R: Evolutionary model fitting with intraspecific variability...

fitBayes {phytools}

R Documentation

Evolutionary model fitting with intraspecific variability using Bayesian MCMC

Description

fitBayes uses Bayesian MCMC to sample terminal states (species means) as well as the parameters of an evolutionary model from their joint posterior distribution, following Revell & Reynolds (2012).

Usage

fitBayes(tree, x, ngen=10000, model="BM", method="reduced", control=list())

Arguments

`tree`	an object of class `"phylo"`.
`x`	a vector of phenotypic values for individuals; `names(x)` should contain the species names (not individual IDs).
`ngen`	a integer indicating the number of generations for the MCMC.
`model`	an evolutionary model: either `"BM"` or `"lambda"`.
`method`	a method: either `"reduced"` or `"full"`.
`control`	a list of control parameters containing the following elements: `sig2`: starting value for `\sigma^2` (BM rate); `lambda`: starting value for the `\lambda` parameter; `a`: starting for the state at the root node; `xbar`: starting values for the states at the tips; `intV`: starting value for the intraspecific variance (reduced method); or `v`: starting value for the vector of intraspecific variances for all species (full method); `pr.mean`: means for the prior distributions in the following order - `sig2`, `lambda` (if applicable), `a`, `xbar`, `intV` or `v` (if applicable), note that the prior probability distribution is exponential for `sig2` and normal for `a` and `y`; `pr.var`: variances on the prior distributions, same order as `pr.mean`.

Value

An object of class "fitBayes" that includes a matrix (mcmc) with a number of rows ngen/control$sample+1 containing the posterior sample and likelihoods.

Matrix columns are labeled by species (for species means and variances), or by the corresponding evolutionary parameter.

Author(s)

Liam Revell liam.revell@umb.edu

References

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

Revell, L. J. and R. G. Reynolds. (2012) A new Bayesian method for fitting evolutionary models to comparative data with intraspecific variation. Evolution, 66, 2697-2707.