diversitree
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Problem with asr.stoch and irreversible model
Dear @richfitz
Nice job on diversitree - I've just started to play with it.
I'm trying to run stochastic mapping using the example of an irreversible mk2 model given here
The following code works fine with asr.joint
and asr.marginal
, but throws an error with asr.stoch
pars <- c(.1, .1, .03, .03, .03, .06)
set.seed(1)
phy <- trees(pars, "bisse", max.taxa=4, max.t=Inf, x0=0)[[1]]
h <- history.from.sim.discrete(phy, 0:1)
plot(h, phy, main="True history")
lik <- make.mk2(phy, phy$tip.state)
argnames(lik)
lik2<-constrain(lik, q10~0)
argnames(lik2)
fit2 = find.mle(lik2,c(.1))
st.s2 <- asr.stoch(lik2, fit2$par)
The above gives the following error:
Error in asr(lik(pars, pars.only = TRUE), ...) :
Exceeding maximum allowed history size
I don't get this for the unconstrained model when doing stochastic mapping. I've also tried calling make.asr.stoch.constrained
explicitly, but I got the same error.