[GGIR] error in part 4

[Gul Satar Ali]

Hi everyone and thanks to Vincent van Hees for the hard work on GGIR,

I'm a sleep researcher currently at Yuan Ze University Taiwan. My aim is to analyze the GENEActive raw accelerometer data "attached the bin file it's around seven hundred MB " ( https://drive.google.com/drive/folders/1_bKaFgli7RuHW2AgOMsEILAd9W0fryGn?usp=sharing) using GGIR. I have 7 days of datasets which I want to analyze  after the process the accelerometers successfully in part 1, 2, and 3, I have an error in part 4 says that ( and also screenshot attached below),

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Part 4
 1Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file 'C:/Users/gulsa/Documents/R/GGIR/output_New folder/meta/ms3.out/NA', probable reason 'No such file or directory'

_______________________________________________________________________________

 

which lead to the failure to process part 4. I wonder if anyone knows how to solve the problem.

I have used with g.shell.GGIR as shown below:

library(GGIR)
 
mode= c(1,2,3,4)
datadir= "C:/Users/gulsa/Documents/R/GGIR/New folder"
outputdir= "C:/Users/gulsa/Documents/R/GGIR"
studyname="test"
f0 = 1
f1 = 2
g.shell.GGIR(
  #-------------------------------
  # General parameters
  #-------------------------------
  mode=mode,
  datadir=datadir,
  outputdir=outputdir,
  studyname=studyname,
  f0=f0,
  f1=f1,
  overwrite = FALSE,
  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 = 1,
  hrs.del.end = 1,
  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= c(5,10),
  anglethreshold=5,
  ignorenonwear = TRUE,
  #-------------------------------
  # Part 4 parameters:
  #-------------------------------
  excludefirstlast = FALSE,
  includenightcrit = 16,
  def.noc.sleep = 1,
  #loglocation= "C:/Users/david/Documents/R/Ali/sleeplog.csv",
  outliers.only = FALSE,
  criterror = 4,
  relyonsleeplog = FALSE,
  sleeplogidnum = TRUE,
  colid=1,
  coln1=2,
  do.visual = TRUE,
  nnights = 9,
  #-------------------------------
  # Part 5 parameters:
  #-------------------------------
  # Key functions: Merging physical activity with sleep analyses
  threshold.lig = c(30,40,50),
  threshold.mod = c(100,120),
  threshold.vig = c(400,500),
  excludefirstlast = FALSE,
  boutcriter = 0.8,
  boutcriter.in = 0.9,
  boutcriter.lig = 0.8,
  boutcriter.mvpa = 0.8,
  boutdur.in = c(10,20,30),
  boutdur.lig = c(1,5,10),
  boutdur.mvpa = c(1,5,10),
  timewindow = c("WW"),
  #-----------------------------------
  # Report generation
  #-------------------------------
  do.report=c(2,4,5))

Thank you,

Ali

ᐧ

[Vincent van Hees]

Hi Ali,

I am able to process your file with all GGIR parts based on the command you shared.

Note that the file does not have an ID number in the header or in the filename as can be seen in part 2 csv report. This will complicate linking the data with your sleeplog.

So, first make sure the ID is correctly extracted. For example, by putting the ID number in the file name before the first underscore and changing idloc to idloc=2. Secondly, check that the ID number as extracted by part2 matches the ID number format in your sleeplog.

If this does not resolve your problem, please share full GGIR console output, you only shared a print screen of the message in red, not the other output above it.

Thanks,

Vincent

Dr. Vincent van Hees

Independent consultant

https://accelting.com/

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[Charles Lucena]

Hi all,

Did you solve your problem?

Unfortunately, my data analyses presented the same problem. Please, have a look below. 

 Part 4
 1Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :

  cannot open compressed file 'D:/Coortes Pelotas Dropbox/Acelerometria Epidemiologia/Acelerometria/Coorte 1982/Lotes - Acompanhamento dos 40 anos/Lote 1 - completo/Results/output_Lote 1 - csv/meta/ms3.out/NA', probable reason 'No such file or directory'

Could you help me, please?