Re: [GGIR] Output not being produced for all participant files

[Vincent van Hees]

Dear Callum

You are specifying f0 = 1 and f1  = 2, which means that GGIR always only processes the first two files. If you do not want this change them to f0 = 1 and f1 = 0.

If your R script does not include f0 = 1 and f1 = 2, then another route is to delete the config.csv file from your output folder such that GGIR falls back on all its default parameter values.

Note that parameter values are obtained in a specific order. First it looks at your R script, then it looks at the available config.csv  in the output folder (if any) and then it falls back on defaults. For details see https://wadpac.github.io/GGIR/articles/chapter2_Pipeline.html#parameter-extraction-order

Best,

Vincent

On Tuesday, 6 May 2025 at 4:30 PM, Callum Regan <callummo...@gmail.com> wrote:

Hi there. Thanks for all the work with GGIR, I really appreciate it, including the new file summary report .

Unfortunately, I am having trouble with my outputs. I have 60 raw gt3x. files where participants wore an actigraph on the hip for one week.

I ran my script and result/meta files were produced only for two out of these sixty participants. At first I was having issues with my advanced sleep diary which I believe I have amended. But then I ran the script without the sleep diary and still encountered that outputs were being produced only for two participants.

I then tried smaller batches e.g., 5 or 8 participants and again output was produced for only two participants. They happen to always be the first two participants.

I have checked that the gt3x can be read by R using "list.files".

Interestingly, when I run my script for only one participant at a time thus only using one gt3x. file, it works completely fine - all outputs are produced.

I am using R version 4.4.2 and GGIR version 3.2.6, although I realise that this issue was happening for me before with the previous GGIR version.

I have attached a meta data file for one participant and the config file when I tried to run my script for 6 participants and again received output for the first two.

Any help with this would be much appreciated.

Thanks,

Callum

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[Callum Regan]

Dear Vincent, 

Thank you for your reply. I realised my mistake and amended accordingly. 

Many thanks, 

Callum