make.geosse.split: Geographic State Speciation and Extinction Model: Split Models

Description

Create a likelihood function for a GeoSSE model where the tree is partitioned into regions with different parameters.

Usage

make.geosse.split(tree, states, nodes, split.t, sampling.f=NULL, strict=TRUE, control=list())
make.geosse.uneven(tree, states, nodes, split.t, sampling.f=NULL, strict=TRUE, control=list())

Arguments

tree

An ultrametric bifurcating phylogenetic tree, in ape “phylo” format.

states

A vector of character states, each of which must be an integer between 0 and 2: see make.geosse. This vector must have names that correspond to the tip labels in the phylogenetic tree (tree$tip.label). Unresolved clades are not supported.

nodes

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

split.t

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

sampling.f

Vector of length 3 where sampling.f[i] is the proportion of species in state i that are present in the phylogeny. A value of c(0.5, 0.75, 1) means that half of species in state 0, three quarters of species in state 1, and all species in state 2 are included in the phylogeny. By default all species are assumed to be known.

strict

The states vector is always checked to make sure that the values are integers on 0:2. If strict is TRUE (the default), then the additional check is made that every state is present. The likelihood models tend to be poorly behaved where states are missing, but there are cases (missing intermediate states for meristic characters) where allowing such models may be useful.

control

List of control parameters for the ODE solver. See details in make.bisse.

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).

The nodes at the top of the split location are specified as a vector of node names. For example, a value of c("nd10", "nd12") means that the splits are along the branches leading from each of these nodes towards the root.