venelin/PCMFit: Maximum likelihood fit and selection of phylogenetic comparative models

PCMFit provides maximum likelihood inference and selection of phylogenetic comparative models (PCMs). Currently, the package implements Gaussian and mixed Gaussian phylogenetic models (MGPMs) 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 approximage 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) and a heuristic-based recursive clade partition search algorithm. The package version 1.0.0 has been used in the 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.

install.packages("remotes")
remotes::install_github("venelin/PCMFit")