View source: R/model-quasse-split.R
make.quasse.split | R Documentation |
Create a likelihood function for a QuaSSE model where the tree is partitioned into regions with different parameters.
make.quasse.split(tree, states, states.sd, lambda, mu, nodes, split.t,
control=NULL, sampling.f=NULL)
tree |
An ultrametric bifurcating phylogenetic tree, in
|
states |
A vector of character states, each of which must be a
numeric real values. Missing values ( |
states.sd |
A scalar or vector corresponding to the standard error around the mean in states (the initial probability distribution is assumed to be normal). |
lambda |
A function to use as the speciation function. The first
argument of this must be |
mu |
A function to use as the extinction function. The first
argument of this must be |
nodes |
Vector of nodes that will be split (see Details). |
split.t |
Vector of split times, same length as |
control |
A list of parameters for tuning the performance of the
integrator. A guess at reasonble values will be made here. See
Details in |
sampling.f |
Scalar with the estimated proportion of extant
species that are included in the phylogeny. A value of |
Branching times can be controlled with the split.t
argument. If this is Inf
, split at the base of the branch (as in
MEDUSA). If 0
, split at the top (closest to the present, as in
the new option for MEDUSA). If 0 < split.t < Inf
then we split
at that time on the tree (zero is the present, with time growing
backwards).
TODO: Describe nodes
and split.t
here.
Richard G. FitzJohn
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