I’m happy to say our paper in Molecular Biology and Evolution on doing PPS in RevBayes is finally out. In this work we streamline the process of posterior predictive simulation, by incoporating all of the necessary tools and test statistics into the backend machinery of RevBayes. Details below.
Tests of absolute model fit are crucial in model-based inference because poorly structured models can lead to biased parameter estimates. In Bayesian inference, posterior predictive simulations can be used to test absolute model fit. However, such tests have not been commonly practiced in phylogenetic inference due to a lack of convenient and flexible software. Here, we describe our newly implemented tests of model fit using posterior predictive testing, based on both data- and inference-based test statistics, in the phylogenetics software RevBayes. This new implementation makes a large spectrum of models available for use through a user-friendly and flexible interface.
Keywords: model testing, Bayesian inference, phylogenetics
Höhna S., Coghill L.M., Mount G.G., Thomson, R.C., Brown, J.M., (2017) P3: Phylogenetic Posterior Prediction in RevBayes. Molecular Biology and Evolution 35:4,1028-1034. doi:10.1093/molbev/msx286.