View source: R/modelbissesplit.R
make.bisse.split  R Documentation 
Create a likelihood function for a BiSSE model where the
tree is partitioned into regions with different parameters.
Alternatively, make.bisse.uneven
can be used where different
regions of the tree have different fractions of species known.
make.bisse.split(tree, states, nodes, split.t, unresolved=NULL,
sampling.f=NULL, nt.extra=10, strict=TRUE, control=list())
make.bisse.uneven(tree, states, nodes, split.t, unresolved=NULL,
sampling.f=NULL, nt.extra=10, strict=TRUE, control=list())
tree 
An ultrametric bifurcating phylogenetic tree, in

states 
A vector of character states, each of which must be 0 or
1, or 
nodes 
Vector of nodes that will be split (see Details). 
split.t 
Vector of split times, same length as 
unresolved 
Unresolved clade information: see section below for structure. 
sampling.f 
Vector of length 2 with the estimated proportion of
extant species in state 0 and 1 that are included in the phylogeny.
A value of 
nt.extra 
The number of species modelled in unresolved clades (this is in addition to the largest observed clade). 
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).
TODO: Describe nodes
and split.t
here.
Richard G. FitzJohn
## Due to a change in sample() behaviour in newer R it is necessary to
## use an older algorithm to replicate the previous examples
if (getRversion() >= "3.6.0") {
RNGkind(sample.kind = "Rounding")
}
pars < c(0.1, 0.2, 0.03, 0.03, 0.01, 0.01)
set.seed(546)
phy < tree.bisse(pars, max.taxa=30, x0=0)
## Here is the phylogeny:
plot(phy, show.node.label=TRUE, label.offset=.1, font=1, cex=.75,
no.margin=TRUE)
## Here is a plain BiSSE function for comparison:
lik.b < make.bisse(phy, phy$tip.state)
lik.b(pars) # 93.62479
## Split this phylogeny at three points: nd15, nd18 and nd26
nodes < c("nd15", "nd18", "nd26")
## This is the index in ape's node indexing:
nodes.i < match(nodes, phy$node.label) + length(phy$tip.label)
nodelabels(node=nodes.i, pch=19, cex=2, col="#FF000099")
## To make a split BiSSE function, pass the node locations and times in:
lik.s < make.bisse.split(phy, phy$tip.state, nodes.i)
## 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]
pars4 < rep(pars, 4)
pars4
## Run the likelihod calculation:
lik.s(pars4) # 93.62479
## These are basically identical (to acceptable tolerance)
lik.s(pars4)  lik.b(pars)
## You can use the labelled nodes rather than indices:
lik.s2 < make.bisse.split(phy, phy$tip.state, nodes)
identical(lik.s(pars4), lik.s2(pars4))
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