View source: R/getMarginalBranchRateMatrix.R
getMarginalBranchRateMatrix | R Documentation |
bammdata
objectFor 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.
getMarginalBranchRateMatrix(ephy, verbose = FALSE)
ephy |
An object of class |
verbose |
Print progress during processing of |
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.
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.
Dan Rabosky
data(whales)
data(events.whales)
ed <- getEventData(whales, events.whales, nsamples = 10)
mbr <- getMarginalBranchRateMatrix(ed)
dim(mbr$lambda_branch_matrix)
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