This might just be a personal thing, but the term agglomeration and referring to the function tax_glom_taxonomy_annotate seems a little confusing and maybe doesn't clearly convey what this function is doing. I think in R the similar but more known action is aggregating and people might be more familiar with this? Up to you.
@elizabethmcd pointed out in #23:
I was copying the syntax/naming of the phyloseq function that does this: https://rdrr.io/bioc/phyloseq/man/tax_glom.html
I wanted to record this feedback because if we keep getting it then I want to change the wording for the function.