Hi Greg,
We have now addressed points 1., 5. and 6. by updating the documentation on the Github repository. For the remaining points some comments:
2.Besides the small unit test dataset, which can be executed in an automated manner, we additionally also provide an option for automatic download of the real-world dataset using curl. Longer term, we would like to integrate the automated download through the plugin dedicated to GNPS integration, which is currently under development.
3.We think that the FeatureTable[Frequency] semantic type is fine for now as it fits the plugin dedicated to GNPS integration semantic output type.
4.We have opened an issue on the q2-issue tracker regarding this subject: Create SimilarityMatrix semantic type · Issue #1 · madeleineernst/q2-cscs · GitHub
7.For now we added the code lines you suggested to compare the two diversity metrics using a Mantel test and Procrustes analysis to the documentation.
Thanks a lot again for your suggestions for improvement! We hope that we were able to address some of them and will continue working on the longer term suggestions once plugins/data becomes available!
Kind regards,
Madeleine and Asker