R Hackathon 1/ContinuousData

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Inferring Models for Continuous Characters in R

Introductory material on continuous models: Brownian motion (BM), Pagel transformations, Ornstein-Uhlenbeck models.

A Note about Multiple Implementations of these Methods

Currently, there are multiple implementations of several of these models across different packages. The results are not always the same across methods, however, because either the purpose of the analysis is slightly different across packages, or the implementations use different computational strategies. The models that currently have multiple implementations as of this writing (13 December 2007) are (i) Brownian motion and (ii) Orstein-Uhlenbeck with one optimum.

Brownian motion Currently, there are three packages that implement inference of the BM model: ape in function ace(), geiger in function fit.continuous(), and ouch in function brown.fit(). The function ace() will return a log-likelihood and a parameter estimate for the BM model, but these are conditional upon the reconstructed trait values of the nodes. This is consistent with the main purpose of ace(), which is to reconstruct ancestral trait values.