- A some point I’ll want to think more seriously about incorporating geographic information into comparative analyses. At some level this data is more available than appropriate continuous traits, as illustrated in the example phylogenetics wiki from Prof. Roderic Page that I just came across.

#### Today’s Goals

- Repeating last night’s bootstraps on the likelihood ratio. Need to clean up and incorporate my bootstrap codes first.
- Should also explore the bootstrapping of the partitioning functions from yesterday.
- Begin implementing stochastic partitioning and stochastic ancestral state painting/inference.

#### Bootstrapping Likelihood ratios

Preliminary bootstrap of the likelihood ratios of the Anoles data (click for larger). Red lines indicate where the true data falls.

Compare to the earlier bootstraps of likelihoods directly: