Quantitative State Speciation and Extinction Model: Split Models
Description
Create a likelihood function for a QuaSSE model where the tree is partitioned into regions with different parameters.
Usage
1 2  make.quasse.split(tree, states, states.sd, lambda, mu, nodes, split.t,
control=NULL, sampling.f=NULL)

Arguments
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 
Details
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.
Author(s)
Richard G. FitzJohn
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