From 8685e5e7428810418d3c89b1bc7bd9000c99303f Mon Sep 17 00:00:00 2001 From: Neha Tiwari Date: Tue, 22 Feb 2022 15:02:46 -0600 Subject: [PATCH] READMEnew.md --- READMEnew.md | 45 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 READMEnew.md diff --git a/READMEnew.md b/READMEnew.md new file mode 100644 index 0000000..4a38f11 --- /dev/null +++ b/READMEnew.md @@ -0,0 +1,45 @@ + +# RevBayes Workshop: Phylogenetic graphical models and Bayesian inference +### UC Berkeley, VLSB 1002 +### February 26-27 2018, 12:00 PM to 4:00 PM +##### Instructor: Will Freyman +##### Coordinator: Carrie Tribble +##### Funded in part by UC Berkeley's Data Science program [DS421](http://ds421.berkeley.edu/) + +[RevBayes](http://revbayes.com) represents a fundamental re-conception of phylogenetic modeling by adopting a graphical model framework in +which all probabilistic models are comprised of modular components that can be assembled in a myriad of ways. +The graphical models are specified using a highly flexible R-like language, `Rev`. + +This workshop will focus on enabling participants to use `Rev` to specify custom arbitrarily complex phylogenetic models from simple component parts. +Instruction will combine short lectures introducing the theoretical and conceptual basis of each inference problem and hands-on computer tutorials +demonstrating how to explore these questions using [RevBayes](http://revbayes.com). +Previous experience with [RevBayes](http://revbayes.com) is not necessary, though familiarity with phylogenetic inference using other software is expected. + +This workshop is open to anyone interested, including students, staff, post-docs, and faculty from IB and beyond. + +Please install the latest version (1.0.7) of [RevBayes](http://revbayes.com) for this workshop. Some of the state-dependent speciation and extinction analyses will not work with earlier versions. + + + +* **February 26** (noon - 4 PM) [[slides]](https://raw.githubusercontent.com/wf8/RevBayes_UC_Berkeley_2018_Workshop/master/slides/Freyman_RevBayes_Graphical_Models.pdf) + - What is a graphical model? + - Discriminative vs generative models + - Linear regression as a graphical model + - Ancestral state estimation as a graphical model + - Linking phylo comparative methods and tree inference through generative graphical models +* **February 27** (noon - 4 PM) + - Correlated evolution of discrete characters [[slides]](https://raw.githubusercontent.com/wf8/RevBayes_UC_Berkeley_2018_Workshop/master/slides/Freyman_RevBayes_Correlated_Evolution.pdf) + - model testing via Bayes factors or reversible-jump MCMC + - State-dependent speciation and extinction (BiSSE/MuSSE) [[tutorial]](https://raw.githubusercontent.com/wf8/RevBayes_UC_Berkeley_2018_Workshop/master/slides/RB_DiversificationRate_CharacterDependent_Tutorial.pdf) + - Hidden Markov models and diversification (HiSSE) + - Cladogenetic SSE models (ClaSSE) and biogeography (DEC-SSE) + +### Scripts and data +* [scripts](https://github.com/wf8/RevBayes_UC_Berkeley_2018_Workshop/tree/master/src) +* [data](https://github.com/wf8/RevBayes_UC_Berkeley_2018_Workshop/tree/master/data) + +The easiest way is to clone this entire repo: +``` +git clone https://github.com/wf8/RevBayes_UC_Berkeley_2018_Workshop.git +``` +