BBMV-package {BBMV} | R Documentation |

Provides a set of functions to fit general macroevolutionary models for continuous traits evolving in adaptive landscapes of any shape. This package implements the Fokker-Planck-Kolmogorov model (FPK), in which the trait evolves under random diffusion but is also subject to a force that pulls it towards specific values - this force can be of any shape. FPK has a version in which hard reflective bounds exist at the extremes of the trait interval: this second model is called BBMV.

Package: | BBMV |

Type: | Package |

Title: | Models for Continuous Traits Evolving in Macroevolutionary Landscapes of any Shape |

Version: | 2.1 |

Date: | 2018-04-23 |

Author: | Florian C. Boucher |

Maintainer: | Florian C. Boucher <flofloboucher@gmail.com> |

Depends: | R (>= 3.1.0), ape |

Suggests: | coda, geiger |

Description: | Provides a set of functions to fit general macroevolutionary models for continuous traits evolving in adaptive landscapes of any shape. This package implements the Fokker-Planck-Kolmogorov model (FPK), in which the trait evolves under random diffusion but is also subject to a force that pulls it towards specific values - this force can be of any shape. FPK has a version in which hard reflective bounds exist at the extremes of the trait interval: this second model is called BBMV. |

License: | GPL-2 |

Index of help topics:

ACE_FPK Ancestral Character Estimation BBMV-package Models for Continuous Traits Evolving in Macroevolutionary Landscapes of any Shape ConvProp_bounds Convolution of the diffusion matrix with the trait density vector. DiffMat_backwards Diffusion matrix building DiffMat_forward Diffusion matrix building FPK_sim_traitgram Simulations with traitgram FormatTree_bounds Tree formatting. LogLik_bounds Likelihood of the FPK model MH_MCMC_FPK MCMC estimation MH_MCMC_FPK_multiclades MCMC estimation on multiple clades Sim_FPK Simulation of the BBM+V process. Uncertainty_FPK Parameter uncertainty VectorPos_bounds Discretization of a continuous trait value into a probability vector. charac_time Characteristic time measurement find.mle_FPK Maximum-likelihood estimation find.mle_FPK_multiple_clades_same_V_different_sig2 Maximum-likelihood estimation fit_FPK_multiple_clades_different_V_different_sig2 Fit independent models in several clades. get.landscape.FPK Plot macroevolutionary landscapes estimated by the FPK or BBM+V models get.landscape.FPK.MCMC Plot posterior distribution of macroevolutionary landscapes. lnL_FPK Creation of the likelihood function lnl_FPK_multiclades_same_V_different_sig2 Likelihood functions for multiple clades log_prior_5pars_root_bounds Prior function. log_prior_nclades_plus_3_pars Prior function. posterior_vs_prior Posterior vs. prior comparison for the FPK model. prep_mat_exp Matrix exponential. proposal_5pars_root_bounds Parameter update for the MCMC function proposal_nclades_plus_3_pars Parameter update for the multiclade MCMC function reformat_multiclade_results Format the output of a multiclade fit trans_from_fixed Linear transformations

Florian C. Boucher Maintainer: Florian C. Boucher <flofloboucher@gmail.com>

Inferring bounded evolution in phenotypic characters from phylogenetic comparative data. F.C. Boucher and V. Demery. Systematic Biology, 65, 651-661, 2016

A general model for estimating macroevolutionary landscapes from phylogenetic comparative data. F.C. Boucher, V. Demery, E. Conti, L. J. Harmon and J. Uyeda. Systematic Biology, syx075, https://doi.org/10.1093/sysbio/syx075

[Package *BBMV* version 2.1 Index]