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 GPG Public Key: 0x15780975
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