I note that Protorosaurus_speneri sits at an unspecified time print(archotreeouch) as(archotreeouch,"data.frame")[137,]
It would be possible for me to verify this is the only problem were you to
provide code that reproduces your problem from scratch. In particular, since
I cannot see how you constructed archotreeouch, I cannot verify that this is
indeed the only problem.
Regarding the initialization of the hansen optimizer (sqrt.alpha, sigma), I
assume you have read '?hansen'. Can you be more specific as to what is not
clear to you?
On Monday, July 25, 2011 08:53:12 AM Roland Sookias wrote:
> OK, well for brown:
>
> brown(logflatnodes,archotreeouch)
>
> and for hansen:
>
> hansen1=hansen(logflatnodes,archotreeouch,diet,sqrt.alpha=0,sigma=1)
>
> I also attach the workspace file. The table from which the diet and log fl
> (femur length) data comes from is called "dietandflatnodes".
>
> Cheers
>
> On Mon, Jul 25, 2011 at 1:37 PM, Aaron King <kin...@umich.edu> wrote:
> > Hi Roland,
> >
> > It looks like it probably has to do ith your data. If you send a code
> > that reproduces the error, we can help you.
> >
> > Aaron
> >
> > On Jul 25, 2011, at 7:44, Roland Sookias <r.sook...@gmail.com> wrote:
> > > Hi
> > >
> > > I posted this on r-help by accident, and realize it's more appropriate
> >
> > here,
> >
> > > so I'll send it here and do ignore the other post.
> > >
> > > I'm trying to use ouch's hansen and brown functions but I get the error:
> > >> brown(logflatnodes,archotreeouch)
> > >
> > > Error in backsolve(l, x, k = k, upper.tri = upper.tri, transpose =
> > > transpose) :
> > > NA/NaN/Inf in foreign function call (arg 1)
> > >
> > > and with hansen also:
> > >
> > > Error in optim(par = c(sqrt.alpha, sigma), fn = function(par) { :
> > > function cannot be evaluated at initial parameters
> > >
> > > I'm not sure what I'm supposed to put in the sqrt.alpha and sigma
> > > parameters. I have several different selective regimes (trophic
> > > guilds).
> >
> > I
> >
> > > have a single continuous character (body size). I read these data in as
> > > a table, and then made the columns into objects (or vectors? i.e. I
> > > did data2=allmydata$data2) and named them by node number. The tree is
> >
> > converted
> >
> > > from ape.
> > >
> > > Thanks very much, and happy to provide more info...
> > >
> > > Traceback for the first error gives:
> > >> traceback()
> > >
> > > 9: .C("bakslv", t = r, ldt = nrow(r), n = k, b = x, ldb = k, nb = nb,
> > >
> > > x = matrix(0, k, nb), job = job, info = integer(1L), DUP = FALSE,
> > > PACKAGE = "base")
> > >
> > > 8: backsolve(l, x, k = k, upper.tri = upper.tri, transpose = transpose)
> > > 7: forwardsolve(vh, a, upper.tri = TRUE, transpose = TRUE)
> > > 6: as.matrix(x)
> > > 5: svd(forwardsolve(vh, a, upper.tri = TRUE, transpose = TRUE))
> > > 4: glssoln(w, x, b)
> > > 3: FUN(X[[1L]], ...)
> > > 2: lapply(dat, function(x) glssoln(w, x, b))
> > > 1: brown(logflatnodes, archotreeouch)
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > R-sig-phylo mailing list
> > > R-sig-phylo@r-project.org
> > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
--
Aaron A. King, Ph.D.
Ecology & Evolutionary Biology
Mathematics
Center for the Study of Complex Systems
University of Michigan
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