error in mode == 0

[Megan Sison]

Hi, 

I am using GGIR to analyse data from axivity sleep trackers for my masters research. I have successfully used this for several weeks now, but it has just stopped working and keeps coming up with the following error message:

Error in mode == 0 :
  comparison (1) is possible only for atomic and list types

I have restarted R, and ensured all packages are up to date. I would really appreciate any guidance as I have little time left to complete my research.

I am using the following R script:

rm(list=ls())
graphics.off()
#==================================================================
f0 = 1  
f1 = 1
mode= c(1,2,3,4)
datadir= "C:/Users/megan/OneDrive/mystudy/mydata"
outputdir= "C:/Users/megan/OneDrive/mystudy/myresults"
studyname="test"
#=================================================
library(GGIR)
g.shell.GGIR(#-------------------------------
             # General parameters
             #-------------------------------
             mode=mode,
             datadir=datadir,
             outputdir=outputdir,
             studyname=studyname,
             f0=f0,
             f1=f1,
             overwrite = TRUE,
             do.imp=TRUE,
             idloc=1,
             print.filename=FALSE,
             storefolderstructure=FALSE,
             #-------------------------------
             # Part 1 parameters:
             #-------------------------------
             windowsizes = c(5,900,3600),
             do.cal=TRUE,
             do.enmo = TRUE,
             do.anglez=TRUE,
             chunksize=1,
             printsummary=TRUE,
             #-------------------------------
             # Part 2 parameters:
             #-------------------------------
             strategy = 1,
             ndayswindow=7,
             hrs.del.start = 0,
             hrs.del.end = 0,
             maxdur = 9,
             includedaycrit = 16,
             L5M5window = c(0,24),
             M5L5res = 10,
             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(100,120),
             #-------------------------------
             # Part 3 parameters:
             #-------------------------------
             timethreshold=5,
             anglethreshold= 5,
             ignorenonwear = TRUE,
             #-------------------------------
             # Part 4 parameters:
             #-------------------------------
             excludefirstlast = FALSE,
             includenightcrit = 16,
             def.noc.sleep = 1,
             # loglocation= "D:/sleeplog.csv,"
             outliers.only = FALSE,
             criterror = 4,
             relyonsleeplog = FALSE,
             sleeplogidnum = TRUE,
             colid=1,
             coln1=2,
             do.visual = TRUE,
             nnights = 9,
             #-------------------------------
             # Report generation
             #-------------------------------
             do.report=c(2,4))
visualreport=TRUE
dofirstpage = TRUE
viewingwindow=2

Thank you in advance,

Megan 

[Vincent van Hees]

Hi Mega,

Can you try replacing g.shell.GGIR( by GGIR(.

I recently added function GGIR as alternative to function g.shell.GGIR. My intention was to preserve g.shell.GGIR functionality, but possibly something went wrong. The idea at least is that when a user call g.shell.GGIR it actually uses GGIR in the background. I will look into it to fix this, but in the mean time replacing g.shell.GGIR by GGIR in your script should address the issue.

Thanks,

Vincent

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