Fast likelihood evaluation for multivariate phylogenetic comparative methods: the PCMBase R package. We introduce an R package, PCMBase, to rapidly calculate the likelihood for multivariate phylogenetic comparative methods. The package is not specific to particular models but offers the user the functionality to very easily implement a wide range of models where the transition along a branch is multivariate normal. We demonstrate the package’s possibilities on the now standard, multitrait Ornstein-Uhlenbeck process as well as the novel multivariate punctuated equilibrium model. The package can handle trees of various types (e.g. ultrametric, nonultrametric, polytomies, e.t.c.), as well as measurement error, missing measurements or non-existing traits for some of the species in the tree.
Keywords for this software
References in zbMATH (referenced in 3 articles , 1 standard article )
Showing results 1 to 3 of 3.
- Mitov, Venelin; Bartoszek, Krzysztof; Asimomitis, Georgios; Stadler, Tanja: Fast likelihood calculation for multivariate Gaussian phylogenetic models with shifts (2020)
- Venelin Mitov; Krzysztof Bartoszek; Georgios Asimomitis; Tanja Stadler: Fast likelihood evaluation for multivariate phylogenetic comparative methods: the PCMBase R package (2018) arXiv
- Venelin Mitov; Tanja Stadler: Parallel likelihood calculation for phylogenetic comparative models: The SPLITT C++ library (2018) not zbMATH