Run key flagging functions — TADA_RunKeyFlagFunctions • EPATADA

This is a shortcut function to run all of the most important flagging functions on a TADA dataset. See ?function documentation for TADA_FlagResultUnit, TADA_FlagFraction, TADA_FindQCActivities, TADA_FlagMeasureQualifierCode, and TADA_FlagSpeciation for more information.

Usage

TADA_RunKeyFlagFunctions(.data, clean = TRUE)

Arguments

.data: A TADA dataframe.
clean: Boolean. Determines whether to keep the suspect rows (or not). Defaults to TRUE.

Value

A TADA dataframe with the following flagging columns: TADA.ResultUnit.Flag, TADA.MethodSpeciation.Flag, TADA.SampleFraction.Flag, TADA.MeasureQualifierCode.Flag and TADA.ActivityType.Flag.

Examples

# Run flagging functions but keep all results
keep_all <- TADA_RunKeyFlagFunctions(Data_6Tribes_5y, clean = FALSE)
#> [1] "Rows with Suspect result value units have been flagged but retained. Review these rows before proceeding and/or set clean = 'suspect_only' or 'both'."
#> [1] "Rows with Suspect sample fractions have been flagged but retained. Review these rows before proceeding and/or set clean = TRUE."
#> [1] "Rows with Suspect speciations have been flagged but retained. Review these rows before proceeding and/or set clean = 'suspect_only' or 'both'."

# Run flagging functions and remove and suspect rows
remove_suspect <- TADA_RunKeyFlagFunctions(Data_6Tribes_5y, clean = TRUE)
#> [1] "Quality control samples have been removed or were not present in the input dataframe. Returning dataframe with TADA.ActivityType.Flag column for tracking."