Hi Emmanuel,
Thanks for answer. I'm using phyml versión 20160328 under xubuntu 14.04
environment, so I'm sure that created files has no extension.
I will try your suggestions.
Thanks,
Christian
El abr. 2, 2016 9:14, "Emmanuel Paradis" <emmanuel.para...@ird.fr> escribió:
> Hi Christian,
>
> It is difficult to see what's going wrong with your problem. Do you use a
> recent version of PhyML? From what I remember about Windows (in case you
> use this OS), the filename extensions (here .txt) are not displayed by the
> file explorer.
>
> If PhyML has run correctly, you should have the files output by PhyML in
> your working directory. Then you can try these lines (assuming you run all
> models from phymltest):
>
> l <- readLines("nnn_stats.txt") # <- adjust the file name to your needs
> l <- grep("Log-likelihood:", l, value = TRUE)
> loglik <- as.numeric(sub(". Log-likelihood:", "", l))
> names(loglik) <- ape:::.phymltest.model
> class(loglik) <- "phymltest"
>
> where 'loglik' is the (expected) output from phymltest(), you can change
> its name (in case you make several runs of this function):
>
> output.phymltest.nnn <- loglik
>
> HTH
>
> Best,
>
> Emmanuel
>
> Le 01/04/2016 15:48, Christian Hodar a écrit :
>
>> I have a problem running phymltest from ape 3.4.
>>
>> The call from R works fine, i can see the phyml running, and in some point
>> an error occurs when the function try to read nnn_stats.txt file, because
>> the output write (at least thats I see in my computer) dont add the "txt"
>> extension. Same thing for the nnn_tree output file.
>> So, any idea how get the summary in order to check the possible paired
>> likelihood tests?
>>
>> ape version 3.4
>> R version 3.2.4
>>
>> Thanks,
>> Christian
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-phylo mailing list - R-sig-phylo@r-project.org
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>>
>>
>> Pour nous remonter une erreur de filtrage, veuillez vous rendre ici :
>> http://f.security-mail.net/301QJWl0hY0
>>
>>
>>
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