no results for part4 and part5 about ggir HOT 9 CLOSED

Thanks for posting this. To get a better understanding of the situation, can you please answer the following questions:

1. Do all your files have .bin.bin extension? This might be problematic for GGIR (I am not entirely sure). Can you try removing one .bin?
2. How does the output of part 2 look like, is it what you expect?
3. Based on the output of part2, can you confirm that the accelerometer was worn in the first 24 hours of the first participant?
4. Can you share your "C:/Alba/03_Data/sleeplog_example.csv", or at least the first couple of rows?

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Hi Vincent,

Many thanks for your check. I tried it again only with one bin file

1. I did it and nothing changed (the file was previously named 14.bin and now is 14)
2. Find attached what I got as part2 output and a screenshot of myresults folder
3. Yes, participants wore the accelerometer since the beginning as it was placed by field nurses.
4. Find attached the sleeplog_example

part2_daysummary.xlsx
part2_summary.xlsx
visualisation_sleep.pdf
sleeplog_example.xlsx

Many thanks and do not hesitate to ask for further information if needed

Alba

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part2 looks good with over 7 days of measurement and wear duration.
maybe inspecting 'QC/plots to check data quality 1.pdf' would be a good extra check to be sure.

Next step is to check that part3 worked well. Can you go to .../meta/sleep.qc and check that there are pdf files in here with meaningful plots of arm angle and sleep classification during the night?

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Hi Vincent,

Here the file 'QC/plots to check data quality 1.pdf' and the pdf with the plots of arm angle

plots_to_check_data_quality_1.pdf

graphperday_id_14.bin_14.bin.pdf

I think they look good, maybe the problem is in step 4...let me know which is the next check

Many thanks,
Alba

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That looks good indeed, maybe something goes wrong in reading the sleeplog data and maybe it has to do with the fact that you only have one sleep night in your sleeplog file.
To test whether this is the problem: Can you copy paste the row with sleeplog_example.csv and paste it a row lower and give it a random other ID number? In that way GGIR may better be able to find the sleeplog data it is looking for. If this is the case, then some improvements need to be made in how GGIR handles sleeplog files with a single row of data.

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I did it and the same error came out (run the script for one bin file (id=14) and the sleeplog with two ids (14 and a random id)

Report part 4
loading all the milestone data from part 4 this can take a few minutes
[1] "report not stored, because no results available"

Report part 5
loading all the milestone data from part 5 this can take a few minutes
generating output for every parameter configurations...
NA-NA-NA-NA-NAreport not stored, because no results available NA-NA-NA-NA-report not stored, because no results available NA-NA-NA--NAreport not stored, because no results available NA-NA-NA--report not stored, because no results available NA-NA--NA-NAreport not stored, because no results available NA-NA--NA-report not stored, because no results available NA-NA---NAreport not stored, because no results available NA-NA---report not stored, because no results available NA--NA-NA-NAreport not stored, because no results available NA--NA-NA-report not stored, because no results available NA--NA--NAreport not stored, because no results available NA--NA--report not stored, because no results available NA---NA-NAreport not stored, because no results available NA---NA-report not stored, because no results available NA----NAreport not stored, because no results available NA----report not stored, because no results available -NA-NA-NA-NAreport not stored, because no results available -NA-NA-NA-r...

Generate visual reports
Warning message:
In rm(outputfinal, outputfinal2) : object 'outputfinal2' not found

sleeplog_example.xlsx

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Do you use that specific xlsx file? Can you convert it to csv, because that is how I designed GGIR.

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Yes, .csv file but here I enclosed the excel file due to it does not allow to attach csv

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Issue resolved, the filename was 14.bin which causes problems:

Part 4 of GGIR expects an underscore after the file identifier as in 14_example.bin
and if that is not recognized it assumed that the name of the raw data file is the identifier itself, so then you will need to fill in 14.bin as identifier in your sleeplog.

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