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
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