Hello,
sorry, I forgot to refer where the problem was. On the beginning, I didn't
check all over thousand trees manually. I found trees on which it was failing
by simple for loop (could be simpler and more straightforward, I know):
Y <- trees.rooted.nexus
class(Y) <- "multiPhylo"
X <- list()
trees.ultra.nexus <- list()
for (i in 1:length(Y)) {
trees.ultra.nexus[[i]] <- chronos(Y[[i]])
X[i] <- i
}
length(X)
length(trees.ultra.nexus)
Last tree there was the last „good“ one. I then checked to following one and
it was just one big polytomy without any structure. No surprise it failed. :-)
After removing several useless „trees“ like that (in several similar steps)
chronos() worked fine as usual. So if anyone would have similar problem...
Sincerely,
VojtěchDne Ne 9. listopadu 2014 17:43:00 jste napsal(a): > Hello, > I have multiPhylo list with consensus trees from MrBayes (*.con.tre). When I > try to get ultrametric trees by trees.ultra.nexus <- > lapply(X=trees.rooted.nexus, FUN=chronos, model=“relaxed“) it start running > and finally it crashes: > > Setting initial dates... > Fitting in progress... get a first set of estimates > Penalised log-lik = -9.32736 > Optimising rates... dates... -9.32736 > Optimising rates... dates... -7.513123 > Done. > Setting initial dates... > Fitting in progress... get a first set of estimates > Penalised log-lik = -10.31663 > Optimising rates... dates... -10.31663 > Optimising rates... dates... -8.40787 > Done. > ... > Setting initial dates... > Fitting in progress... get a first set of estimates > Penalised log-lik = -9.084298 > Optimising rates... dates... -9.084298 > Optimising rates... dates... -3.934602 > Optimising rates... dates... -3.931579 > Done. > Setting initial dates... > Fitting in progress... get a first set of estimates > Penalised log-lik = -10.27628 > Optimising rates... dates... -10.27628 > Optimising rates... dates... -7.097138 > Done. > Setting initial dates... > Fitting in progress... get a first set of estimates > Error in sapply(A_ki, function(x) sum(tmp[x])) - tmp2 : > non-numeric argument to binary operator > Calls: lapply ... FUN -> nlminb -> gradient -> gradient -> gradient.poisson > In addition: There were 50 or more warnings (use warnings() to see the first > 50) > Error in sapply(A_ki, function(x) sum(tmp[x])) - tmp2 : > non-numeric argument to binary operator > Calls: lapply ... FUN -> nlminb -> gradient -> gradient -> gradient.poisson > I tried to change parameters, no change... When I display warnings, I see: > Warning messages: > 1: In nlminb(start.para, f, g, control = opt.ctrl, lower = LOW, ... : > NAs introduced by coercion > 2: In nlminb(start.para, f, g, control = opt.ctrl, lower = LOW, ... : > NAs introduced by coercion > 3: In nlminb(start.para, f, g, control = opt.ctrl, lower = LOW, ... : > ... > When I tried with trees from *.trprobs files, it worked perfectly. Any idea > what could be wrong? > Sincerely, > Vojtěch -- Vojtěch Zeisek http://trapa.cz/en/ Department of Botany, Faculty of Science Charles University in Prague Benátská 2, Prague, 12801, CZ http://botany.natur.cuni.cz/en/ Institute of Botany, Academy of Science Zámek 1, Průhonice, 25243, CZ http://www.ibot.cas.cz/en/ Czech Republic
signature.asc
Description: This is a digitally signed message part.
_______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
