6. How GGIR Deals with Invalid Data

Imputation of invalid epoch data

All time segments classified as non-wear or clipping (see Chapter 3) and those masked by the study protocol (see Chapter 5) are treated as invalid data. In GGIR part 2, the epoch level metric values are imputed, while a log is kept of which epochs were imputed. For most of the subsequent analysis done by GGIR, the imputed time series is used. The time series without invalid segments are used only for a few analyses:

• Weighted average of full recording

• Cosinor analysis (see Chapter 10)

• A very specific non-default configuration of sleep analysis (see Chapter 8)

The imputation of epoch data is done based on the mean metric value corresponding to the valid values from the same time in the day on other days in the recording. However, if the same time interval is marked as invalid across all recorded days, the value is imputed by zero, except for metric EN which is imputed by 1.

For example, imagine a 5-day recording with the following ENMO metric data for two specific epochs in the day across five days:

Time	Mon	Tue	Wed	Thu	Fri
8:59:55 – 9:00:00	3	4	3	invalid	3
9:00:00 – 9:00:05	invalid	invalid	invalid	invalid	invalid

The above would be imputed as shown below because the average of 3, 4, 3 and 3 is 3.25:

Time	Mon	Tue	Wed	Thu	Fri
8:59:55 – 9:00:00	3	4	3	3.25	3
9:00:00 – 9:00:05	0	0	0	0	0

Controlling the imputation

It is worth noting that you have the option to disable the imputation by setting parameter do.imp = FALSE. This means that values are kept as they are and not imputed or omitted. Disabling the imputation is not recommended for most use-cases, but can be relevant for studies in a controlled sleep or exercise laboratories where the sensor is known to be worn throughout the experiment.

An alternative way to control the imputation is to specify time segments in which the invalid epochs are to be imputed by zeros (or ones for the metric EN) instead of following the standard GGIR imputation method. To do this, you should use the parameter TimeSegments2ZeroFile.

Key parameters

• do.imp,
• TimeSegments2ZeroFile

Related output

• In GGIR part 2, plots to check the data quality highlight the segments of the file that were considered invalid and imputed. These plots can be found in the folder “results/QC/”.
• In GGIR part 5, time series are produced and optionally stored within the folder “meta/ms5out.raw/” in either csv or RData format. These time series contain an indicator of the epochs that were considered invalid and imputed.