# Overview

RevBayes has as its central idea that any statistical model, for example a phylogenetic model, is composed of smaller parts that can be decomposed and put back together in a modular fashion (Höhna et al. 2016). This comes from considering (phylogenetic) models as probabilistic graphical models, which lends flexibility and enhances the capabilities of the program. Users interact with RevBayes via an interactive shell. Users communicate commands using a language specifically designed for RevBayes, called Rev; an R-like language (complete with control statements, user-defined functions, and loops) that enables the user to build up (phylogenetic) models from simple parts (random variables, variable/parameter transformations, models, and constants of different sorts).

Here we assume that you have successfully installed RevBayes. If this isn’t the case, then please consult our website on how to install RevBayes.

# Getting Started

For the examples outlined in each tutorial, we will use RevBayes interactively by typing commands in the command-line console. For the exercises you can either use RevBayes interactively or run an entire script. Execute the RevBayes binary. If this program is in your path, then you can simply type in your Unix terminal:

• ’$rb’\ When you execute the program, you will see a brief program information, including the current version number. Remember that more information can be obtained from www.RevBayes.com. When you execute the program with an additional filename, e.g., • ’$ rb my_analysis.Rev’\

then RevBayes will run all commands specified in your file.

You may want to run RevBayes in parallel using multiple processes. This can be done by starting RevBayes with

# Getting help in RevBayes

RevBayes provides an elaborate help system. Most of the help is found online on our website\ http://www.RevBayes.com. Within RevBayes you can display the help for a function, distribution or any other type using the ? symbol followed by the command you want help for:

?dnNorm
?mcmc
?mcmc.run


Additionally, RevBayes will print the correct usage of a function if you only type in its name and hit return:

mcmc

       MCMC function (Model model, Monitor[] monitors, Move[] moves, String moveschedule = "sequential" | "random" | "single", Natural nruns)


## RevBayes Users’ Forum

An email list has been created for users of RevBayes to discuss RevBayes-related topics, including: RevBayes installation and use, scripting and programming, phylogenetics, population genetics, models of evolution, graphical models, etc. The forum is hosted by Google Groups:

1. Höhna S., Landis M.J., Heath T.A., Boussau B., Lartillot N., Moore B.R., Huelsenbeck J.P., Ronquist F. 2016. RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language. Systematic Biology. 65:726–736. 10.1093/sysbio/syw021
2. Höhna S., Heath T.A., Boussau B., Landis M.J., Ronquist F., Huelsenbeck J.P. 2014. Probabilistic Graphical Model Representation in Phylogenetics. Systematic Biology. 63:753–771. 10.1093/sysbio/syu039