[DOCUMENTATION] example of reference taxon identifiability constraint

[adw96]

Hi @svteichman! I just had an awesome meeting with some folx interested in using the reference taxon constraint for radEmu. Would you mind putting together a vignette showing how to do this? We don't have one, to my knowledge 🙀

It can be short and sweet, eg roughly following

• "This vignette shows you how to change the identifiability constraint in radEmu to use a reference taxon. It assumes familiarity with the basic usage of radEmu."
• "We'll use the dataset of Wirbel et al. Check out the introductory vignette for more info."
• Here's how you fit the model with eg F praus as the reference taxon...
• The interpretation of the parameters changes when you change the constraint. Here's how you interpret the estimates and inference results... Recall that's this is the old interpretation (under smooth median)...
• "We just fit a single categorical predictor here, but you can do the same with multiple covariates as well as cluster-correlated (eg longitudinal) data."
• "Don't forget to let us know your questions "
• link to the vignette in the wiki

Thank you for your help and please let me know your questions!

Others -- feel free to chime in with any other specific requests for documentation.

PS. I think these folx actually need fastEmu -- they were very enthusiastic when I told them it's in the works😻

[svteichman]

Great idea, will do - thanks for the helpful outline!