As a reviewer of the pirouette manuscript pointed out, a site model has
- a gamma site model
- a substitution model
Therefore, create_jc69_site_model(id = NA, gamma_site_model = create_gamma_site_model()) is a minor misnomer.
Better would be: create_site_model(id = NA, gamma_site_model = create_gamma_site_model(), subst_model = create_jc69_nsm()).
As a reviewer of the
pirouettemanuscript pointed out, a site model hasTherefore,
create_jc69_site_model(id = NA, gamma_site_model = create_gamma_site_model())is a minor misnomer.Better would be:
create_site_model(id = NA, gamma_site_model = create_gamma_site_model(), subst_model = create_jc69_nsm()).