Package: PCMBase
Type: Package
Title: Simulation and Likelihood Calculation of Phylogenetic
        Comparative Models
Version: 1.2.15
Authors@R: c(person("Venelin", "Mitov", email = "vmitov@gmail.com",
                    comment = '<a href="https://venelin.github.io">venelin.github.io</a>',
                    role = c("aut", "cre", "cph")),
             person("Krzysztof", "Bartoszek",
                    role = c("ctb")),
             person("Georgios", "Asimomitis",
                    role = c("ctb")),
             person("Tanja", "Stadler",
                    role = c("ths")))
Maintainer: Venelin Mitov <vmitov@gmail.com>
Description: 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.
Encoding: UTF-8
License: GPL (>= 3.0)
LazyData: true
Depends: R (>= 3.1.0)
Imports: ape, abind, expm, mvtnorm, data.table, ggplot2, xtable
Suggests: testthat, knitr, rmarkdown, ggtree, cowplot, covr, mvSLOUCH,
        BiocManager
RoxygenNote: 7.3.2
ByteCompile: yes
VignetteBuilder: knitr, rmarkdown
URL: https://venelin.github.io/PCMBase/, https://venelin.github.io
BugReports: https://github.com/venelin/PCMBase/issues
NeedsCompilation: no
Repository: https://venelin.r-universe.dev
Date/Publication: 2025-09-01 14:00:00 UTC
RemoteUrl: https://github.com/venelin/pcmbase
RemoteRef: HEAD
RemoteSha: 24d769dce3f31bc8d3fb540f869925265aef7ce4
Packaged: 2026-07-03 06:22:21 UTC; root
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]