Viariable "dur_day_spt_min" in part5_personsummary_MM

[ZHANG JIAQI]

Hi, Vincent,

Thank you for all the effort in GGIR.

We are currently using GGIR package 3.2 for PA analyses. However, when looking at the variable "dur_day_spt_min" in the output file "part5_personsummary_MM_L30M100V245_T5A5", the time spent in sleep and wake totaled exceeding 24 hr (1440 min). Since this is midnight to midnight window, I assume that every window size should be equivalent to 1440 min. Then, I checked the "part5_daysummary_full_MM_L30M100V245_T5A5" from the QC file and found that every ID had their "dur_day_spt_min" around 2880 min in their last window. I was quite confused by the results and I hope you can help me figure out what went wrong in my analyses.

Many thanks,

Jiaqi

Below are my scripts:

GGIR(mode=c(1,2,3,4,5),
     datadir = "F:/!! File Transfer/Full Raw Data",
     outputdir = "F:/!! File Transfer",
     do.parallel = TRUE,
     chunksize = 0.2,
     
     do.report=c(2,4,5),
     idloc = 5,
     dynrange = 8,
     
     printsummary = TRUE,
     #=====================
     # Part 2
     #=====================
     data_masking_strategy = 1,
     hrs.del.start = 0,          hrs.del.end = 0,
     maxdur = 7,                 includedaycrit = 16,
     Sadeh_axis = "Y",
     qlevels = c(c(840/1440), c(1140/1440), c(1320/1440), c(1380/1440),
                 c(1410/1440), c(1415/1440), c(1420/1440), c(1425/1440),
                 c(1430/1440), c(1435/1440), c(1439/1440)),
     qwindow=c(0,24),
     mvpathreshold =c(100),
     mvpadur = c(1, 5, 10),
     boutcriter = 0.8,
     includenightcrit = 16,
     iglevels = TRUE,
     
     #=====================
     # Part 3 + 4
     #=====================
     excludefirstlast = TRUE,
     def.noc.sleep = 1,
     criterror = 2,
     do.visual = TRUE,
     
     #=====================
     # Part 5
     #=====================
     threshold.lig = c(30),  threshold.mod = c(100),  threshold.vig = c(245),
     boutcriter.in = 0.9,    boutcriter.lig = 0.8,
     boutcriter.mvpa = 0.8,
     boutdur.in = c(10, 30), boutdur.lig = c(1, 5, 10),
     boutdur.mvpa = c(1, 5, 10),
     includedaycrit.part5 = 2/3,
     winhr = c (0.017, 0.083, 0.167, 0.25, 0.333, 0.417, 0.5, 1, 2, 5, 10),
     qM5L5 = 0.25,
     require_complete_lastnight_part5 = TRUE,

     #=====================
     # Visual report
     #=====================
     timewindow = c("MM","WW"),
     visualreport=TRUE)

[Vincent van Hees]

Dear Jiaqi,

Thanks for reporting this.

To allow me to reproduce and investigate the error could you share with me an example .RData file from the meta/basic output subfolder?

Thanks,

Vincent

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

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[ZHANG JIAQI]

Thanks for your reply. I have attached two examples of .RData file from the meta/basic output subfolder of my dataset.

Regards,

Jiaqi

[Vincent van Hees]

Thanks Jiaqi,

I identified a bug that is specific tot the combined use of excludefirstlast = TRUE and timewindow = "MM".

I have drafted a fix which you can test by installing GGIR via:

remotes::install_github("wadpac/GGIR", ref = "issue1292_define_days_when_nights_excluded")

My plan is to merge it in the upcoming days and to include it in the next GGIR release..

Thanks,

Vincent

To view this discussion, visit https://groups.google.com/d/msgid/RpackageGGIR/0335bb2a-f240-401d-8e79-a6342948f059n%40googlegroups.com.

[ZHANG JIAQI]

Dear Vincent,

Thank you very much for your prompt response and assistance with this matter.

I have tested the code you provided and observed that the variable dur_day_spt_min in the output file part5_personsummary_MM_L30M100V245_T5A5 has been successfully corrected. However, I noticed slight changes in the values of other variables as well following the modification.

Could you please kindly inform whether these changes are expected and align with the intended adjustments?

Thank you for your support.

Regards,

Jiaqi

[Vincent van Hees]

Dear Jiaqi,

Thanks for reporting back. Yes, if the definition of a day window changes as was the case than all variables for that day are likely to change since they are calculated over a different time window and by that different data. However, for the days for which the duration has remained unchanged the other values should also be the same.

Please note that I have integrated this update in the new GGIR 3.2-6 release.

Best regards,

Vincent

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

To view this discussion, visit https://groups.google.com/d/msgid/RpackageGGIR/bd2613ab-6624-4a01-b5f3-1ae6f8bbcda7n%40googlegroups.com.