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

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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)