Auto-updating back to SPT even though sleep log is supplied and option is set to TimeinBed

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Milan Zarchev

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Dec 20, 2021, 8:58:51 AM12/20/21
to R package GGIR
Hi,

I'm running into some trouble when trying to calculate the sleep efficiency metric. I have a sleep diary with time in bed data that I am able to read with no errors using the g.loadlog function (see attached script and sleep diary for 20 participants). However, when I supply the same sleep log to the GGIR main function and run the analyses, I get the message: 

Auto-updating sleepwindowType to SPT because nog sleeplog used and neither HASPT.algo HorAngle used.

It's weird because obviously the sleep log is not only loaded but also used, as the part4_nigtsummary output shows (sleeplog_used = 1 for all rows). So now I am completely confused as to why I GGIR is switching back to SPT and I do not get sleep efficiency metrics.

Additionally, I am also getting these error messages which could be relevant? 

In `[<-.factor`(`*tmp*`, iseq, value = "9.2625") :
  invalid factor level, NA generated


The same ones show up however when I am trying to just do the SPT analysis (I have a different diary for sleep time not time in bed) and everything seems in order there despite the errors.

Any help here would be very much appreciated!
sleeplog_formatted.csv
part4_nightsummary_sleep_cleaned.csv
GGIR_sleep_efficiency.R

Vincent van Hees

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Dec 23, 2021, 5:08:14 AM12/23/21
to Milan Zarchev, R package GGIR
Sorry to hear that Milan,
This issue may have been fixed already. Can you try again with the latest development version. To install it, please run the following R commands:

install.packages("remotes")
library(remotes)
remotes::install_github("wadpac/GGIR")

Thanks,
Vincent

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

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Dec 23, 2021, 5:27:31 AM12/23/21
to R package GGIR
Thank you for the help Vincent, its much appreciated! 

I will report on whether the development version solves this when I have access to my work computer early January.

Milan Zarchev

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Jan 6, 2022, 5:47:37 AMJan 6
to R package GGIR
Just an update for anyone else that might be encountering a similar issue - Vincent's newest dev version of GGIR solves the issue and I am able to obtain sleep efficiency metrics now with the same code I used before. 

Thank you once again Vincent for your tireless work on developing and assisting with GGIR!

Milan

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