DESCRIPTION

Package: PCMFit
Type: Package
Title: Maximum likelihood fit and selection of phylogenetic comparative models
Version: 1.0.0
Authors@R: c(person("Venelin", "Mitov", email = "vmitov@gmail.com",
                 role = c("aut", "cre", "cph")))
Maintainer: Venelin Mitov <vmitov@gmail.com>
Description: The goal of PCMFit is to provide a generic tool for inference and 
  selection of phylogenetic comparative models (PCMs). Currently, the package 
  implements Gaussian and mixed Gaussian phylogenetic models (MGPM) over all 
  tree types (including non-ultrametric and polytomic trees). The package 
  supports non-existing traits or missing measurements for some of the traits on 
  some of the species. The package supports specifying measurement error 
  associated with each tip of the tree or inferring a measurement error 
  parameter for a group of tips. The Gaussian phylogenetic models include 
  various parametrizations of Brownian motion (BM) and Ornstein-Uhlenbeck (OU) 
  multivariate branching processes. The mixed Gaussian models represent models 
  with shifts in the model parameters as well as the type of model at points of 
  the tree. Each shift-point is described as a pair of a shift-node and 
  associated type of model (e.g. OU or BM) driving the trait evolution from the 
  beginning of the branch leading to the shift-node toward the shift-node and 
  its descendants until reaching a tip or another shift-point. The function 
  PCMFit is used to fit a given PCM or a MGPM for a given tree with specified 
  shift-points. The function PCMFitMixed is used to fit an ensemble of possible 
  MGPMs over a tree for which the shift-points are unknown. This function can 
  perform model selection of the best MGPM for a given tree and data according 
  to an information loss function such as the Akaike information criterion 
  (AIC). The package has been thoroughly tested and applied to real data in the 
  related research article Mitov et al. 2019 <doi:10.1073/pnas.1813823116>. 
  Currently, the package is available from <https://github.com/venelin/PCMFit>. 
  The web-page <https://venelin.github.io/PCMFit/> provides access to 
  documentation and related resources.
Encoding: UTF-8
License: GPL (>= 3.0)
LazyData: true
Depends:
    R (>= 3.1.0)
Imports:
    ape,
    PCMBase,
    foreach,
    iterators,
    digest,
    data.table
Suggests:
    PCMBaseCpp,
    testthat,
    knitr,
    rmarkdown
RoxygenNote: 6.1.1
VignetteBuilder: knitr
URL: https://venelin.github.io/PCMFit/index.html, 
    https://github.com/venelin/PCMFit, https://doi.org/10.3929/ethz-b-000315296
BugReports: https://github.com/venelin/PCMFit/issues