Leo Lahti

Can you provide a reproducible example? We also recommend shifting to SummarizeExperiment-based systems https://microbiome.github.io/OMA/

It seems that after averaging over nationality, there are no groups any more. The function is not intended to be used this way, so we should add a warning or...

Hmm yes, we were planning to just remove this functionality but perhaps it could be mentioned more explicitly or with a link to some online tutorial example.

naming changed now - functionality issue not

Hi - this function is for fast preliminary exploration only. Do the examples on [this page](https://microbiome.github.io/tutorials/Heatmap.html) help? We are aiming to improve the tutorial over time so suggestions are welcome.

This visualization has been constantly problematic. We will need a more robust solution than what is currently available. Implementing such may take some time i.e. no quick fix is possible...

As far as I can see, none of the above-mentioned functions are maintaiend in the microbiome R pkg. This functionality and examples would be useful, though, but not currently implemented....

I agree, this would be useful. If you could afford the time to prepare an example, we could add it in the tutorial? Otherwise, I'll leave this open for now...

Sure, excellent idea, and tutorials do play a key role in dissemination of these methods. The microbiome package currently focuses on downstream analyses of phyloseq objects, and provides some functionality...

How about an example of selecting core microbiota based on user defined detection and prevalence cutoffs; and subsequent visualizations of the core? The "core" function should be intuitive and useful,...