Error in Part 3

[Abby Yeung]

Dear GGIR community,

I am processing the .csv file converted from 60sec .agd file via the Actilife software. We are using Actigraph GT9X devices and data are collected with 60-Hz. 

This is the example of the resulting csv: (with axis, 1 to 3, steps and vm from left to right)

I am using the code below and returns with error. 

The error message: "Error in quantile.default(x, probs = HDCZA_threshold[1]/100) :missing values and NaN's not allowed if 'na.rm' is FALSE" 

Your assistance is greatly appreciated!

Regards,

Abby 

[奥田昌之]

Hi, Abby,

You can use a raw data file.

It was available two years ago. 

A GGIR code for the same csv file with the same parameters  does not work now in my situation. 

It was available two years ago. 

Changes are updates of GGIR and R.  

Now, however, GGIR can read raw datafile, .gt3x, which could not read it two year ago.

It may take a little longer time in process.

Masayuki 

2025年6月13日金曜日 15:59:23 UTC+9 Abby Yeung:

[Vincent van Hees]

Dear Abby,

If you use non-raw data (counts) the default sleep detection algorithms do not work as they rely on angle to be extracted from the (raw) data.

So, you would have to select an alternative algorithms. I am not sure how to detect sleep from ActiGraph count data as I have not worked with this that much. Maybe try:

HASIB.algo = "Sadeh1994" and HASPT.algo = "HLRB"

Best,

Vincent

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

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[Vincent van Hees]

Good point Masayuki,

If you use ActiGraph GT9X you should be able to store the raw data, which has gt3x file extension and is much bigger in file size compared with the 60 second files.

Best,

Vincent

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[Abby Yeung]

Thank you, Vincent and Masayuki,

I will try to use the raw data file! thanks 

Abby