Calculate macroevolutionary rate changes on a phylogeny from BAMM output
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.
An object of class
A numeric that specifies the size (as a fraction of tree height) of the segments that each branch will be discretized into.
An integer vector indexing which posterior samples to include in the calculation.
A logical. If
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 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.
bammdata object with a new component named "dtrates", which
is a list with two or three components:
tau The parameter value of
tauused in the calculation.
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.
If there are zero length branches in the input tree
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