A question regarding day segment analyses with GGIR

[Julia ZZ]

Hi all,

I wonder if anyone has the experience with day segment analyses. I keep meeting a warning in the process:

Report part 2
 1 2 3Warning message:
In g.conv.actlog(qwindow, qwindow_dateformat) :
 Date not recognised in activity diary. We expect format /%d-/%m-/%Y but we see 04-11-2020 04-11-2020 25-10-2020 23-10-2020 23-10-2020 25-10-2020. You need to update the qwindow_dateformat argument, and check that dates are in a consistent format.

However, my activity log did show the date as 04-11-2020 (Nov 4th, 2020), 04-11-2020 (Nov 4th, 2020), 25-10-2020 (Oct 25th, 2020),  23-10-2020 (Oct 25th, 2020), 23-10-2020 (Oct 23rd, 2020),  and 25-10-2020 (Oct 25th, 2020). In addition, I did specify the qwindow_dateformat as "/%d-/%m-/%Y".  So, I am a little bit confused. Can anyone help me with it? Thank you very much. 

Sincerely,

Julia

[Vincent van Hees]

Hi Julia,

That is indeed peculiar.

I am not an Excel expert but I am now wondering whether it is possible that the dates are stored as m/d/Y even though you may have changed the way they are visually formatted. What happens if you specify "/%m-/%d-/%Y"?

Also, if you could send me your .csv file that be helpful. Just snapshot of the first couple of lines should be sufficient.

Thanks, Vincent

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[Julia ZZ]

Hi Vincent,

Thank you very much for the reply. I tried to specify "/%m-/%d-/%Y", it shows similar warning. So I put the current codes, 2 basic files, and activity logs (both excel and csv version) to the email. Can you help me with it?

library(GGIR)
datadir="V:/ACOI/.../CSV_all"
outputdir="V:/ACOI/.../test_activitylog"

g.shell.GGIR(

  datadir=datadir,
  outputdir=outputdir,
  studyname="Attempt1",
  idloc=6,
  f0=1,
  f1=2,
  mode=c(2),
  #mode = 1:2, # <= run GGIR parts 1 and 2 #revised based on the vignettes
  do.report = 2, # <= generate csv-report for GGIR part 2 #revised based on the vignettes
  qwindow = "V:/ACOI/.../activitylog_test_2files.csv", #revised based on the vignettes
  overwrite=TRUE,
#part 1#
        windowsizes = c(5,900,3600),
        do.anglez=TRUE,
        chunksize = c(1),
        printsummary=TRUE,
 
#part 2#
        strategy = 2 , # this strategy gets rid of first data before first midnight and last midnight
        includedaycrit = 16, M5L5res = 10, #already in default
        winhr = 5,
        #qwindow=c(0,24), #revised based on the vignettes
        qwindow_dateformat = "/%d-/%m-/%Y", #revised based on the vignettes
        #qwindow_dateformat = "/%md-/%d-/%y", #revised based on the vignettes
        qlevels = c(c(1380/1440),c(1410/1440)),
        ilevels = c(0,36, 201, 707, 8000),
        mvpathreshold = c(201),
        boutcriter = 0.8,
              bout.metric = 6 ,
        epochvalues2csv=TRUE,
        mvpadur=c(1,5,10),
        iglevels = TRUE, #this function calculates intensity gradient
        do.parallel = TRUE)

warnings()

Sincerely, 

Julia

[Julia ZZ]

Hi Vincent,

I am very sorry to bother you again, but I have an additional question beside my last post. After I update GGIR to 2.6.0, the segment file GGIR processing keeps showing error "Error in strptime(x, format, tz = "GMT") : invalid 'format' argument". It was no error when I used the last version. I wonder if you have any answers for it and my last questions regarding "/%d-/%m-/%Y warning". Thank you very much.

Sincerely,

Julia

On Monday, January 31, 2022 at 7:59:31 AM UTC-5 Vincent van Hees wrote:

[Vincent van Hees]

This should now be fixed in the GGIR development version. Please install for the time being with: 

library(remotes)

remotes::install_github("wadpac/GGIR")

Further,

• use  "%d-%m-%Y" without the forward slashes.
• Remove the dots in your activitylog file. Cells for missing values should be left empty.

Vincent

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[Julia ZZ]

Hi Vincent,

Thank you for your reply. I am using the most updated GGIR version and revise the activity log as you suggested, however it keeps showing the following information:

when process part 2:

Errors and warnings for meta_1034RAW.csv.RData$message
[1] "NA/NaN argument"

$call
fi:(fi - 1 + length(ML5colna))

when generate the part 2 report: 

Error: cannot allocate vector of size 1.1 Gb

I am very confused about those two messages. I wonder if you have any answers for it. Thank you very much.

Sincerely,

Julia

[Vincent van Hees]

Hi Julie,

See below the R code I used on your data a couple weeks ago, and it worked then. Can you try and see whether it works for you on the same files you send me?

g.shell.GGIR( 

  datadir=datadir,

  outputdir=outputdir,

  studyname=studyname,

  idloc=6,

  f0=1,

  f1=2,

  mode=c(2),

  #mode = 1:2, # <= run GGIR parts 1 and 2 #revised based on the vignettes

  do.report = 2, # <= generate csv-report for GGIR part 2 #revised based on the vignettes

  qwindow = "/home/vincent/data/investigating_issues/JuliaZZ/activitylog_test_2files.csv", #revised based on the vignettes

  overwrite=TRUE,

  #part 1#

  windowsizes = c(5,900,3600),

  do.anglez=TRUE,

  chunksize = c(1),

  printsummary=TRUE,

 

  #part 2#

  strategy = 2 , # this strategy gets rid of first data before first midnight and last midnight

  includedaycrit = 16, M5L5res = 10, #already in default

  winhr = 5,

  #qwindow=c(0,24), #revised based on the vignettes

  qwindow_dateformat = "%d-%m-%Y", #revised based on the vignettes

  #qwindow_dateformat = "/%md-/%d-/%y", #revised based on the vignettes

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

  ilevels = c(0,36, 201, 707, 8000),

  mvpathreshold = c(201),

  boutcriter = 0.8,

  bout.metric = 6 ,

  epochvalues2csv=TRUE,

  mvpadur=c(1,5,10),

  iglevels = TRUE, #this function calculates intensity gradient

  do.parallel = FALSE

  ) #viewingwindow of visual report: 1 centres at day and 2 centers at night

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