Michael McLaren

See https://github.com/joey711/phyloseq/issues/1335#issue-625661877

in order to avoid problems that can arise from misspelling optional arguments. See https://principles.tidyverse.org/dots-inspect.html for one idea

Create a method for testing equivalence between phyloseq objects

1

Currently, you can test if two phyloseq objects are literally equal with `all.equal`, but this function will return false if the taxa or sample order differs. It is useful for...

that can be used to run the `merge_taxa_vec()` ASV-to-OTU clustering example and possible future examples that require a phyloseq object with a `refseq` slot. One possibility is the Callahan et...

When doing a `tax_glom` with a `taxrank`where many taxa are unassigned and `NArm = TRUE`, then `tax_glom()` can be bottlenecked by the initial call to `prune_taxa()` to remove the taxa...

Compare distance and clustering methods for tip_glom

1

In phyloseq::tip_glom, the line ```r dd

Otherwise can fail with cryptic message; See https://github.com/joey711/phyloseq/issues/1110 (the message is different for speedyseq's tax_glom, but similarly unhelpful): ``` Error in `taxa_names

Specifically regarding functions from phyloseq. See recent issue with calling `t()` on a phyloseq object within the tax_glom function #6 for the sort of thing we need to make sure...

It might be convenient to have a function that performs a simple plug-in approach to the the 'reference-species' approach to calibration described by https://github.com/mikemc/differential-abundance-theory. In its simplest form, the function...