PCMBase - Simulation and Likelihood Calculation of Phylogenetic
Comparative Models
Phylogenetic comparative methods represent models of
continuous trait data associated with the tips of a
phylogenetic tree. Examples of such models are Gaussian
continuous time branching stochastic processes such as Brownian
motion (BM) and Ornstein-Uhlenbeck (OU) processes, which regard
the data at the tips of the tree as an observed (final) state
of a Markov process starting from an initial state at the root
and evolving along the branches of the tree. The PCMBase R
package provides a general framework for manipulating such
models. This framework consists of an application programming
interface for specifying data and model parameters, and
efficient algorithms for simulating trait evolution under a
model and calculating the likelihood of model parameters for an
assumed model and trait data. The package implements a growing
collection of models, which currently includes BM, OU, BM/OU
with jumps, two-speed OU as well as mixed Gaussian models, in
which different types of the above models can be associated
with different branches of the tree. The PCMBase package is
limited to trait-simulation and likelihood calculation of
(mixed) Gaussian phylogenetic models. The PCMFit package
provides functionality for inference of these models to tree
and trait data. The package web-site
<https://venelin.github.io/PCMBase/> provides access to the
documentation and other resources.
