I posted an updated version of the preprint that introduces the new method ecoevolity. The updates are relatively minor, but there are new plots in the Supporting Information that illustrate the model-choice accuracy of the new method, which complement the plots that show the accuracy of estimating the number of divergence events.
Also, thanks to the workshop at the SSB Meeting in June, the documentation is much improved. Checkout the open-science repository for the project if you want all the details.