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Calculate Total Nitrogen and Phosphorus

Source: R/Transformations.R
TADA_CalculateTotalNP.Rd

Apply nutrient aggregation logic from EPA's Enforcement and Compliance History Online (ECHO) Water Pollutant Loading Tool to add nitrogen subspecies and phosphorus forms together to approximate total nitrogen (TN) and total phosphorus (TP) by site and day.

Usage

TADA_CalculateTotalNP(.data, sum_ref, daily_agg = "max")

Arguments

.data

TADA dataframe. TADA_AutoClean() should have been run and TADA.ResultMeasureValueDataTypes.Flag must be present. The function will run required flag functions if needed. Suspect/invalid combinations are excluded.

sum_ref

Optional custom summation reference dataframe with the same columns as the internal reference; if omitted, the internal reference is used.

daily_agg

Aggregation function used to collapse multiple measurements per day/site/metadata combination. One of "max", "min", or "mean". Defaults to "max".

Value

The input dataframe plus additional rows representing TN and TP totals, with explanatory flags: TADA.NutrientSummation.Flag, TADA.NutrientSummationGroup, and TADA.NutrientSummationEquation. Original rows not used in summations are preserved.

Details

Before summing, the function aggregates measurements to a single daily value per characteristic–unit–fraction–speciation–media combination using the chosen daily_agg. Where needed, it converts nitrogen subspecies to "AS N" and phosphorus forms to "AS P" using conversion factors in the summation reference. The internal summation reference can be customized and supplied via sum_ref.

  • If required QA/QC flagging columns are absent, the function runs TADA_FindQCActivities() (clean = FALSE), TADA_FlagResultUnit() (clean = "none"), TADA_FlagFraction() (clean = FALSE), and TADA_FlagSpeciation() (clean = "none"), and excludes invalid or suspect combinations from TN/TP summations.

  • The function will not run a second time on the same data: if TADA.ResultMeasureValueDataTypes.Flag already contains "TN/TP estimated...", the input is returned unchanged.

  • Daily aggregation uses daily_agg ("max", "min", or "mean") per site/day and metadata combination. Rows considered but not selected are preserved with explanatory flags.

  • Keys are normalized (trim whitespace; "" and "NONE" become NA) before matching to the summation reference; the join is NA-aware (dplyr >= 1.1.0).

  • Speciation conversions are applied where a conversion factor is provided.

  • New rows for TN/TP totals are added with deterministic ResultIdentifier values based on site/date/group to ease testing and traceability.

Note

Requires dplyr >= 1.1.0 for NA-aware joins when matching to the summation ref.

See also

TADA_AggregateMeasurements(), TADA_FlagResultUnit(), TADA_FlagFraction(), TADA_FlagSpeciation(), TADA_HarmonizeSynonyms(), TADA_GetNutrientSummationRef()

Examples

if (FALSE) { # \dontrun{
df <- TADA_DataRetrieval(
  statecode = "UT",
  startDate = "2024-06-01",
  endDate = "2024-07-01",
  characteristicType = "Nutrient",
  applyautoclean = TRUE,
  ask = FALSE
)

df2 <- TADA_SimpleCensoredMethods(
  df, nd_method = "multiplier", nd_multiplier = 0.5,
  od_method = "as-is", od_multiplier = "null"
)

df2 <- TADA_RunKeyFlagFunctions(df2, clean = TRUE)
df2 <- TADA_HarmonizeSynonyms(df2)

out <- TADA_CalculateTotalNP(df2, daily_agg = "max")
} # }