"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
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