simulate  R Documentation 
Evolves one or more trees under the BiSSE (Binary State Speciation and Extinction), MuSSE (MultiState Speciation and Extinction), BiSSEness (BiSSEnode enhanced state shift), ClaSSE (Cladogenetic State change Speciation and Extinction), or GeoSSE (Geographic State Speciation and Extinction) model, or a simple character independent birthdeath model. For the SSE models, it simultaneously evolves a character that affects speciation and/or extinction, and the tree itself.
trees(pars, type=c("bisse", "bisseness", "bd", "classe", "geosse",
"musse", "quasse", "yule"), n=1, max.taxa=Inf, max.t=Inf,
include.extinct=FALSE, ...)
tree.bisse(pars, max.taxa=Inf, max.t=Inf, include.extinct=FALSE,
x0=NA)
tree.musse(pars, max.taxa=Inf, max.t=Inf, include.extinct=FALSE,
x0=NA)
tree.musse.multitrait(pars, n.trait, depth, max.taxa=Inf, max.t=Inf,
include.extinct=FALSE, x0=NA)
tree.quasse(pars, max.taxa=Inf, max.t=Inf, include.extinct=FALSE, x0=NA,
single.lineage=TRUE, verbose=FALSE)
tree.bisseness(pars, max.taxa=Inf, max.t=Inf, include.extinct=FALSE,
x0=NA)
tree.classe(pars, max.taxa=Inf, max.t=Inf, include.extinct=FALSE,
x0=NA)
tree.geosse(pars, max.taxa=Inf, max.t=Inf, include.extinct=FALSE,
x0=NA)
tree.bd(pars, max.taxa=Inf, max.t=Inf, include.extinct=FALSE)
tree.yule(pars, max.taxa=Inf, max.t=Inf, include.extinct=FALSE)
prune(phy, to.drop=NULL)
pars 
Vector of parameters. The parameters must be in the same
order as an unconstrained likelihood function returned by

type 
Type of tree to generate: May be "bisse" or "bd". 
n 
How many trees to generate? 
max.taxa 
Maximum number of taxa to include in the tree. If

max.t 
Maximum length to evolve the phylogeny over. If

include.extinct 
Logical: should extinct taxa be included in
the final phylogeny? And should extinct trees be returned by

x0 
Initial character state at the root (state 0 or 1). A value
of 
n.trait , depth 
For 
single.lineage 
( 
verbose 
( 
... 
Additional arguments 
phy 
A phylogeny, possibly with extinct species, produced by one of the tree evolving functions. 
to.drop 
Optional vector with the species names to drop. 
The phylogeny will begin from a single lineage in state x0
, but
the final phylogeny will include only branches above the first split.
tree.bisse
may return an extinct phylogeny, and trees
might return extinct phylogenies if include.extinct
is
TRUE
.
A phylo
phylogenetic tree (ape format), or for
bisse.trees
, a list
of phylo
trees.
The trees will have an element tip.state
that contains the
binary state information.
There are some logic problems around the creation of zero and one species trees; this will cause occasional errors when running the above functions. Things will change to fix this soon. All these functions may change in the near future.
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(3)
phy < tree.bisse(pars, max.taxa=30, x0=0)
phy$tip.state
h < history.from.sim.discrete(phy, 0:1)
plot(h, phy)
## Retain extinct species:
set.seed(3)
phy2 < tree.bisse(pars, max.taxa=30, x0=0, include.extinct=TRUE)
h2 < history.from.sim.discrete(phy2, 0:1)
plot(h2, phy2)
#### MuSSE:
## Two states
pars < c(.1, .2, .03, .04, 0.05, 0.1)
set.seed(2)
phy < tree.musse(pars, 20, x0=1)
h < history.from.sim.discrete(phy, 1:2)
plot(h, phy)
## A 3state example where movement is only allowed between neighbouring
## states (1 <> 2 <> 3), and where speciation and extinction rates
## increase moving from 1 > 2 > 3:
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
set.seed(2)
phy < tree.musse(pars, 30, x0=1, include.extinct=TRUE)
h < history.from.sim.discrete(phy, 1:3)
plot(h, phy, cex=.7)
## And with extinct taxa pruned:
phy2 < prune(phy)
h2 < history.from.sim.discrete(phy2, 1:3)
plot(h2, phy2, cex=.7)
## This can all be done in one step (and is by default):
set.seed(2)
phy < tree.musse(pars, 30, x0=1)
h < history.from.sim.discrete(phy, 1:3)
plot(h, phy, cex=.7)
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