Birth-Death-Shift Analyses

Here, you can find the Rev scripts used in the study

Höhna, S., W A. Freyman, Z. Nolen, J. P. Huelsenbeck, M. R. May, B. Rannala,
   and B. R. Moore. Submitted. A general approach for inferring branch-
   specific rates of lineage diversification.

1. Likelihood surface for primates analysis under different implementations.
2. Prior and posterior distribution of the number of shifts when all categories are equal.
3. Comparison of data augmentation and stochastic mapping approaches for estimating branch-specific speciation rates.
4. Compare ESS between stochastic mapping and data agumentation.
5. Simulations confirming coverage probabilities.
6. Analyses investigating the sensitivity of the method to the number of discrete categories for the base distributions.
7. Prior sensitivity analysis of the shift rate prior on branch-specific speciation rates and the estimated number of shifts.
8. Empirical case study using a hyperprior approach.
9. Scripts for the path sampling analyses to calculate the Bayes Factor for the primate data.
10. Simulation study.
11. Various tree files, including the primate data tree file.