User:Carl Boettiger/Notebook/Comparative Phylogenetics/2010/05/12

Comparative Phylogenetics

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Roi and Sam Comparative Phylogenetics R Workshop Day 2: 4p - 6:30p Attending the R workshop by Roi Holzmann and Sam Price from the Wainwright lab. Missed the introductory session on Monday. Course data currently available here. Resources: Springer R books pdfs available through UC Davis. In particular: R book w/ ape. Speciation & Diversification 3rd session (4:10 - 5:10 pm): Packages: Laser, Geiger, Ape, apTreeshape & Diversitree Lineage through time plots ape and laser: ltt.plot() or plotLtt() Simulating trees (Yule and Birth/Death) Tree statistics (gamma statistic – Pybus & Harvey etc.) Laser MEDUSA – shifts in diversification rates (in Gieger) Discrete data 4th session (5:30 - 6:30 pm): Packages: Ape & Geiger Ancestral state reconstruction Fitting models of evolution (fitDiscrete in Geiger)