Utilizing maticce to estimate transitions in continuous character evolution

This document provides an overview of the maticce package, which serves three primary purposes. First, it implements an information-theoretic approach to estimating where on a phylogeny there has been a transition in a continuous character. As currently implemented, the approach assumes that (1) such transitions are appropriately modeled as shifts in optimum / equilibrium of a character evolving according to an Ornstein-Uhlenbeck process; (2) strength of constraint / rate of evolution toward the optimum is constant over the tree, as is variance; and (3) all branches on which a change could occur are identified. These assumptions can be relaxed in future versions if needed. Second, the package provides helper functions for the ouch package, in which all likelihood calculations are performed. For example, the package automates the process of painting regimes (described in the Painting Regimes section below) for the hansen function of ouch, specifying nodes at which the regime changes. It also provides functions for identifying most recent common ancestors and all descendents of a particular node. Users of ouch who want to handle large numbers of analyses may find the routines for summarizing analyses over trees and over regimes useful as well. Finally, maticce provides a flexible set of simulation functions for visualizing how different model parameters affect (i.e., what they ’say’ about) our inference of the evolution of a continuous character on a phylogenetic tree. This document also provides a worked example of analyzing a continuous character dataset that illustrates most of the maticce features. Working through this example will I expect address most questions that should come up during a typical analysis.