No Part 5 outputs, would appreciate advice

[Rose Evard]

Hello, 

I am currently trying to understand and use GGIR for examining wrist-worn actigraph data over a 12-24 hour wear period to analyze PA intensity patterns.   I'm trying to use the Hildebrand cut points.  I'm able to receive the night summaries from Part 4, but not the output PDF that I see in the GGIR tutorial YouTube video or the Part 5 summaries.  I have adjusted the includedcrit.part5 and the minimum_MM_length.part5.  

Within my Part 2 person-level summary, the ENMO_fullRecordingMean is NaN across all four participants' data that I am testing with.  I feel like this could be part of the issue, but I don't know how to solve that. 

Any advice?  Here are my current configurations, which I made following the GGIR vignette: 

---- 

Part 2: 

do.enmo= TRUE,

acc.metric="ENMO",

idloc = 2,

-----

Part 5: 

threshold.lig =  c(44.8),

  threshold.mod = c(100.6),

  threshold.vig = c(428.8),

  includedaycrit.part5 = 1/3,

  minimum_MM_length.part5 = 12

If any more information is needed let me know!

Thank you,

Rose Evard

[Vincent van Hees]

Hello Rose,

Can you process the file without specifying any argument, except: datadir="yourdatafolderpath", outputdir="youroutputfolderpath", mode = c(1,2), do.report = 2, overwrite= TRUE.

Ideally, the part 2 reports in the results folder and the pdf file in the QC folder will give you an impression of how long the recording lasted and whether the accelerometer was worn at all.

Best,

Vincent

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[Sarah Burkart]

Good morning,

I am also running into an error that I haven't seen before when processing 24-hour Axivity data. I've run several files without issue, but one file does not produce part 5 output. I have inspected the part 2 and part 4 output and it appears that I have 21 days with at least 16 hours of wear (valid day).  I have also updated and restarted R/RStudio. When I try to process the file, I receive the error below:

Errors and warnings for 76664_0017930101.cwa.RData$message

[1] "invalid 'trim' argument"

$call

format.default(ts$time[sse[ts$diur[sse] == 0]], "%H")

I have included some code below if it is needed:

  #=====================

  # Parts 1 & 2

  #=====================

  do.enmoa = TRUE, do.enmo = FALSE,  

  strategy = 2,               ndayswindow= 1,

  hrs.del.start = 0,          hrs.del.end = 0,

  maxdur = 0,                 includedaycrit = 16,

  winhr = c(5,10),

  qlevels = c(c(1380/1440),c(1410/1440)),

  qwindow=c(0,24),

  ilevels = c(seq(0,400,by=50),8000),

  mvpathreshold =c(100.4),

  bout.metric = 4,

  closedbout= FALSE,

  overwrite=FALSE,

  epochvalues2csv= TRUE,

  #=====================

  # Part 5

  #=====================

  threshold.lig = c(61.8), threshold.mod = c(100.4), 

  boutcriter = 0.8,      boutcriter.in = 0.9,     boutcriter.lig = 0.8,

  boutcriter.mvpa = 0.8, boutdur.in = c(1), boutdur.lig = c(1),

  boutdur.mvpa = c(1), save_ms5rawlevels = TRUE,

Thank you in advance for your suggestions!

-Sarah