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BBMV (version 2.1)

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.

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Version

Install

install.packages('BBMV')

Monthly Downloads

25

Version

2.1

License

GPL-2

Maintainer

Florian Boucher

Last Published

April 30th, 2018

Functions in BBMV (2.1)

proposal_nclades_plus_3_pars

Parameter update for the multiclade MCMC function

reformat_multiclade_results

Format the output of a multiclade fit

lnl_FPK_multiclades_same_V_different_sig2

Likelihood functions for multiple clades

proposal_5pars_root_bounds

Parameter update for the MCMC function

Uncertainty_FPK

Parameter uncertainty

log_prior_5pars_root_bounds

Prior function.

Matrix exponential.

posterior_vs_prior

Posterior vs. prior comparison for the FPK model.

log_prior_nclades_plus_3_pars

Prior function.

trans_from_fixed

Linear transformations

Likelihood of the FPK model

FormatTree_bounds

Tree formatting.

get.landscape.FPK

Plot macroevolutionary landscapes estimated by the FPK or BBM+V models

Creation of the likelihood function

ConvProp_bounds

Convolution of the diffusion matrix with the trait density vector.

Maximum-likelihood estimation

DiffMat_backwards

Diffusion matrix building

Ancestral Character 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.

DiffMat_forward

Diffusion matrix building

FPK_sim_traitgram

Simulations with traitgram

Simulation of the BBM+V process.

get.landscape.FPK.MCMC

Plot posterior distribution of macroevolutionary landscapes.

MCMC estimation

MH_MCMC_FPK_multiclades

MCMC estimation on multiple clades

VectorPos_bounds

Discretization of a continuous trait value into a probability vector.

Characteristic time measurement