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

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 * style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]] Comparative Phylogenetics
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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

ltt.plot or plotLtt
 * Lineage through time plots ape and laser:
 * 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)


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