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.

Version:	1.2.14
Depends:	R (≥ 3.1.0)
Imports:	ape, abind, expm, mvtnorm, data.table, ggplot2, xtable
Suggests:	testthat, knitr, rmarkdown, ggtree, cowplot, covr, mvSLOUCH, BiocManager
Published:	2024-03-15
DOI:	10.32614/CRAN.package.PCMBase
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 at gmail.com>
BugReports:	https://github.com/venelin/PCMBase/issues
License:	GPL (≥ 3.0)
URL:	https://venelin.github.io/PCMBase/, https://venelin.github.io
NeedsCompilation:	no
Citation:	PCMBase citation info
Materials:	README NEWS
CRAN checks:	PCMBase results

Documentation:

Reference manual:	PCMBase.pdf
Vignettes:	Getting started Creating a Custom Model in the PCMBase Framework The PCMBase Parametrization API Tracing the likelihood calculation of a Gaussian model

Downloads:

Package source:	PCMBase_1.2.14.tar.gz
Windows binaries:	r-devel: PCMBase_1.2.14.zip, r-release: PCMBase_1.2.14.zip, r-oldrel: PCMBase_1.2.14.zip
macOS binaries:	r-release (arm64): PCMBase_1.2.14.tgz, r-oldrel (arm64): PCMBase_1.2.14.tgz, r-release (x86_64): PCMBase_1.2.14.tgz, r-oldrel (x86_64): PCMBase_1.2.14.tgz
Old sources:	PCMBase archive

Reverse dependencies:

Reverse imports:

mvSLOUCH, PCMBaseCpp

Linking:

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