Analyses of Physical activity - no sleep data and activity thresholds

[Naomi Chapman]

Hi all, 

I have a couple of questions relating to the analyses of Physical activity from the Actigraph GTX3 worn on the hip for the waking hours only (i.e. participants were advised to remove for sleep and don on waking up).

1) As participants only wore for waking hours and I am only interested in physical activity data is this the correct GGIR script or do I not need to include Part 3 and 4 as I have no sleep data?

library(GGIR)
GGIR(mode=c(1,2,3,4,5),
     datadir="C:/Users/nchapman/Documents/GGIR data",
     outputdir="C:/Users/nchapman/Documents/GGIR test output working",
     dataFormat="raw",
     desiredtz = "Australia/Perth",
     do.report=c(2,5), 
     
     
     #part1
     idloc=6,
     dynrange=NULL,
     do.enmo = TRUE,
     acc.metric = "ENMO",
     
     #part2  
     strategy=2,
     includedaycrit=8,
     sensor.location="hip",
     qwindow=c(0,24),
     do.imp=TRUE, 
     mvpathreshold=c(69.1),
     excludefirstlast=FALSE,
     
     #Part 3 and 4
     timethreshold=(5),
     anglethreshold=5,
     ignorenonwear=TRUE,
     def.noc.sleep=1,
     
     #Part5
  threshold.lig=c(47.4),
  threshold.mod=c(69.1),
  threshold.vig=c(258.7) ,
  bout.criter=0.8,
  boutcriter.in=0.9,
  boutcriter.lig=0.8,
  boutcriter.mvpa=0.8,
  boutdur.in=c(1, 10, 30),
  boutdur.lig=c(1, 10),
  boutdur.mvpa=c(1, 10),
  includedaycrit.part5=8,#includedaycrit would be 16hours if I had night measurement
  part5_agg2_60seconds = TRUE,     

     #visual report
     timewindow=c("MM"),
     visualreport=TRUE,
     week_weekend_aggregate.part5=TRUE)

2) Regarding the thresholds (I am using Hildebrand), how does the analyses work given there is only one number defined. Does the script automatically detect that light is between the values defined for light and moderate (47.4 and 69.1), moderate between the values for moderate and vigorous (69.1 and 258.7) and vigorous above that defined for vigorous (258.7) or is it worked out some other way? 

3) If I am not interested in bouts for physical activity can I just remove those lines from my R script?

Hopefully that makes sense and thanks in advance for the help. 

Naomi 

[Vincent van Hees]

Hi Naomi,

The GGIR documentation should answer all your questions. For example here, here, and here.

If you need additional help, please consider hiring my for support.

Best wishes,

Vincent

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