Create a likelihood function for a GeoSSE model where the tree is partitioned into regions with different parameters.
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())
An ultrametric bifurcating phylogenetic tree, in
ape “phylo” format.
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.
Vector of nodes that will be split (see Details).
Vector of split times, same length as nodes (see
Details).
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.
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.
List of control parameters for the ODE solver. See
details in make.bisse.
Emma E. Goldberg
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.