Part 5 Error

[stuart.ro...@googlemail.com]

Hi all

I have been using GGIR for a while but with my recent batch of analysis i can run parts 2-4 but when running part 5 i get the following error 

Report part 5

 loading all the milestone data from part 5 this can take a few minutes

Error in (function (..., deparse.level = 1)  :

  number of columns of matrices must match (see arg 284)

This is not something i have encountered before.

The GGIR code i am using is below when trying to run part 5 alone after successfully running parts 2-4.

If anyone else has encountered this and came up with a solution then let me know.

Cheers

Stuart

g.shell.GGIR(#=======================================
             # INPUT NEEDED:
             mode=c(5),
             datadir="xxxx",
             outputdir="xxx",
             f0=1, f1=c(),
             overwrite = FALSE,
             #-------------------------------
             # Part 1:
             #-------------------------------
             # Key functions: reading file, auto-calibration, and extracting features
             do.enmo = TRUE,             do.anglez=TRUE,
             desiredtz="Asia/Kuwait",
             chunksize=1,                printsummary=TRUE,
             #-------------------------------
             # Part 2:
             #-------------------------------
             strategy = 1,               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(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24),
            doilevels = TRUE,
             ilevels = c(0, 30, 100, 200, 300, 400, 8000),
             mvpathreshold =c(100),
             bout.metric = 4,
             closedbout=FALSE,
             iglevels=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 = 16,
             def.noc.sleep = c(1),
             outliers.only = TRUE,
             criterror = 4,
             relyonsleeplog = FALSE,
             colid=1,
             coln1=2,
             do.visual = FALSE,
             nnights = 9,
             #-------------------------------
             # Part 5:
             # Key functions: Merging physical activity with sleep analyses
             #-------------------------------
             threshold.lig = c(30), threshold.mod = c(100),  threshold.vig = c(400),
             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"), frag.metrics = "all",
             part5_agg2_60seconds= TRUE,
             #-----------------------------------
             # Report generation
             #-------------------------------
             # Key functions: Generating reports based on meta-data
             do.report=c(2,4,5),
             visualreport=FALSE,     dofirstpage = FALSE,
             viewingwindow=1)

[Vincent van Hees]

Hi Stuart,

I think it is a bug in GGIR specific to when using argument storefolderstructure = TRUE, small chance that is also affects other configurations, I have now drafted a fix to this.

Would you mind installing the development version of GGIR with the following code:

install.packages("remotes")

library(remotes)

remotes::install_github("wadpac/GGIR", ref= issue484_columnmatches")

library(GGIR)

Next, please re-run part 5 (argument: mode = 5) and re-create the report (argument: do.report = 5).

Let met know if this addresses the issue.

Cheers, Vincent

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[stuart.ro...@googlemail.com]

Hi Vincent

You are a star - that has fixed it.

Thanks again for all the help and work you do on GGIR!

Cheers

Stuart

[Julia]

Hi Vincent,

I have a follow-up question on this topic. 

I had the same problem and tried the suggested code. I received the following error after installing 'remotes':

remotes::install_github("wadpac/GGIR", ref= "issue484_columnmatches") 

Downloading GitHub repo wadpac/GGIR@issue484_columnmatches

Error in utils::download.file(url, path, method = method, quiet = quiet,  : cannot open URL 'https://api.github.com/repos/wadpac/GGIR/tarball/issue484_columnmatches' >

Do you have a suggestion to solve this problem?

Thank you!

Best, 

Julia 

Op woensdag 12 januari 2022 om 17:35:02 UTC+1 schreef Vincent van Hees:

[Jairo Hidalgo Migueles]

Hi Julia,

The branch  "issue484_columnmatches" is from 1 year ago, so I would say that the changes in that branch are already implemented in the current GGIR version. Try to install GGIR with

install.packages("GGIR")

Make sure you are using the version 2.8-2 and re-run your script.

Best,
Jairo

[Julia]

Hi Jairo,

Thank you for answering.

I still experience a smilar problem, but in the report of part 4.

 Report part 4   

loading all the milestone data from part 4 this can take a few minutes 

Error in (function (..., deparse.level = 1)  :    

number of columns of matrices must match (see arg 2)

It does not give this error when I run the script on less patient files. 

Do you have any suggestions?

Thank you!

Best,

 Julia 

Op zaterdag 4 februari 2023 om 10:03:53 UTC+1 schreef jairo.hidal...@gmail.com:

[Vincent van Hees]

Hi Julia,

Just sharing an error message does not make it easy for others to help you.

Please share as much detail as possible to help others help you, ideally with a reproducible small example of the error, including:

• GGIR call used
• Example .RData file from the meta/basic folder
• Description of what you have tried to understand the issue
• Description of what differs between the files for which the code worked.

Thanks,

Vincent

Dr. Vincent van Hees | Independent consultant | https://accelting.com/

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