make.musse  R Documentation 
Prepare to run MuSSE (MultiState Speciation and Extinction) on a phylogenetic tree and character distribution. This function creates a likelihood function that can be used in maximum likelihood or Bayesian inference.
MuSSE is agnostic as to whether multiple states or multiple traits are modelled (following Pagel 1994). Instead, a transition rate matrix amongst possible trait/state combinations is constructed and the analysis is conducted on this.
The helper function make.musse.multitrait
wraps the
basic MuSSE model for the case of a combination of several binary
traits; its argument handling are a little different; please see the
help page for more information.
make.musse(tree, states, k, sampling.f=NULL, strict=TRUE,
control=list())
starting.point.musse(tree, k, q.div=5, yule=FALSE)
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. 
sampling.f 
Vector of length 
strict 
The 
control 
List of control parameters for the ODE solver. See
details in 
q.div 
Ratio of diversification rate to character change rate. Eventually this will be changed to allow for Mk2 to be used for estimating q parameters. 
yule 
Logical: should starting parameters be Yule estimates rather than birthdeath estimates? 
With more than 9 states, qij can be ambiguous (e.g. is q113 1>13 or 11>3?). To avoid this, the numbers are zero padded (so that the above would be q0113 or q1103 for 1>13 and 11>3 respectively). It might be easier to rename the arguments in practice though.
Richard G. FitzJohn
make.bisse
for the basic binary model, and
make.musse.multitrait
for the case where the data are
really combinations of binary traits.
## 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")
}
## 1: BiSSE equivalence
pars < c(.1, .2, .03, .04, 0.05, 0.1)
set.seed(2)
phy < tree.musse(pars, 20, x0=1)
## Show that the likelihood functions give the same answers. Ignore the
## warning when creating the MuSSE function.
lik.b < make.bisse(phy, phy$tip.state1)
lik.m < make.musse(phy, phy$tip.state, 2)
all.equal(lik.b(pars), lik.m(pars), tolerance=1e7)
## Notice that default argument names are different between BiSSE and
## MuSSE, but that the order is the same.
argnames(lik.b) # BiSSE: 0/1
argnames(lik.m) # MuSSE: 1/2
## 2: 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:
## You can get the expected argument order for any number of states
## this way (sorry  clunky). The help file also lists the order.
diversitree:::default.argnames.musse(3)
## Here are the parameters:
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)
## Extract history from simulated tree and plot
## (colours are 1: black, 2: red, 3: blue)
col < c("blue", "orange", "red")
h < history.from.sim.discrete(phy, 1:3)
plot(h, phy, cex=.7, col=col)
## The states are numbered 1:3, rather than 0:1 in bisse.
states < phy$tip.state
table(states)
## 2: Likelihood
## Making a likelihood function is basically identical to bisse. The
## third argument needs to be the number of states. In a future
## version this will probably be max(states), but there are some
## pitfalls about this that I am still worried about.
lik < make.musse(phy, states, 3)
## Here are the arguments. Even with three states, this is getting
## ridiculous.
argnames(lik)
## Start with a fully constrained model, but still enforcing stepwise
## changes (disallowing 1 <> 3 shifts)
lik.base < constrain(lik, lambda2 ~ lambda1, lambda3 ~ lambda1,
mu2 ~ mu1, mu3 ~ mu1,
q13 ~ 0, q21 ~ q12, q23 ~ q12, q31 ~ 0, q32 ~ q12)
## Not run:
p < starting.point.musse(phy, 3)
fit.base < find.mle(lik.base, p[argnames(lik.base)])
## Now, allow the speciation rates to vary:
lik.lambda < constrain(lik, mu2 ~ mu1, mu3 ~ mu1,
q13 ~ 0, q21 ~ q12, q23 ~ q12, q31 ~ 0, q32 ~ q12)
fit.lambda < find.mle(lik.lambda, p[argnames(lik.lambda)])
## Very little improvement in fit (this *is* a small tree)
anova(fit.base, lambda=fit.lambda)
## Run an MCMC with this set. Priors will be necessary (using the
## usual exponential with mean of 2r)
prior < make.prior.exponential(1 / (2 * (p[1]  p[4])))
samples < mcmc(lik.lambda, coef(fit.lambda), nstep=1000, w=1,
prior=prior, print.every=50)
## Posterior probability profile plots for the three speciation rates.
profiles.plot(samples[2:4], col)
abline(v=c(.1, .15, .2), col=col)
## End(Not run)
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