make.musse.split {diversitree}  R Documentation 
Create a likelihood function for a MuSSE model where the tree is partitioned into regions with different parameters.
make.musse.split(tree, states, k, nodes, split.t,
sampling.f=NULL, strict=TRUE, control=list())
tree 
An ultrametric bifurcating phylogenetic tree, in

states 
A vector of character states, each of which must be an
integer between 1 and 
k 
The number of states. 
nodes 
Vector of nodes that will be split (see Details). 
split.t 
Vector of split times, same length as 
sampling.f 
Vector of length 
strict 
The 
control 
List of control parameters for the ODE solver. See
details in 
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).
Richard G. FitzJohn
## This example picks up from the tree used in the ?make.musse example.
## First, simulate the tree:
set.seed(2)
pars < c(.1, .15, .2, # lambda 1, 2, 3
.03, .045, .06, # mu 1, 2, 3
.05, 0, # q12, q13
.05, .05, # q21, q23
0, .05) # q31, q32
phy < tree.musse(pars, 30, x0=1)
## Here is the phylogeny, with true character history superposed:
h < history.from.sim.discrete(phy, 1:3)
plot(h, phy, show.node.label=TRUE, font=1, cex=.75, no.margin=TRUE)
## Here is a plain MuSSE function for later comparison:
lik.m < make.musse(phy, phy$tip.state, 3)
lik.m(pars) # 110.8364
## Split this phylogeny at three points: nd16 and nd25, splitting it
## into three chunks
nodes < c("nd16", "nd25")
nodelabels(node=match(nodes, phy$node.label) + length(phy$tip.label),
pch=19, cex=2, col="#FF000099")
## To make a split BiSSE function, pass the node locations and times
## in. Here, we'll use 'Inf' as the split time to mimick MEDUSA's
## behaviour of placing the split at the base of the branch subtended by
## a node.
lik.s < make.musse.split(phy, phy$tip.state, 3, nodes, split.t=Inf)
## The parameters must be a list of the same length as the number of
## partitions. Partition '1' is the root partition, and partition i is
## the partition rooted at the node[i1]:
argnames(lik.s)
## Because we have two nodes, there are three sets of parameters.
## Replicate the original list to get a starting point for the analysis:
pars.s < rep(pars, 3)
names(pars.s) < argnames(lik.s)
lik.s(pars.s) # 110.8364
## This is basically identical (to acceptable tolerance) to the plain
## MuSSE version:
lik.s(pars.s)  lik.m(pars)
## The resulting likelihood function can be used in ML analyses with
## find.mle. However, because of the large number of parameters, this
## may take some time (especially with as few species as there are in
## this tree  getting convergence in a reasonable number of iterations
## is difficult).
## Not run:
fit.s < find.mle(lik.s, pars.s, control=list(maxit=20000))
## End(Not run)
## Bayesian analysis also works, using the mcmc function. Given the
## large number of parameters, priors will be essential, as there will
## be no signal for several parameters. Here, I am using an exponential
## distribution with a mean of twice the stateindependent
## diversification rate.
## Not run:
prior < make.prior.exponential(1/(2*diff(starting.point.bd(phy))))
samples < mcmc(lik.s, pars.s, 100, prior=prior, w=1, print.every=10)
## End(Not run)