Leo Lahti

minimal data is now available in mia https://github.com/microbiome/mia/blob/devel/data/Tito2024QMP.rda

Great! It might be good to summarize also in OMA the basis for selecting this particular implementation with just 1-3 sentences, when you update relevant part there.

That's a good point. Would it be good to check what options are available for the other one, too, and choose the optimal one if there are relevant differences?

It should be also clear for user if they use the weighted or unweighted version. Ideally, both will be available.

Ok.. should we then provide all available options by using arguments `weighted` (TRUE/FALSE) and `normalized` (TRUE/FALSE)? Then the wrapper will internally choose the right method for the given combination (and...

In that link phyloseq seems to yield systematically different methods than others. We can do more benchmarks but I am not sure if that is needed at this point. If...

1. if the fast algorithm yields the same results than slow algorithm then the only thing with practical importance is the choices on normalization & weighting? Why should we support...

We can certainly add another MAE demo data set in mia, for instance. It should be about microbiome research (which is indeed so far less covered in terms of multiomics...

@stefpeschel would be great to hear your thoughts on this; SECOM seems to have good performance compared to SparCC & SPIEC-EASI. Would it be worth incorporating into the network section...

Let's at least cite SECOM in the network chapter in a suitable place?