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Brian O ’ Meara http:// www.brianomeara.info PowerPoint Presentation
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Brian O ’ Meara http:// www.brianomeara.info

Brian O ’ Meara http:// www.brianomeara.info

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Brian O ’ Meara http:// www.brianomeara.info

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  1. Brian O’Meara • http://www.brianomeara.info http://www.youtube.com/watch?v=9R8hpPY_9kY Get out laptop, fire up R

  2. install.packages("ctv") library(ctv) install.views("Phylogenetics") install.packages("corHMM")

  3. Model selection

  4. Likelihood ratio test test statistic = 2(ln L1 - ln L0)

  5. Likelihood ratio test

  6. Likelihood ratio test Posada and Crandal 1998

  7. Akaike information criterion AICi = -2 ln Li + ki AIC is estimator as distance between truth and approximating model “Truth drops out as a constant”-- Burnham and Anderson 2004

  8. Bayes Factors

  9. Reversible jump MCMC Model 1 Model 1 Model 2 Model 2

  10. Organize by: Question Method • Continuous time Markov Chain • Birth death process • Multivariate normal • BiSSE and friends • Tree stretching • Correlation of herbivory with group living • Crepuscular foraging being intermediate between nocturnal and diurnal • Biogeography • Causes of diversification • Rate of trait evolution • What limits the number of species

  11. Flour, sugar, egg, butter, leavening, liquid

  12. Continuous time Markov chain finite state space A, T, G, C woody, herbaceous susceptible, infected, recovered herbivorous, omnivorous, carnivorous 0, 2, 4, 6, 8, ..., 100 legs

  13. Per day: What is probability of it leaving the store that day? If it leaves, what is the probability it was paid for? What is the probability it stays in the store ≥ two days?

  14. Per ∆t:

  15. Per ∆t:

  16. Per ∆t:

  17. Per ∆t:

  18. Per ∆t:

  19. Does the store ever get Twinkies back? [Do people return Twinkies for a refund?] H0: r*-store = 0 H1: r*-store > 0

  20. Do adults give to kids at the same rate kids give to adults? H0: rchild-adult = radult-child H1: rchild-adult ≠ radult-child

  21. From this basic model: • Hypotheses about rates for a single character (are some equal? are some zero?) • Hypotheses about correlation between characters • Tree inference • Ancestral state inference

  22. Continuous time Markov chain finite state space

  23. Currie et al. 2010 Nature

  24. Currie et al. 2010 Nature

  25. Currie et al. 2010 Nature

  26. Currie et al. 2010 Nature

  27. 0 0 0 0 0 0 0 0 0 Currie et al. 2010 Nature

  28. 0 0 0 0 0 0 Currie et al. 2010 Nature

  29. Currie et al. 2010 Nature

  30. Currie et al. 2010 Nature

  31. Currie et al. 2010 Nature

  32. Currie et al. 2010 Nature

  33. 0 A 1 A 0 B 1 B No social play No sex play No social play Yes sex play No sex play Yes social play Yes sex play Yes social play

  34. 0 0 0 0

  35. 0 A 1 A 0 B 1 B No social play No sex play No social play Yes sex play No sex play Yes social play Yes sex play Yes social play

  36. No social play No sex play 0 A No social play Yes sex play No sex play Yes social play 1 A 0 B 1 B Yes sex play Yes social play

  37. Pagel 1994

  38. Barker & Pagel 2005

  39. 0 1 1 1 0 0 1 0

  40. Barker & Pagel 2005

  41. Barker & Pagel 2005

  42. ... ... up to maximum number of genes ... ... where a, b, etc. are just f(i, j, birthdeath rate)

  43. Ree & Smith 2008

  44. Ree & Smith 2008

  45. Courtesy Nicolas Salamin

  46. Joint: Choose values for x, y, z, w that together maximize likelihood