Censored test error

[ant...@gmail.com]

Hello everyone,

while trying to run the censored rate test  in RBrownie on simulated data (sims run in motmot), the runs fail with the following error message:

...
Starting to execute NEXUS file
   Entering TAXA block...done
   Entering TREES block...done
   Entering CHARACTERS block...ERROR: Cannot find taxon -
terminate called after throwing an instance of 'TaxaBlock::nosuchtaxon'
Aborted

This does not happen to all simulated datasets, but once it happens the runs fall alltogether. My question is two-fold:

1) I have tried to figure out why this happens, but could not associate it to any characteristics of the simulated data. I guess this could be some kind of convergence issue with the likelihood optimizer? Any other ideas on why this happens?

2) Although I am running the runCensored() command within a try(..., silent=T) function, it does not seem to combine well with try(), which makes it impossible to skip the failing runs and continue running the rest of simulated datasets. Any ideas on how I might deal with this?

Thanks a lot!
Antigoni

[Brian O'Meara]

With errors like this, the first thing to try is getting rid of "funny" characters in taxon names. Especially when going from R to C++, like in RBrownie, characters like spaces, dashes, etc. can have different meanings. I'd get rid of spaces, single or double quotes, underscores, dashes, periods, dollar signs, etc. and see if it's still a problem.

Best,
Brian

_______________________________________
Brian O'Meara
Assistant Professor
Dept. of Ecology & Evolutionary Biology
U. of Tennessee, Knoxville
http://www.brianomeara.info

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[Antigoni Kaliontzopoulou]

Thanks for this Brian, but unfortunately it doesn't work. In any case, I only had spaces in taxon names, but even removing those the same thing happens.

A potentially important point is that this happens while running simulation cycles. I mean, it is not like I cannot run the analysis at all, so this seems to indicate the problem is not "technical" (i.e. some error with the taxa or variable names or the trees), as I can run some analyses alright. It only appears at some point (possibly when simulating data with somehow "extreme" characteristics"). The problem is that as this error I mentioned aborts R altogether, I cannot even figure out WHEN it happens (i.e. R is aborted and I cannot get back into my loops and try to understand which conditions exactly make RBrownie crash). I will try outputting simulation conditions in an external file in every cycle to see if I can figure it out, but if you or anyone else have any other ideas, I will be very happy to give them a try.

Thanks again
Antigoni

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Antigoni Kaliontzopoulou

CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos
Campus Agrário de Vairão, 4485-661 Vairão
PORTUGAL
Department of Ecology, Evolution, and Organismal Biology
Iowa State University, Ames,
Iowa 50011, USA

tel: +351 91 3086188
mail to: ant...@gmail.com
            anti...@mail.icav.up.pt

[luca...@umich.edu]

Hi Antigoni,

You may have solved this already, but I recently received the same error while trying to read a file in to Brownie. I figured out that the error was caused by the notation of the character values, i.e., very small and very large values being written in scientific notation with the letter "E". Once I converted my values into decimal format, Brownie was able to read my file just fine.

Cheers,
Lucy