This function looks for replicate samples and pairs them to their original or parent sample for further analysis. Replicate samples without an associated original sample are flagged as orphan samples.
Usage
TADA_PairReplicates(.data, type = c("QC_replicate"), time_difference = 600)Arguments
- .data
TADA dataframe which must include the columns 'OrganizationIdentifier', 'ActivityTypeCode', 'ActivityStartDate', 'ActivityStartDateTime', 'ResultIdentifier', 'ActivityRelativeDepthName', 'TADA.LatitudeMeasure', 'TADA.LongitudeMeasure', 'TADA.ResultMeasureValue', 'TADA.ComparableDataIdentifier', 'TADA.ActivityType.Flag', 'TADA.ActivityDepthHeightMeasure.MeasureValue', 'TADA.ResultDepthHeightMeasure.MeasureValue', 'TADA.ActivityTopDepthHeightMeasure.MeasureValue', and 'TADA.ActivityBottomDepthHeightMeasure.MeasureValue'.
- type
Character argument identifying which Activity Types to look for while pairing replicates to their parent samples. The default type is "QC_replicate", which includes Activity Type Codes: "Quality Control Field Replicate Habitat Assessment", "Quality Control Field Replicate Msr/Obs", "Quality Control Field Replicate Portable Data Logger", "Quality Control Field Replicate Sample-Composite", and "Quality Control Sample-Field Replicate".
- time_difference
Numeric argument defining the maximum time difference in seconds to search for parent samples. The default time window is 600 seconds or 10 minutes. The time_difference can be as large as the user would like, but parent-replicate pairs will only be identified if they were collected on the same date.
Value
This function adds one column to the original data frame: 'TADA.ReplicateSampleID'. 'TADA.ReplicateSampleID' contains the 'ResultIdentifier' value from the replicate sample if a parent sample match is identified. Both the replicate sample and the parent sample will have the same 'ResultIdentifier' code in this column, marking them as a pair. If a sample was identified as a replicate sample in the 'TADA.ActivityType.Flag' column but does not have an associated parent sample in the data frame, the 'TADA.ReplicateSampleID' column will contain the flag 'Orphan'. If more than one parent or replicate sample is identified in the data frame, the 'TADA.ReplicateSampleID' column for all samples will contain the 'ResultIdentifier' value from one of the replicate samples marking them as a grouping.
Examples
# Load example dataset:
data(Data_NCTCShepherdstown_HUC12)
# Run TADA_FindQCActivities to add TADA.ActivityType.Flag column:
df <- TADA_FindQCActivities(Data_NCTCShepherdstown_HUC12)
# Find pairs for all data flagged as "QC_replicate" in the TADA.ActivityType.Flag column:
df_all_pairs <- TADA_PairReplicates(df)
# Find pairs for only data with ActivityTypeCode "Quality Control Sample-Field Replicate":
df_fieldrep_pairs <- TADA_PairReplicates(df, type = "Quality Control Sample-Field Replicate")
# Find pairs for all data flagged as "QC_replicate" within a 5-minute time window:
df_all_pairs_5min <- TADA_PairReplicates(df, time_difference = 300)