Output interpretation in GGIR

[Kerstin Blom]

Hi,

I'm currently working with understanding the outliers proposed by the package, to determine how to handle that data, before doing my statistics for a large insomnia treatment study.

Two questions have arisen, and I cannot find the answers in the otherwise very helpful support material:

1. in the file plots_to_check_data_quality_1.pdf: at what time does Day start, i.e. the marked starting point 0, 1, 2 etc. on the x-axis?
2. in the file visualization_sleep.pdf: what does the colour yellow/lime signify?
   

I would greatly appreciate your help!

Best regards,

Kerstin Blom

[ben_m...@hotmail.com]

Hi Kerstin,

See my answers below:

1. in the file plots_to_check_data_quality_1.pdf: at what time does Day start, i.e. the marked starting point 0, 1, 2 etc. on the x-axis?
   

1. The tick mark on the axis for each day is midnight as these plots are made during the earlier stages of GGIR and are therefore midnight-midnight summaries of the data as per part 2 outputs

1. in the file visualization_sleep.pdf: what does the colour yellow/lime signify?
   

1. Information for this can be found here: https://cran.r-project.org/web/packages/GGIR/vignettes/GGIR.html#5_Motivation_and_clarification in the 4.2 Output part 4, then on the 4.2.3 visualisation_sleep.pdf tab just underneath. Pasted in the description anyway for you:
   "Explanation of the image: Each line represents one night. Colours are used to distinguish definitions of sustained inactivity bouts (2 definitions in this case) and to indicate existence or absence of overlap with the sleeplog. When argument outliers.only is set to FALSE it will visualise all available nights in the dataset. If outliers.only is set to TRUE it will visualise only nights with a difference in onset or waking time between sleeplog and sustained inactivity bouts larger than the value of argument criterror.
   This visualisation with outliers.only set to TRUE and critererror set to 4 was very powerful to identify entry errors in sleeplog data in van Hees et al PLoSONE 2015. We had over 25 thousand nights of data, and this visualisation allowed us to quickly zoom in on the most problematic nights to investigate possible mistakes in GGIR or mistakes in data entry."

Hope that helps,

Ben

[Kerstin Blom]

Thank you Ben! Very helpful! However, I don't find (or understand?) how the description in 4.2.3 helps me understand what the yellow/lime colour signifies? Is it inactivity that is not defined as sleep?

Best regards

Kerstin

[Vincent van Hees]

Hi Ben en Kerstin,

The two shades of green/yellow/lime represent two definition of sustained inactivity (possibly sleep) according to the algorithm. For example, if anglethreshold is set to c(5,10), GGIR will generate two sleep estimates: One with anglegthreshold=5 and one with anglethreshold=10.

In the updated version of GGIR (2.5-0 accessible later this week) this image will have a legend that should hopefully clarify better what is what.

Best, Vincent

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[Vincent van Hees]

Responding to:

"...

1. in the file plots_to_check_data_quality_1.pdf: at what time does Day start, i.e. the marked starting point 0, 1, 2 etc. on the x-axis?

The tick mark on the axis for each day is midnight as these plots are made during the earlier stages of GGIR and are therefore midnight-midnight summaries of the data as per part 2 outputs"

>> This is not entirely correct. the ticks represent 24 hours blocks of data. If your recording did not start at midnight then these are not midnights.

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[Kerstin Blom]

Thanks Vincent for the clarifications! I'm quite relieved the "Day" doesn't start at midnight, our data would have been very confusing if this was the case. So I assume it's the variable  start_time in  part2_summary.csv  that indicates when the 24-hour cycle begins?

BR Kerstin

[Vincent van Hees]

>  So I assume it's the variable  start_time in  part2_summary.csv  that indicates when the 24-hour cycle begins?

Yes, that is correct

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