Please cite more references for the "beta diversity metric" vignette

[cstawitz]

The decision tree in the vignette "selecting a beta diversity metric" is very helpful, but lacks citations. I would expect such an authoritative resource to cite where the recommendations for different diversity metrics comes from, as I expect it draws upon a lof expert opinion. I'm not an expert in microbial ecology, so I can't verify the accuracy of the guide, but at minimum it should provide a reference list so researchers can cite why they chose a specific diversity metric.

There are also a few missing explanatory statements from this vignette. For example, the vignette recommends different alpha levels for the UniFrac method without explaining what alpha is.

[dansmith01]

Thank you for your valuable feedback regarding the "Selecting a Beta Diversity Metric" vignette. We have revised the document to ensure it serves as an authoritative and well-referenced resource:

• Citations: We have extensively updated the decision tree to include primary literature citations for every metric recommendation. The guide now references key studies (e.g., Lozupone & Knight 2005, Gloor et al. 2017, Chen et al. 2021, Kers & Saccenti 2022) to substantiate the decision points regarding phylogenetic signal, compositionality, and sparsity.

• Clarification of UniFrac Parameters: We have streamlined the Generalized UniFrac recommendation to focus on the method's ecological utility (balancing dominant and rare taxa) rather than specific parameter tuning. The discussion of specific alpha parameter values has been moved to the generalized_unifrac() function documentation, where the mathematical definition is now explicitly provided.

We believe these updates provide the necessary context and rigour for researchers to confidently cite and justify their metric selection.