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509 the foramt of the reference table from epatadas tada getsynonymref function #510

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hillarymarler merged 3 commits into from
Aug 14, 2024
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509 the foramt of the reference table from epatadas tada getsynonymref function #510

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1cf0eeb
Update TADARefTables.R
hillarymarler Aug 13, 2024
5e27c9b
Update Transformations.R
hillarymarler Aug 13, 2024
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Documentation updates
hillarymarler Aug 13, 2024
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28 changes: 12 additions & 16 deletions R/TADARefTables.R
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Expand Up @@ -18,22 +18,18 @@ TADA_GetNutrientSummationRef <- function() {

#' Generate Unique Synonym Reference Table
#'
#' Function generates a synonym reference table containing all unique
#' combinations of TADA.CharacteristicName, TADA.ResultSampleFractionText,
#' TADA.MethodSpeciationName, 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.MethodSpeciationName, 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.).
#' Function generates a synonym reference table containing all unique combinations of
#' TADA.CharacteristicName, TADA.ResultSampleFractionText, and TADA.MethodSpeciationName. 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 forTADA.CharacteristicName, TADA.ResultSampleFractionText,
#' and TADA.MethodSpeciationName. 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 alreadyrun 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.
#'
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7 changes: 3 additions & 4 deletions R/Transformations.R
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Expand Up @@ -8,10 +8,9 @@
#' suggested synonym naming for some priority characteristics. Where a suggested
#' characteristic name, fraction, speciation, or unit is present, the function
#' will convert the TADA.CharacteristicName, TADA.ResultSampleFractionText,
#' TADA.MethodSpeciationName, and/or TADA.ResultMeasure.MeasureUnitCode to
#' the target format. In cases where a target unit or speciation differs from
#' the existing unit or speciation, the reference table will also apply
#' multiplication conversion factors to the TADA.ResultMeasureValue.
#' and TADA.MethodSpeciationName to the target format. In cases where a target
#' speciation differs from the existing speciation, the reference table will
#' also apply multiplication conversion factors to the TADA.ResultMeasureValue.
#'
#' @param .data TADA dataframe
#' @param ref Optional argument to specify which dataframe to use as a reference
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28 changes: 12 additions & 16 deletions man/TADA_GetSynonymRef.Rd
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7 changes: 3 additions & 4 deletions man/TADA_HarmonizeSynonyms.Rd
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