phytools: evol.rate.mcmc – R documentation

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evol.rate.mcmc

Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny

Description

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.

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 σ_1^2; `sig2`: starting value for σ_2^2; `a`: starting value for a; `sd1`: standard deviation for the normal proposal distribution for σ_1^2; `sd2`: standard deviation for the normal proposal distribution for σ_2^2; `kloc`: scaling parameter for tree move proposals - 1/λ for the reflected exponential distribution; `sdlnr`: standard deviation on the log-normal prior on σ_1^2/σ_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

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

Value

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

`mcmc`	results from the MCMC run.
`tips`	list of stips in rate σ_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. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

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.