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
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