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 inference 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 


Author  Venelin Mitov [aut, cre, cph] (<a href="https://venelin.github.io">venelin.github.io</a>), Krzysztof Bartoszek [ctb], Georgios Asimomitis [ctb], Tanja Stadler [ths] 
Maintainer  Venelin Mitov <vmitov@gmail.com> 
License  GPL (>= 3.0) 
Version  1.2.14 
URL  https://venelin.github.io/PCMBase/ https://venelin.github.io 
Package repository  View on CRAN 
Installation 
Install the latest version of this package by entering the following in R:

Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.