Simulation and Likelihood Calculation of Phylogenetic Comparative Models.

PCMBase : Simulation and likelihood calculation of phylogenetic comparative methods

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. Note that the PCMBase package does not implement model inference. Due to the enormous variety of models and possible model inference methods, this functionality is delegated to other packages that, taking advantage of PCMBase’s fast likelihood calculation, can implement maximum likelihood (ML) or Bayesian inference methods. For example, the PCMFit package provides heuristic-based ML fit of (mixed) Gaussian phylogenetic models (Mitov, Bartoszek, and Stadler 2019).

Installation

An optional but highly recommended dependency

The function PCMTreePlot in the package is implemented based on the R-package ggtree, which is not on CRAN. It is highly recommended to install this package in order to visualize trees with colored parts corresponding to different evolutionary regimes. If ggtree is not installed, the package will fail to run examples and generate the vignettes. At the time of writing this documentation, ggtree can be installed from bioconductor through the following code (if that does not work, check the ggtree home page):

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ggtree", version = "3.8")

Installing PCMBase from CRAN

A stable but possibly old version of PCMBase is available on CRAN and can be installed with this command:

install.packages("PCMBase")

Github

The newest but possibly less stable and tested version of the package can be installed using:

devtools::install_github("venelin/PCMBase")

Resources

The user guides and technical reference for the library are available from the PCMBase web-page.

• The Getting started guide
• The PCMBase parameterizations guide
• The Tracing the likelihood calculation of a Gaussian mode guide
• The Creating a Custom Model in the PCMBase Framework guide

The research article “Fast likelihood calculation for multivariate Gaussian phylogenetic models with shifts”, published in Theoretical Population Biology provides a thorough description of the likelihood calculation algorithm currently implemented in PCMBase. Appendix A of this article gives an overview of the modular structure and the features of the package.

The PCMBase source code is located in the PCMBase github repository.

Feature requests, bugs, etc can be reported in the PCMBase issues list.

Citing PCMBase

To give credit to the PCMBase package in a publication, please cite the following article:

Mitov, V., Bartoszek, K., Asimomitis, G., & Stadler, T. (2019). Fast likelihood calculation for multivariate Gaussian phylogenetic models with shifts. Theor. Popul. Biol. https://doi.org/10.1016/j.tpb.2019.11.005

Used R-packages

The PCMBase R-package uses the following 3rd party R-packages:

• For tree processing in R: ape v5.5 (Paradis et al. 2018), data.table v1.14.2 (Dowle and Srinivasan 2019);
• For algebraic manipulation: expm v0.999.6 (Goulet et al. 2018), mvtnorm v1.1.3 (Genz et al. 2018);
• For plotting: ggtree v3.2.1 (Yu and Lam 2019), ggplot2 v3.3.5 (Wickham et al. 2018);
• For unit-testing: testthat v3.1.1 (Wickham 2018), covr v3.5.1 (Hester 2018);
• For documentation and web-site generation: roxygen2 v7.1.2 (Wickham, Danenberg, and Eugster 2018), pkgdown v2.0.1 (Wickham and Hesselberth 2018);

Licence and copyright

Copyright 2016-2021 Venelin Mitov

Source code to PCMBase is made available under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. PCMBase is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

References