This function determines if detection limit type and detection condition are parsimonious before applying simple tools for non-detect and over-detect data handling, including filling in the values as-is, X times the detection limit, or a random number between 0 and the LOWER detection limit. These methods do NOT depend upon censored data frequency in the data frame.
Usage
TADA_SimpleCensoredMethods(
.data,
nd_method = "multiplier",
nd_multiplier = 0.5,
od_method = "as-is",
od_multiplier = "null"
)Arguments
- .data
A TADA dataframe
- nd_method
A text string indicating the type of method used to populate a non-detect (lower limit) data value. Can be set to "multiplier" (default),"randombelowlimit", or "as-is".
- nd_multiplier
A number to be multiplied to the LOWER detection limit for each entry to obtain the censored data value. Must be supplied if nd_method = "multiplier". Defaults to 0.5, or half the detection limit.
- od_method
A text string indicating the type of method used to populate an over-detect (upper limit) data value. Can be set to "multiplier" or "as-is" (default).
- od_multiplier
A number to be multiplied to the UPPER detection limit for each entry to obtain the censored data value. Must be supplied if od_method = "multiplier". Defaults to 0.5, or half the detection limit.
Value
A TADA dataframe with the additional column TADA.CensoredMethod, which documents the method used to fill censored data values. If user has not previously run TADA_IDCensoredData or TADA_FlagMeasureQualifierCode, this function will also run those and add the columns TADA.CensoredData.Flag, TADA.MeasureQualifierCode.Flag and TADA.MeasureQualifierCode.Def.
Details
This function runs TADA_IDCensoredData within it which adds the column TADA.CensoredData.Flag. Enter ?TADA_IDCensoredData into the console for more information.
Examples
# Load example data frame:
data(Data_Nutrients_UT)
# Check for agreement between detection condition and detection limit type,
# and in instances where the measurement is non-detect, set the result value
# to half of the detection limit value. For over-detect measurements, retain
# the detection limit value as the result value as-is.
Data_Nutrients_UT_CensoredFlag <- TADA_SimpleCensoredMethods(Data_Nutrients_UT, nd_method = "multiplier", nd_multiplier = 0.5, od_method = "as-is", od_multiplier = "null")
#> [1] "TADA_IDCensoredData: There are 12 results in your data frame that are missing ResultDetectionConditionText. TADA requires BOTH ResultDetectionConditionText and DetectionQuantitationLimitTypeName fields to be populated in order to categorize censored data."
# Check for agreement between detection condition and detection limit type, and in instances where the measurement is non-detect, set the result value to a random value between 0 and the detection limit value. For over-detect measurements, retain the detection limit value as the result value as-is.
Data_Nutrients_UT_CensoredFlag <- TADA_SimpleCensoredMethods(Data_Nutrients_UT, nd_method = "randombelowlimit", nd_multiplier = "null", od_method = "as-is", od_multiplier = "null")
#> [1] "TADA_IDCensoredData: There are 12 results in your data frame that are missing ResultDetectionConditionText. TADA requires BOTH ResultDetectionConditionText and DetectionQuantitationLimitTypeName fields to be populated in order to categorize censored data."