Visual report not being generated

[Leticia Sewaybricker]

Hi all,

With GGIR version 2.9-5 everything is running smoothly but the visual report. I am getting this error:

Generate visual reports Error in if (P2daysummary_tmp$`N hours`[1] < 24 & P2daysummary_tmp$`N hours`[1] > : missing value where TRUE/FALSE needed

Does anybody have any thoughts?

I confess that I was wondering if it could be somewhat linked to what is being presented by Krista in the conversation entitled " Error in part 4: Error in if (WKN2 > SLN2 )".

Please, find below the script being used. Attached there is the config file, the.RData file from meta/basic folder.

##GGIR analysis for WEBS##
##Run first this if wants step counts
source("***/verisense_count_steps.R") # update to local path to verisense_count_steps.R file
myfun =  list(FUN=verisense_count_steps,
              parameters= c(3, 5, 15, -0.5, 3, 4, 0.001, 1.2),
              expected_sample_rate= 15,
              expected_unit="g",
              colnames = c("step_count"),
              outputres = 1,
              minlength = 1,
              outputtype="numeric",
              aggfunction = sum,
              timestamp=F,
              reporttype="event")

##CLEANER version##
library(GGIR)
GGIR(datadir=" C:/ ***",
     outputdir=" C:/ ***",
     configfile = "C:/***/config_webs2.csv",
     WornDuringSleep = TRUE,
     part2ImpWithZero = FALSE,
     part2ExcludeNonwear = TRUE,
     includedaycrit = 8,
     ndayswindow = 0,
     strategy = 1,
     maxdur = 8,
     hrs.del.start = 4,
     hrs.del.end = 0,
     includedaycrit.part5 = 0.33333333,
     excludefirstlast.part5 = FALSE,
     do.imp = FALSE,
     minimum_MM_length.part5 = 8,
     excludefirstlast = FALSE,
     includenightcrit = 8,
     excludefirst.part4 = FALSE,
     excludelast.part4 = FALSE,
     max_calendar_days = 8,
     imputeTimegaps = FALSE,
     myfun = myfun)

Thanks!

Leticia

[Jairo Hidalgo Migueles]

Hi Leticia,

May I ask how the part 2 daysummary report look like for this file? Can you see the variables N hours and N validhours there?

Best,
Jairo

[Leticia Sewaybricker]

Hi Jairo, great point.

I can see both N hours and N validhours and they both look right. Attached part 2 daysummary report in case it helps.

Thanks for digging into it.

Leticia

[Jairo Hidalgo Migueles]

Did you also get meta data for parts 3 and 4? If so, the visualreport should be generated. Can you share meta data from part 1 so that I can have a look? You'll find that in the output folder (meta/basic/).

Best,
Jairo

[Leticia Sewaybricker]

Hi Jairo,

please see attached 3 files

1) "meta_001" - file from meta/basic/ folder

2) "001_ms3" (renamed for sharing purpose) - file from meta/ms3.out folder

3) "001_ms4" (renamed for sharing purpose) - file from meta/ms4.out folder

Let me know if anything else would be helpful.

Thanks!

Leticia

[Vincent van Hees]

Hi Leticia,

I see your reply to Jairo has not been answered yet. I just had a look at the files

and I managed to fix the issue by adding argument 'do.part3.pdf = FALSE' to your code. This will tell GGIR not to created a pdf visualisation in part 3, which is where I think the bug is. The visualisation is probably not that important. In the new GGIR 2.10-1 (more about that in my email later today) you may want to consider setting visualreport_without_invalid = FALSE.

Best,

Vincent

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

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[Leticia Sewaybricker]

Hi Vincent,

Thank you for investigating further and sharing this option.

I will run more tests on my end - specially now with the new GGIR 2.10-1 (exciting news!!) - and share any updates I have.

Thank you once more.

Best wishes,

Leticia

[Jairo Hidalgo Migueles]

Hi Leticia,

I'm sorry I couldn't look at this before. I have just run your file through GGIR version 2.10-1 (current version in CRAN) and everything run well, even with do.part3.pdf = TRUE. The only thing I had to change in your script is the definition of the desiredtz, as I observed your timestamps contained "-0700", so I defined desiredtz = "Etc/GMT+7". If, by any chance, you are processing the data in a different timezone where they were collected, you would also need to define desiredtz as I did.

Additionally, I was able to reproduce the error that you first reported in this thread:

Error in if (P2daysummary_tmp$`N hours`[1] < 24 & P2daysummary_tmp$`N hours`[1] > : missing value where TRUE/FALSE needed

This error appears in the generation of the file summary reports (pdf visualizations), so it is not affecting your output, just the visualizations. I am working on a solution for this now.

Best,
Jairo