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 OrnsteinUhlenbeck (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, twospeed 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 traitsimulation and likelihood calculation of (mixed) Gaussian phylogenetic models. The PCMFit package provides functionality for ML and Bayesian fit of these models to tree and trait data. The package website <https://venelin.github.io/PCMBase/> provides access to the documentation and other resources.
Package details 


Maintainer  Venelin Mitov <[email protected]> 
License  GPL (>= 3.0) 
Version  1.2.11 
URL  https://venelin.github.io/PCMBase/ https://github.com/venelin/PCMBase 
Package repository  View on GitHub 
Installation 
Install the latest version of this package by entering the following in R:

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