Dear all,
It seems that fitting an equal-rate model of ancestral state
reconstruction with a root constraint now returns an error message. It
looks like a recent bug.
It has something to do with a function called internally by find.mle
{diversitree}, but I am not able to understand the exact nature of this
problem.
Below is an example to reproduce the issue.
I am using diversitree 0.9-7.
Thanks for the precious help.
Sébastien
-------------------------------------------------------------------
> library(diversitree)
> pars <- c(.1, .1, .03, .03, .1, .2)
> set.seed(3)
> phy <- trees(pars, "bisse", max.taxa=25, max.t=Inf, x0=0)[[1]]
> #fitting a Mk2 model without and with root constraint
> lik <- make.mk2(phy, phy$tip.state)
> fit.mk2 <- find.mle(lik, c(.1, .1))
> fit.mk2.root <- find.mle(lik,c(.1,.1), root=ROOT.GIVEN, root.p=c(0,1))
> #fitting an ER model without and with root constraint
> lik2=constrain(lik,q01~q10)
> fit.er <- find.mle(lik2, 0.1)
> fit.er.root <- find.mle(lik2, 0.1, root=ROOT.GIVEN, root.p=c(0,1))
Error in set.defaults(func, defaults = list(...)) : Unknown defaults
-------------------------------------------------------------------
--
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Sébastien Lavergne
Laboratoire d'Ecologie Alpine, UMR 5553
CNRS - Université Grenoble Alpes
BP 53, 38041 Grenoble Cedex 9, France
tel 0033 476 514 497
http://seb.lavergne.free.fr/
http://www-leca.ujf-grenoble.fr/membres/lavergne.htm
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