R: Bayesian MCMC method for identifying exceptional phenotypic...

evol.rate.mcmc {phytools}

R Documentation

Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny

Description

Estimates the phylogenetic location of a single rate shift on the tree using Bayesian MCMC (as described in Revell et al., 2012b).

Usage

evol.rate.mcmc(tree, x, ngen=10000, control=list(), ...)
## S3 method for class 'evol.rate.mcmc'
print(x, ...)
## S3 method for class 'evol.rate.mcmc'
summary(object, ...)
## S3 method for class 'summary.evol.rate.mcmc'
print(x, ...)
## S3 method for class 'summary.evol.rate.mcmc'
plot(x, ...)

Arguments

`tree`	an object of class `"phylo"` (a phylogenetic tree).
`x`	a vector of tip values for species in which `names(x)` contains the species names of `tree`, an object of class `"evol.rate.mcmc"`, or (in the case of the S3 `summary` method) an object of class `"summary.evol.rate.mcmc"`.
`ngen`	an integer value indicating the number of generations for the MCMC.
`control`	a list of control parameters containing the following elements: `sig1`: starting value for `\sigma_1^2`; `sig2`: starting value for `\sigma_2^2`; `a`: starting value for a; `sd1`: standard deviation for the normal proposal distribution for `\sigma_1^2`; `sd2`: standard deviation for the normal proposal distribution for `\sigma_2^2`; `kloc`: scaling parameter for tree move proposals - `1/\lambda` for the reflected exponential distribution; `sdlnr`: standard deviation on the log-normal prior on `\sigma_1^2/\sigma_2^2`; `rand.shift`: probability of proposing a random shift in the tree (improves mixing); `print`: print frequency for the MCMC; `sample`: sample frequency.
`object`	for the S3 `summary` method, an object of class `"evol.rate.mcmc"`.
`...`	other optional arguments.

Details

This function takes a phylogenetic tree and data for a single continuously valued character and uses a Bayesian MCMC approach to identify the phylogenetic location of a shift in the evolutionary rate through time.

Default values of control are given in Revell et al. (2012b).

Value

An object of class "evol.rate.mcmc" consisting of at least the following elements:

`mcmc`	results from the MCMC run.
`tips`	list of tips in rate `\sigma_1^2` for each sampled generation of MCMC (to polarize the rate shift).

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., D. L. Mahler, P. Peres-Neto, and B. D. Redelings (2012) A new method for identifying exceptional phenotypic diversification. Evolution, 66, 135-146.