Ordination methods, interpretation

[TuomasBorman]

The ordination method section does only describe available methods, but does not really say the difference between them, and when to use them. (the differences in interpretation)

• The UMAP section could cite to this paper for instance. It can give misleading results, but could be used in clustering.
• Aithcison vs Bray-Curtis in MDS. Could describe the differences in interpretation. AIthcison measures linear relationship of abundances. --> samples close to each other have similar abundances. Bray-Curtis measures how large portion of species in communities is shared between samples A and B. @antagomir Is there better ecological interpretation?

[antagomir]

When ordination section text is updated it would be necessary to cite key literature, where those interpretations and ways to summarize them are available. I can pick suitable refs when someone opens a PR on this for comments.

[antagomir]

UMAP is generally not so recommended, I would leave that out entirely and focus on the methods that are commonly used & accepted in the microbiome field (e.g. PCA, PCoA/MDS, NMDS, dbRDA, possibly some other but not too many)

[antagomir]

For dissimilarities, the following are very relevant at least: Aitchison, Jaccard, Bray-Curtis, Unifrac.