make.quasse.split: Quantitative State Speciation and Extinction Model: Split...

In richfitz/diversitree: Comparative 'Phylogenetic' Analyses of Diversification

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).
mu	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.

Author(s)

Richard G. FitzJohn

richfitz/diversitree documentation built on Oct. 3, 2023, 8:57 p.m.