Part 5 Error

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stuart.ro...@googlemail.com

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Jan 11, 2022, 4:33:26 PMJan 11
to R package GGIR
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

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Jan 12, 2022, 11:35:02 AMJan 12
to stuart.ro...@googlemail.com, R package GGIR
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

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Jan 12, 2022, 1:10:20 PMJan 12
to R package GGIR
Hi Vincent

You are a star - that has fixed it.

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

Cheers
Stuart

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