dtRates: Calculate macroevolutionary rate changes on a phylogeny from...

In BAMMtools: Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees

Calculate macroevolutionary rate changes on a phylogeny from BAMM output

Description

dtRates calculates the mean of the marginal posterior density of the rate of speciation/extinction or trait evolution for small segments along each branch in a phylogeny.

Usage

dtRates(ephy, tau, ism = NULL, tmat = FALSE)

Arguments

ephy	An object of class bammdata.
tau	A numeric that specifies the size (as a fraction of tree height) of the segments that each branch will be discretized into.
ism	An integer vector indexing which posterior samples to include in the calculation.
tmat	A logical. If TRUE the matrix of branch segments is returned.

Details

dtRates bins the phylogeny into windows of time and calculates average rates of speciation/extinction or phenotypic evolution along each segment of a branch within a window. The width of each window is determined by tau. tau is a fraction of the root to tip distance so a value of tau = 0.01 bins the phylogeny into 100 time windows of equal width.

Value

A bammdata object with a new component named "dtrates", which is a list with two or three components:

• tau: The parameter value of tau used in the calculation.

• rates: If ephy$type = "trait": a numeric vector with the phenotypic rates of each segment on each branch. If ephy$type = "diversification": a list with two components. The first component is a numeric vector of speciation rates. The second component is a numeric vector of extinction rates.

• tmat: A matrix of the starting and ending times of the segments on each branch. Only if tmat = TRUE.

Note

If there are zero length branches in the input tree NAs will result.

Author(s)

Mike Grundler

References

http://bamm-project.org/

See Also

plot.bammdata

Examples

data(whales, events.whales)
ed <- getEventData(whales, events.whales, burnin=0.25, nsamples=500)

# use all posterior samples
ed <- dtRates(ed, tau=0.01)

# use specified range of posterior samples
ed <- dtRates(ed, tau=0.01, ism=50:150)

BAMMtools documentation built on Sept. 13, 2024, 1:10 a.m.