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| Original file line number | Diff line number | Diff line change |
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| #' Nutrient Summation Reference Key | ||
| #' | ||
| #' Function downloads and returns the newest available nutrient summation | ||
| #' reference dataframe. This dataframe is used in TADA_CalculateTotalNitrogen as | ||
| #' the basis for the combinations added together to get total nitrogen. Users | ||
| #' may customize this reference table for their own dataset and use the custom | ||
| #' dataframe as an input in TADA_CalculateTotalNitrogen. | ||
| #' | ||
| #' @return Dataframe of nutrient summation combinations | ||
| #' | ||
| #' @export | ||
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| TADA_GetNutrientSummationRef <- function() { | ||
| ref <- utils::read.csv(system.file("extdata", "NPsummation_key.csv", package = "TADA")) | ||
| return(ref) | ||
| } | ||
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| #' Generate Unique Synonym Reference Table | ||
| #' | ||
| #' Function generates a synonym reference table containing all unique | ||
| #' combinations of TADA.CharacteristicName, TADA.ResultSampleFractionText, | ||
| #' TADA.MethodSpecificationName, and TADA.ResultMeasure.MeasureUnitCode. The | ||
| #' function also joins in some TADA-specific suggested synonyms for nutrients | ||
| #' and priority parameters. These target synonyms (denoted in the reference | ||
| #' table with the prefix "Target.") are intended to help the user aggregate | ||
| #' synonymous data that may be uploaded with slightly different metadata | ||
| #' conventions and prepare nutrient data for total N and P summations. Users can | ||
| #' review how their input data relates to target synonyms for | ||
| #' TADA.CharacteristicName, TADA.ResultSampleFractionText, | ||
| #' TADA.MethodSpecificationName, and TADA.ResultMeasure.MeasureUnitCode. Once | ||
| #' the synonym table is created, users may optionally edit the target columns in | ||
| #' the reference table to meet their needs. Additionally, the function assumes | ||
| #' the user has already removed any data containing invalid | ||
| #' characteristic-unit-fraction-speciation combinations (i.e. user has already | ||
| #' run TADA_FlagFraction, TADA_FlagSpeciation, TADA_FlagResultUnit, etc.). | ||
| #' | ||
| #' @param .data TADA dataframe. If a data frame is not provided, the function will return the default internal reference table. | ||
| #' | ||
| #' @return Synonym Reference Table unique to the input dataframe | ||
| #' | ||
| #' @export | ||
| #' | ||
| #' @examples | ||
| #' # Load example dataset: | ||
| #' data(Data_6Tribes_5y) | ||
| #' | ||
| #' # Create a synonym reference table for flagged, cleaned dataframe: | ||
| #' Data_6Tribes_5yClean <- subset(Data_6Tribes_5y, !is.na(Data_6Tribes_5y$TADA.ResultMeasureValue)) | ||
| #' Data_6Tribes_5yClean <- TADA_FlagFraction(Data_6Tribes_5yClean, clean = TRUE) | ||
| #' Data_6Tribes_5yClean <- TADA_FlagResultUnit(Data_6Tribes_5yClean, clean = "invalid_only") | ||
| #' Data_6Tribes_5yClean <- TADA_FlagSpeciation(Data_6Tribes_5yClean, clean = "invalid_only") | ||
| #' Data_6Tribes_5yClean <- TADA_FlagMethod(Data_6Tribes_5yClean, clean = TRUE) | ||
| #' CreateRefTable <- TADA_GetSynonymRef(Data_6Tribes_5yClean) | ||
| #' | ||
| #' # Get internal synonym reference table | ||
| #' reference <- TADA_GetSynonymRef() | ||
| TADA_GetSynonymRef <- function(.data) { | ||
| if (missing(.data)) { | ||
| ref <- utils::read.csv(system.file("extdata", "HarmonizationTemplate.csv", package = "TADA")) | ||
| return(ref) | ||
| } | ||
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| # check .data is data.frame | ||
| TADA_CheckType(.data, "data.frame", "Input object") | ||
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| # check .data has the required columns | ||
| expected_cols <- c( | ||
| "TADA.CharacteristicName", | ||
| "TADA.ResultSampleFractionText", | ||
| "TADA.MethodSpecificationName", | ||
| "TADA.ResultMeasure.MeasureUnitCode" | ||
| ) | ||
| TADA_CheckColumns(.data, expected_cols) | ||
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| if (!any(c("TADA.MethodSpeciation.Flag", "TADA.SampleFraction.Flag", "TADA.ResultUnit.Flag") %in% names(.data))) { | ||
| print("Warning: This dataframe is missing TADA QC flagging columns, indicating that you have not yet run the TADA_FlagResultUnit, TADA_FlagFraction, or TADA_FlagSpeciation functions. It is highly recommended you run these flagging functions and remove Invalid combinations before proceeding to this step.") | ||
| } | ||
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| # check to see if any invalid data flags exist | ||
| check_inv <- .data[, names(.data) %in% c("TADA.MethodSpeciation.Flag", "TADA.SampleFraction.Flag", "TADA.ResultUnit.Flag")] | ||
| check_inv <- check_inv %>% | ||
| tidyr::pivot_longer(cols = names(check_inv), names_to = "Flag_Column") %>% | ||
| dplyr::filter(value == "Invalid") | ||
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| if (dim(check_inv)[1] > 0) { | ||
| check_inv <- check_inv %>% | ||
| dplyr::group_by(Flag_Column) %>% | ||
| dplyr::summarise("Result Count" = length(value)) | ||
| print("Warning: Your dataframe contains invalid metadata combinations in the following flag columns:") | ||
| print(as.data.frame(check_inv)) | ||
| } | ||
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| # execute function after checks are passed | ||
| # define raw harmonization table as an object | ||
| harm.raw <- utils::read.csv(system.file("extdata", "HarmonizationTemplate.csv", package = "TADA")) | ||
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| join.data <- merge(unique(.data[, expected_cols]), | ||
| harm.raw, | ||
| by = expected_cols, | ||
| all.x = TRUE | ||
| ) | ||
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| # trim join.data to include only unique combos of char-frac-spec-unit | ||
| unique.data <- join.data %>% dplyr::distinct() | ||
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| unique.data <- unique.data[, names(harm.raw)] | ||
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| # return unique.data | ||
| return(unique.data) | ||
| } | ||
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| #' Nutrient Summation Reference Key | ||
| #' | ||
| #' This internal reference file includes USGS only units/speciations. It was | ||
| #' created in July 2023 using the pcodes domain table from NWIS | ||
| #' (https://help.waterdata.usgs.gov/codes-and-parameters/parameters). All USGS units | ||
| #' and speciations are given a target unit and speciation that is synonymous, but | ||
| #' adheres to the WQX schema (WQX measure unit domain table). | ||
| #' | ||
| #' This reference file is used in the TADA_ConvertResultUnits() function where | ||
| #' synonymous units and speciations are harmonized before units are then also | ||
| #' harmonized/converted to WQX targets. | ||
| #' | ||
| #' | ||
| #' @return Dataframe of USGS only units and speciations and their WQX compatible | ||
| #' targets/synonyms. | ||
| #' | ||
| #' @export | ||
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| TADA_GetUSGSSynonymRef <- function() { | ||
| ref <- utils::read.csv(system.file("extdata", "USGS_units_speciation.csv", package = "TADA")) | ||
| return(ref) | ||
| } |
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