Try plot(archotreeouch,node.names=TRUE) ?paint Best practice is tricky. I don't think there is a general answer to that question: the best practice probably depends strongly on the data and the scientific question. Certainly I know of no reason to suppose that specifying internal selective regimes is invalid.
A.
On Monday, July 25, 2011 11:11:49 AM Roland Sookias wrote:
> Cheers. Yes it seems to have been the tree somehow, as you say. Can I also
> ask, is it possible to see the tree with node numbers properly so one can
> assign selective regimes to internal nodes? Or is the best practice just to
> assign them to terminal ones?
>
> Thanks
>
> On Mon, Jul 25, 2011 at 3:21 PM, Aaron A. King <kin...@umich.edu> wrote:
> > "Code" means a sequence of R commands that I can run to reproduce your
> > problem. As opposed to a narrative that I have to take guesses on,
> > possibly
> > wasting both your time and mine. You might have a look at
> >
> > ?savehistory
> >
> > to get a quick way to obtain such a thing.
> >
> > Your problem is caused by the fact that your data are incomplete. You do
> > not
> > have information on the depth of that node. This is strange, and I think
> > that
> > you must have done something to the tree. When I do
> >
> > load("ouch.RData")
> > archotreeouch <- ape2ouch(archotree)
> > brown(logflatnodes,archotreeouch)
> > hansen(logflatnodes,archotreeouch,diet,sqrt.alpha=1,sigma=1)
> >
> > I do not get errors.
> >
> > As for the problem with the initialization of hansen, you have discovered
> > a typo in the documentation, for which I am grateful to you! It should
> > read 'nchar*(nchar+1)/2'. In your case, you must supply a scalar value,
> > a guess as
> > to what the square root of alpha should be.
> >
> > I will repair the documentation and upload a new version of ouch to CRAN
> > soon.
> >
> > Aaron
> >
> > On Monday, July 25, 2011 10:03:13 AM Roland Sookias wrote:
> > > Right. Um well the tree was made by ape2ouch(archotree) (also in the
> > > workspace file). I'm not sure what you mean by code...
> > >
> > > I have indeed read ?hansen. All I could find was:
> > >
> > > "Each matrix can be parameterized by nchar*(nchar+1) parameters, where
> > > nchar is the number of quantitative characters."
> > >
> > > I have one character, so as far as I could understand it that would
> > > imply "2" should be specified. I tried that to no avail.
> >
> > --
> > Aaron A. King, Ph.D.
> > Ecology & Evolutionary Biology
> > Mathematics
> > Center for the Study of Complex Systems
> > University of Michigan
> > GPG Public Key: 0x15780975
--
Aaron A. King, Ph.D.
Ecology & Evolutionary Biology
Mathematics
Center for the Study of Complex Systems
University of Michigan
GPG Public Key: 0x15780975
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