ANCOMBC arguments/output issues in NUI Galway Metagenomics Workshop

[cmirzayi]

Currently knitting this workshop fails due to a few issues I've identified:

ancombcResults <-
  mia::makePhyloseqFromTreeSE(countryData) |>
  ancombc("country")

fails due to a missing formula. Updating to formula="country" appears to resolve, but it doesn't seem to give the same results as the original analysis. The results are about slightly different from the original. For instance, Catenibacterium mitsuokai has a B of -8.69 in the vignette (available here: https://waldronlab.io/curatedMetagenomicDataAnalyses/articles/NUI-Galway-Metagenomics-Workshop.html#modeling-bacteria-by-country) but a B of -8.51 when I run it now. @lwaldron is this expected?

The next step is that there are issues converting the list of results from ANCOMBC into a data.frame. It appears that the format is very different from what it was in 2021 and will require some updates which I will begin documenting soon.

[lwaldron]

I assume it's because there have been more samples added to cMD since 2021, wouldn't worry about small changes in the coefficients.

[cmirzayi]

I spent some time today plugging away at this. I should have a pull request with the updated and fixed Galway workshop vignette tomorrow.

[cmirzayi]

#52 resolves this issue.