READMEnew.md

READMEnew.md

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+# 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 <http://willfreyman.org>
+##### Coordinator: Carrie Tribble <https://carrietribble.weebly.com/>
+##### 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
+```
+