# NOT RUN {
## Not run
library(diversitree)
pars <- c(0.1, 0.2, 0.03, 0.03, 0.01, 0.01)
set.seed(4)
phy <- tree.bisse(pars, max.t=30, x0=0)
sim.dat <- data.frame(names(phy$tip.state), phy$tip.state)
## Now fit HiSSE equivalent with a hidden state for state 1:
trans.rates.hisse <- TransMatMaker(hidden.states=TRUE)
trans.rates.hisse <- ParDrop(trans.rates.hisse, c(2,3,5,7,8,9,10,12))
pp.hisse <- hisse(phy, sim.dat, hidden.states=TRUE, turnover.anc=c(1,2,0,3),
eps.anc=c(1,2,0,3), trans.rate=trans.rates.hisse)
##Now reconstruct the likeliest states under this model:
pp <- MarginRecon(phy, sim.dat, f=c(1,1), pars=pp.hisse$solution,
hidden.states=TRUE)
# }
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