BBMV-package {BBMV}R Documentation

Models for Continuous Traits Evolving in Macroevolutionary Landscapes of any Shape

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.

Details

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

Author(s)

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

References

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]