Issue #140 resolved
Lluís Revilla created an issue

I was doing the cases as in the website, when I noticed that they aren't run with the latest version of mixOmics.

The case I have trouble with is the sPLS

network(liver.spls, comp = 1:2, shape.node = c("rectangle", "rectangle"),
        color.node = c("white", "pink"), color.edge = color.edge, threshold = 0.8)
Error in network(liver.spls, comp = 1:2, shape.node = c("rectangle", "rectangle"),  : 
  unused argument (threshold = 0.8)

It only works when I remove the threshold parameter:

network(liver.spls, comp = 1:2, shape.node = c("rectangle", "rectangle"),
        color.node = c("white", "pink"), color.edge = color.edge )

Maybe it would work better to run these cases as vignettes inside the package. That way the code and content will be up to date.

Comments (4)

  1. Lluís Revilla reporter

    There is another tutorial that I'm having problems, it reports some warnings which make me doubt of the results

    perf.srbct <- perf(splsda.srbct, validation = "Mfold", folds = 5,
                        dist = 'max.dist', nrepeat = 10,
                        progressBar = FALSE) 
    Warning messages:
    1: The SGCCA algorithm did not converge 
    2: The SGCCA algorithm did not converge 
    
  2. Kim-Anh Le Cao repo owner

    Thanks Lluis we will fix that on the website. Many things to do on our end and we running at a stretch.

    There might be some convergence issue using perf, it depends on the random folds. I would not be worried though as this happened (here) twice in a 5 folds x 10 repeats = 50 runs and we average the results. I would be concerned however if that happened on a splsda() final model though (which is not the case here).

    I am closing this issue.

  3. GENET Carine

    The argument Threshold was replaced by cutoff. so the spls command should be :

    network(liver.spls, comp = 1:2, shape.node = c("rectangle", "rectangle"),
            color.node = c("white", "pink"), color.edge = color.edge, cutoff= 0.8 )
    

    Regards Carine Ca

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