Error in Part 3

[Juan Pablo Espinoza]

Hello everyone,

I'm encountering an issue when running some specific ".gt3x" files in GGIR. During Part 3, I receive the following error message: Error in seq.int(0, to0 - from, by) : 'to' must be a finite number. However, I noticed that when I change the "desiredtz" parameter to a different time zone, the files process correctly and generate the reports as expected.

Does anyone know why this happens, and how problematic it might be to change the time zone in order to analyze these files?

Thank you so much for your help,
Juan Pablo.

[Vincent van Hees]

Hi Juan,

I am not sure, and can have a look. Would you mind sending me for the recording that triggers this error:

• The RData file
• You GGIR parameters: your R script or config.csv file

Thanks,

Vincent

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[Juan Pablo Espinoza]

Hi Vincent,  

Thank you so much for your interest in my issue. I've attached my R script, the link to download raw data file, and a photo of the error message.  

Best regards,

Juan Pablo.

Download raw file link: https://drive.google.com/file/d/1XOIf9Xo2f8H-2R0N7r6Z_oFlO-fPtLLZ/view?usp=sharing

Script: 

library(GGIR)
# General parameters
GGIR(datadir = "~/Desktop/GGIR/EyeFit/Pendientes/",
     outputdir = "~/Desktop/GGIR/EyeFit/OUTPUT_x/",
     studyname="EyeFit",
     desiredtz = "Chile/Continental",
     mode = (1:5),
     # Part 2 parameters
     strategy = 1,
     ndayswindow=7,
     hrs.del.start = 0,
     hrs.del.end = 0,
     maxdur = 7,
     qwindow=c(0, 24),
     windowsizes = c(5,900,3600),
     qlevels = c((24-2) /24, # MI20
                 (24-1)/24, #M60
                 (24-0.5) /24, #M30
                 (24-0.25) /24, #M15
                 (1440-5)/3440), #M05
     ilevels = c(0,50,100,200,8000),
     iglevels = 1,
     mvpathreshold =c(100.6),
     # Part 3+4 parameters
     def.noc.sleep = 1,
     HASPT.algo ="HDZA",
     do.visual = TRUE,
     includenightcrit = 16,
     excludefirst.part4 = FALSE,
     excludelast.part4 = FALSE,
     # Part 5 parameters
     # Physical activity and inactivity threshold / Cut-points Hildebrand 2014; Hildebrand 2016
     do.enmo = TRUE,
     acc.metric = "ENMO",
     threshold.lig = c(44.8), threshold.mod = c(100.6),threshold.vig = c(428.8),
     # Bout durations
     boutdur.in = c(10,20,30), boutdur.lig = c(10), boutdur.mvpa = c(1, 5, 10),
     #Fraction of a bout that need to meet thresholds
     boutcriter = 0.8,
     boutcriter.in = 0.9, boutcriter.lig = 0.8, boutcriter.mvpa = 0.8,
     # Data cleaning
     includedaycrit.part5 = 2/3,
     # Report generation
     week_weekend_aggregate.part5 = FALSE, #Poner TRUE si necesito saber sobre solo la semana
     do.report=c(2, 4, 5))

[Vincent van Hees]

Thanks, this is an error outside GGIR and I have reported it.

In the meantime a workaround for you would be to use: do.part3.pdf = TRUE, which skips the generation of the GGIR part 3 plot.

Vincent

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[Vincent van Hees]

... I meant to type: do.part3.pdf = FALSE

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