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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