ActCR Circadian Rhythms Package Implementation in GGIR

[joeck...@gmail.com]

Hello,

I have a question over the ActCR package for extracting circadian rhythm metrics from actigraphy. I am a novice with accelerometry so if anyone knows the answer to my question, the help would be highly appreciated!

Does anyone know how the ActCR package handles invalid or missing data? I have set  includedaycrit = 16 in GGIR Part 2 so that any day with less than 16 hours is invalid and excluded. However, the circadian rhythm outputs from the ActCR package are reporting that cosinor_ndays and cosinorExt_ndays (which reports the number of days that are modeled to produce the Cosinor and Extended Cosinor Analysis) are equal to all days of actigraphy data, even the days that are invalid and have less than 16 hours of data. My concern is that the circadian rhythm outputs are reflective of missing and invalid data and are thus incorrect. I cannot figure out from existing documentation how the ActCR package handles missing data to determine if my current circadian rhythm outputs are correct, or if I need to somehow manually adjust the ActCR code to exclude invalid days. 

Thank you very much for your time and assistance. 

Joanna 

[Vincent van Hees]

Hello Joanna,

Does anyone know how the ActCR package handles invalid or missing data?

As of the ActCR release from May 2022 (0.3.0) cosinor and extended cosinor analyses are flexible to handle both time series with missing data and with imputed data. I had the same concern as you and this is why I made that contribution to the ActCR code.

Inside GGIR, ActCR is used for cosinor and extended cosinor analyses where invalid time points are set to NA and by that ignored. This is also discussed in the GGIR vignette: https://cran.r-project.org/web/packages/GGIR/vignettes/GGIR.html#5102_Cosinor_analysis_and_Extended_Cosinor_analysis

Note that even if a day has less than 16 valid hours GGIR will use the available valid data points for the cosinor analyses.

Best, Vincent

Dr. Vincent van Hees | Independent consultant | https://accelting.com/

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