Tracking when I made the `core_summary_lists.rda` I have been using

[jibarozzo]

Summary

I've identified the history of the core_summary_lists.rda object that has been used throughout our analyses. There appears to be a fundamental flaw in how this object was generated.

Timeline

• Commit 0743de9: First successful implementation of ExtractCore() function, which created spatial_core.rda
• Commit d38af24: Renamed the object from spatial_core to core_summary_lists

Issue Details

All subsequent analyses have been performed using this core_summary_lists.rda object. However, I've identified that it is fundamentally flawed because it identified "core" ASVs based on dplyr::last(), which we have now determined to be unsuitable for our analyses. Based on germs-lab/BRCore/issues/17, first handled in germs-lab/BRCore/issues/5

Impact

This issue affects all downstream analyses that depend on the correct identification of core ASVs, which includes most of our ordination analyses, dbRDA models, and microbial community comparisons across BRCs.

Next Steps

We need to:

1. Regenerate the core microbiome using an appropriate method
2. Re-run affected analyses with the corrected core ASV set
3. Validate that the new results are methodologically sound
4. Update relevant figures and tables for the manuscript