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.

c(person("Venelin", "Mitov", email = "vmitov@gmail.com",
role = c("aut", "cre", "cph")),
person("Krzysztof", "Bartoszek",
role = c("ctb")),
person("Georgios", "Asimomitis",
role = c("ctb")),
person("Tanja", "Stadler",
role = c("ctb")))
testthat, knitr, rmarkdown, abind, ggtree, covr
Venelin Mitov [aut, cre, cph],
Krzysztof Bartoszek [ctb],
Georgios Asimomitis [ctb],
Tanja Stadler [ctb]

testthat, knitr, rmarkdown, abind, ggtree, cowplot, covr

Fast Likelihood Calculation for Phylogenetic Comparative Models
c(person("Venelin", "Mitov", email = "vmitov@gmail.com",
role = c("aut", "cre", "cph")))
Provides a C++ backend for multivariate phylogenetic comparative
models implemented in the R-package 'PCMBase'. Can be used in combination
with 'PCMBase' to enable fast and parallel likelihood calculation. Implements
the pruning likelihood calculation algorithm described in Mitov et al. (2018)
<arXiv:1809.09014>. Uses the 'SPLITT' C++ library for parallel tree traversal
described in Mitov and Stadler (2018) <doi:10.1111/2041-210X.13136>.