BAMMtools (version 2.1.0)

getMarginalBranchRateMatrix: compute mean branch rates for bammdata object

Description

For each sample in the posterior, computes the mean rate for each branch in the focal phylogeny (speciation, extinction, trait evolution). If the bammdata object contains nsamples samples and the target phylogeny has nbranches branches, the function will compute a matrix of nbranches x nsamples.

Usage

getMarginalBranchRateMatrix(ephy, verbose = FALSE)

Arguments

ephy

an object of class bammdata

verbose

print progress during processing of bammdata object

Value

• Returns a list with the following components:
• lambda_branch_matrix
  A nbranches x nsamples matrix of mean speciation rates for each branch.
• mu_branch_matrix
  A nbranches x nsamples matrix of mean extinction rates for each branch.
• beta_branch_matrix
  A nbranches x nsamples matrix of mean phenotypic rates for each branch.

Details

If a type = 'diversification' bammdata object is passed as an argument, the function will return matrices for both speciation and extinction. If type = 'trait' object, the matrix will simply be the corresponding phenotypic rates. Branch-specific rates are the mean rates computed by integrating the relevant rate-through-time function along each branch, then dividing by the length of the branch.

Examples

data(whales)
data(events.whales)
ed <- getEventData(whales, events.whales, nsamples = 10)
mbr <- getMarginalBranchRateMatrix(ed)
dim(mbr$lambda_branch_matrix)