make.quasse.split: 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

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 ape phylo format.

states

A vector of character states, each of which must be a numeric real values. Missing values (NA) are not yet handled. This vector must have names that correspond to the tip labels in the phylogenetic tree (tree$tip.label

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 x (see Details).

A function to use as the extinction function. The first argument of this must be x (see Details.)

nodes

Vector of nodes that will be split (see Details).

split.t

Vector of split times, same length as nodes (see Details).

control

A list of parameters for tuning the performance of the integrator. A guess at reasonble values will be made here. See Details in make.quasse for possible entries.

sampling.f

Scalar with the estimated proportion of extant species that are included in the phylogeny. A value of 0.75 means that three quarters of extant species are included in the phylogeny. By default all species are assumed to be known

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.