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.)
- 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)