Part 4 Sleep Summary Missing Days

[Taren Sanders]

Hi All,

We've been processing some accelerometer data with more than a week's worth of observations. We are getting the expected number of days in the part 2 day summary csv, however the part 4 night summary csv never presents more than 7 nights worth of data. There are definitely more than 7 nights worth of data. If I inspect the sleep qc PDFs, I can see the expected number of nights are present. We have the excludefirstlast set to FALSE, and we are not using any log data. Am I missing a setting?

Thanks,

Taren

[Vincent van Hees]

Hi Taren,

The file "part4_nightsummary_sleep_full.csv" in the results/QC folder may help to clarify this with variable cleaningcode, see also function documentation of part 4.

An explanation could be the non-wear criteria settings that cause GGIR to ignore certain nights if the monitor was not worn for enough hours in the day.

Vincent

[Taren Sanders]

Hi Vincent,

Very much appreciate the response. I had a look at the _full night summary, and these still only show 7 nights. That is, it is not that the nights are being excluded (we had turned down all of the variables used to exclude to test this), rather that these nights just don't seem to be processed.It looks like others are having similar problems (https://groups.google.com/forum/#!topic/rpackageggir/7SEDKUM5fLQ). 

If helpful, I've posted the script used below. Again, appreciate any suggestions you have.

Kind regards,

Taren

     

 g.shell.GGIR(#=======================================

                   # INPUT NEEDED:

                   mode=c(2,3,4),

                   metadatadir=c("s:/7-IPPE Data Folder/iPLAY Data/Data/Main Study/Geneactiv Temp Output"),

                   outputdir="s:/7-IPPE Data Folder/iPLAY Data/Data/Main Study/Geneactiv Temp Output", 

                   f0=1, f1=c(), 

                   desiredtz="Australia/Sydney", 

                   overwrite=TRUE,

                   studyname = "MAROOTA_BL",

                   #-------------------------------

                   # Part 1:

                   #-------------------------------

                   # Key functions: reading file, auto-calibration, and extracting features

                   do.enmo = TRUE,             do.anglez=TRUE,

                   chunksize=1,                printsummary=TRUE,

                   windowsizes = c(5,900,3600), 

                   #-------------------------------

                   # Part 2:

                   #-------------------------------

                   strategy = 3,               ndayswindow=7, 

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

                   #maxdur = 9,                 includedaycrit = 16,

                   winhr = c(5,10),

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

                   qwindow=c(0,24),

                   ilevels = c(0,56.3,191.6,695.8,8000),

                   mvpathreshold =c(191.6, 695.8), 

                   bout.metric = 4,

                   closedbout=FALSE,

                   do.imp=TRUE, 

                   #-------------------------------

                   # Part 3:

                   #-------------------------------

                   # Key functions: Sleep detection

                   timethreshold= c(5),        anglethreshold=5,

                   ignorenonwear = TRUE,

                   #-------------------------------

                   # Part 4:

                   #-------------------------------

                   # Key functions: Integrating sleep log (if available) with sleep detection

                   # storing day and person specific summaries of sleep

                   excludefirstlast = FALSE,

                   includenightcrit = 0,

                   def.noc.sleep = c(),

                   # loglocation= "C:/mydata/sleeplog.csv",

                   outliers.only = FALSE,

                   criterror = 4,

                   relyonsleeplog = FALSE,

                   # sleeplogidnum = TRUE,

                   # colid=1,

                   # coln1=2,

                   do.visual = TRUE,

                   # nnights = 9,

                   #-------------------------------

                   # Part 5:

                   # Key functions: Merging physical activity with sleep analyses

                   #-------------------------------

                   threshold.lig = c(56.3), threshold.mod = c(191.6),threshold.vig = c(695.8),

                   boutcriter = 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),   timewindow = c("WW"),

                   #-----------------------------------

                   # Report generation

                   #-------------------------------

                   # Key functions: Generating reports based on meta-data

                   do.report=c(2,4),

                   visualreport=TRUE,     dofirstpage = TRUE,

                   viewingwindow=1)

[Vincent van Hees]

Hi Taren,

Jairo has now looked into this and has proposed some improvements to the g.part5 function to help you and others extract more days of results with part 5.

Later this week I will go through his proposed changes and hopefully soon after that we will be able to incorporate it in a new version of GGIR.

Best regards,

Vincent

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