getCladeRates {BAMMtools} | R Documentation |
Compute clade-specific mean rates
Description
Computes marginal clade-specific rates of speciation,
extinction, or (if relevant) trait evolution from BAMM
output.
Usage
getCladeRates(ephy, node = NULL, nodetype = "include", verbose = FALSE)
Arguments
ephy |
An object of class |
node |
If computing rates for a specific portion of tree, the node
subtending the relevant subtree. If multiple nodes are supplied, then
the equivalent number of |
nodetype |
Either "include" or "exclude". If |
verbose |
Logical. If |
Details
Computes the time-weighted mean evolutionary rate for a given
clade. Conversely, one can compute the rate for a given phylogeny
while excluding a clade; this operation will give the "background"
rate. It is important to understand several aspects of these mean
rates. First, rates in the BAMM
framework are not constant
through time. Hence, the function computes the mean time-integrated
rates across the subtree. Operationally, this is done by integrating
the speciation rate with respect to time along each branch in the
subtree. These time-integrated rates are then summed, and the sum
is divided by the total sum of branch lengths for the subtree.
The function computes a rate for each sample in the posterior, and returns a list of rate vectors. Each rate in the corresponding vector is a mean rate for a particular sample from the posterior. Hence, you can think of the return value for this function as an estimate of the marginal distribution of rates for the focal clade. You can compute means, medians, quantiles, etc from these vectors.
Value
A list with the following components:
lambda: A vector of speciation rates (if applicable), with the i'th rate corresponding to the mean rate from the i'th sample in the posterior.
mu: A vector of extinction rates (if applicable), with the i'th rate corresponding to the mean rate from the i'th sample in the posterior.
beta: A vector of phenotypic rates (if applicable), with the i'th rate corresponding to the mean rate from the i'th sample in the posterior.
Author(s)
Dan Rabosky
References
Examples
data(events.whales, whales)
ed <- getEventData(whales, events.whales, nsamples=500)
all_rates <- getCladeRates(ed)
mean(all_rates$lambda)
mean(all_rates$mu)
# joint density of mean speciation and extinction rates:
plot(all_rates$mu ~ all_rates$lambda)
# clade specific rates: here for Dolphin subtree:
dol_rates <- getCladeRates(ed, node=140)
mean(dol_rates$lambda)
mean(dol_rates$mu)
# defining multiple nodes
mean(getCladeRates(ed, node=c(132, 140),
nodetype=c('include','exclude'))$lambda)