This R package wraps a small C++ library that uses expectation propagation to calculate a variational approximation to the likelihood of the phylogenetic threshold model. The advantage of the approximation is that it scales to a nearly arbitrary number of traits and tips.
For examples of use, see the functions testcase_continuous() (for continuous traits), testcase_categorical() (for binary traits), and testcase_mixed() (for mixed continuous-binary traits).
Slides decribing the method and implementation are found here.