diversitree: Worked Examples

Here some worked code examples. Each is compiled from a script file using sowsear, which produces a knitr file, which is compiled into markdown and converted into HTML using pandoc.

The version of diversitree they were compiled with is indicated at the bottom of the file (note that this may be a prerelease version).

These are smaller examples than in the main tutorial, and cover a specific problem.

• Unreplicated correlated evolution
  Unlike phylogenetic independent contrasts, Markov trait evolution methods (such as Pagel 1994) and BiSSE-type methods can be mislead where there is no phylogenetic replication. This demonstrates the problem on a simulated tree. (created 9 May 2012)

• Ornstein-Uhlenbeck calculations on non-ultrametric trees, under two algorithms. The OU calculations in diversitree differ from those in other packages (e.g., geiger) by avoiding working with the phylogenetic variance-covariance matrix. While the different approaches agree exactly on ultrametric trees, the calculations differ on non-ultrametric trees. (created 10 May 2012)