{[(Perfluoroundecyl)sulfonyl]amino}acetic acid","Accepted","" +"λ-Cyhalothrin","Accepted","" diff --git a/man/TADA_AutoFilter.Rd b/man/TADA_AutoFilter.Rd index 0b403eff..710181ff 100644 --- a/man/TADA_AutoFilter.Rd +++ b/man/TADA_AutoFilter.Rd @@ -23,7 +23,7 @@ This function removes rows where the result value is not numeric to prepare a dataframe for quantitative analyses. Ideally, this function should be run after other data cleaning, QA/QC, and harmonization steps are completed using other TADA package functions, or manually. Specifically, . -this function removes rows with "Text","Coerced to NA", and "Blank" +this function removes rows with "Text","Coerced to NA", and "NA - Not Applicable" in the TADA.ResultMeasureValueDataTypes.Flag column, or NA in the TADA.ResultMeasureValue column. @@ -31,7 +31,7 @@ This function removes rows where the result value is not numeric to prepare a dataframe for quantitative analyses. Ideally, this function should be run after other data cleaning, QA/QC, and harmonization steps are completed using other TADA package functions, or manually. Specifically, . -this function removes rows with "Text","Coerced to NA", and "Blank" +this function removes rows with "Text","Coerced to NA", and "NA - Not Applicable" in the TADA.ResultMeasureValueDataTypes.Flag column, or NA in the TADA.ResultMeasureValue column. } diff --git a/man/TADA_FlagMeasureQualifierCode.Rd b/man/TADA_FlagMeasureQualifierCode.Rd index 7316e386..ce488f83 100644 --- a/man/TADA_FlagMeasureQualifierCode.Rd +++ b/man/TADA_FlagMeasureQualifierCode.Rd @@ -55,4 +55,8 @@ MeasureQualifierCode_flags_only <- TADA_FlagMeasureQualifierCode(Data_6Tribes_5y # Remove all suspect samples: MeasureQualifierCode_clean <- TADA_FlagMeasureQualifierCode(Data_6Tribes_5y, clean = TRUE) + +# Remove all suspect samples and DO NOT include a new column with +# qualifier definitions (TADA.MeasureQualifierCode.Def): +MeasureQualifierCode_clean_nodefs <- TADA_FlagMeasureQualifierCode(Data_6Tribes_5y, clean = TRUE, define = FALSE) } diff --git a/vignettes/TADAModule1.Rmd b/vignettes/TADAModule1.Rmd index 486511bc..a782b74a 100644 --- a/vignettes/TADAModule1.Rmd +++ b/vignettes/TADAModule1.Rmd @@ -75,7 +75,7 @@ remotes::install_github("USEPA/TADA", # when developing the package, update this chunk to the current repository branch, so it runs with all of the new features prior to a PR to develop remotes::install_github("USEPA/TADA", - ref = "12-7-23-cm", + ref = "cm-harmonize", dependencies = TRUE ) ``` @@ -754,15 +754,20 @@ TADA_FieldValuesPie(TADAProfileClean4, "MeasureQualifierCode") ``` MeasureQualifierCode definitions are available -[here](https://cdx.epa.gov/wqx/download/DomainValues/ResultMeasureQualifier.CSV){style="font-size: 12pt;"}. +[here](https://cdx.epa.gov/wqx/download/DomainValues/ResultMeasureQualifier.CSV){style="font-size: 12pt;"}. TADA_FlagMeasureQualifierCode will automatically add applicable definitions to the input dataframe in a new column +called "TADA.MeasureQualifierCode.Def". + + +In this example, we show how to use the function TADA_FlagMeasureQualifierCode to add definitiond and flag and/or remove rows with specific codes under MeasureQualifierCode that are categorized as "SUSPECT". -In this example, we show how to use the function TADA_FlagMeasureQualifierCode to remove rows with specific ResultMeasureQualifier that are flagged as "SUSPECT". There See ?TADA_FlagMeasureQualifierCode for more information. ```{r FilterMeasureQualifierCodes} +# flag only Review_TADAProfileClean4 <- TADA_FlagMeasureQualifierCode(TADAProfileClean4, clean = FALSE, - flaggedonly = TRUE + flaggedonly = TRUE, + define = TRUE ) # Review_TADAProfileClean4 is empty because we did not find any Suspect samples @@ -856,10 +861,10 @@ sum(is.na(TADAProfileClean4$TADA.ResultMeasureValue)) ``` Filter down to only numeric data. Remove data where the -TADA.ResultMeasureValueDataTypes.Flag = "Text","Coerced to NA",or "Blank". +TADA.ResultMeasureValueDataTypes.Flag = "Text","Coerced to NA",or "NA - Not Applicable". ```{r filter_out_NAs} -# Removes rows where the result value is not numeric. Specifically, removes rows with "Text","Coerced to NA", or "Blank" in the TADA.ResultMeasureValueDataTypes.Flag column, or NA in the TADA.ResultMeasureValue column. +# Removes rows where the result value is not numeric. Specifically, removes rows with "Text","Coerced to NA", or "NA - Not Applicable" in the TADA.ResultMeasureValueDataTypes.Flag column, or NA in the TADA.ResultMeasureValue column. TADAProfileClean5 <- TADA_AutoFilter(TADAProfileClean4) ```