[R] RAxML using R

Rui Barradas ruipbarradas at sapo.pt
Mon Dec 29 12:18:51 CET 2014


You can put the code of that function in a separate file, say "raxml.R" 
and then use source("raxml.R"). See the help page ?source.

Hope this helps,

Rui Barradas

Em 28-12-2014 23:09, Luigi Marongiu escreveu:
> Dear all,
> I would like to run RAxML for phylogenetic analysis as indicated on
> Paradis' "Analysis of phylogenetic and evolution with R" (p. 158) thus I
> tried to use the package phyloch and its function raxml(). I am using
> Linux Ubuntu 14 and I was able to successfully install RAxML on my machine.
> However phyloch is not supported by CRAN and the package as provided by
> the author on http://www.christophheibl.de/Rpackages.html cannot be
> installed -- or at least I could not using the Software centre.
> I found a function on http://www.christophheibl.de/raxml.R that should
> be the actual script of the function raxml(). However I do not know how
> to implement such function. Shall I just copy it into my script? But
> then I will have hundreds of lines of code that will mess with my
> script. Can I create a kind of package that I can call from my code? Or
> is there another way to send the data to the linux shell and call the
> raxml function?
> Could anybody help?
> Thank you
> Luigi
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

More information about the R-help mailing list