RevBayes is a computer program that uses directed acyclic graphs (DAG's) to specify any type of model, to hold the model and data in memory, and to compute the likelihood of the parameters of the model. DAG's provide a framework for the construction of modular models. Models can easily be extended and/or parts of the model exchanged (e.g., the substitution process and clock model) and several models can be combined. The design of RevBayes should allow the implementation of any extension to existing models. RevBayes is mainly developed for Bayesian phylogenetic analyses, but it can be extended to any inference on probabilistic models.
In this talk, I will give a brief introduction to the concept of DAG's and how they are used to construct a model. Once the model is specified, I will show how to simulate new observations under the model and how to estimate its parameters. I will demonstrate this in the RevLanguage, which is an R-like language for building DAG's for phylogenetic problems. The RevLanguage is used interactively to specify the model, as done with R. I will show how a full phylogenetic model is specified, step-by-step. I will mainly focus on various standard substitution models, relaxed clock models, and divergence times priors. Specifically, I will show a new birth-death model with speciation and extinction rates varying over time and use this in a integrative analysis. In the integrative analysis I condition only on the alignment (only the alignment is considered to be known) and estimate the tree and divergence times simultaneously as well as the speciation and extinction rates.
| West Coast USA: | 11:00 (11:00 AM) on Wednesday, February 29 |
| East Coast USA: | 14:00 (02:00 PM) on Wednesday, February 29 |
| England: | 19:00 (07:00 PM) on Wednesday, February 29 |
| France: | 20:00 (08:00 PM) on Wednesday, February 29 |
| Japan: | 04:00 (04:00 AM) on Thursday, March 01 |
| New Zealand: | 08:00 (08:00 AM) on Thursday, March 01 |
Learn how to connect ahead of time. To hear about upcoming talks, send an email to phyloseminar+subscribe@googlegroups.com or follow @ematsen.
If you can't make it, don't fret— you can always watch the recording.