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mwpennell / arbutus

Assessing the adequacy of phylogenetic models of quantitative trait evolution
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Unit tree with arbitrary parameters #7

Open richfitz opened 10 years ago

richfitz commented 10 years ago

Issue by richfitz from Tuesday Oct 01, 2013 at 06:05 GMT Originally opened as https://github.com/richfitz/modeladequacy/issues/21

It should be easy enough to write a method based on the fit.mle ones that takes a vector of parameters and makes a unit tree. This is easiest for BM with one parameter, but given we have a standard list of names, we could require (or assume) those.

richfitz commented 10 years ago

Comment by mwpennell from Thursday Oct 03, 2013 at 06:20 GMT

just saw this

assuming you mean for the simple models (multipeak OU and auteur models would be VERY hard)

like as.unit.tree(tree, data=data, pars=c(sigsq=1, alpha=0.5))

that sort of thing? sure we could do this. do you think this would be useful??

richfitz commented 10 years ago

Comment by richfitz from Thursday Oct 03, 2013 at 06:27 GMT

I think that there are limited cases where this could be useful; there is one such case in the "BM tree rescaling worked (diversitree, mcmc)" test in test-unit-tree.R (see lines 64-67 here, which could be replaced by as.unit.tree(lik.bm, coef(samples.bm)[idx,] if we allowed something like this. Not sure if it's worth it, but not too much work either.

Yeah, for things like multipeak OU and auteur models it could be a bit harder, but with a likelihood function at least the order of the arguments is well defined.

richfitz commented 10 years ago

Comment by mwpennell from Thursday Oct 03, 2013 at 06:33 GMT

i see. if you feel like writing something like and think it would be useful, go ahead and give it a go.