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
Hello, 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.
Dear Rui, thanks for the reply. I tried it but there were serious problems with the function itself: I can't use it as is because there were different error messages according to the parameters passed to it. Such function has to be re-written on purpose or I should call the RAxML function from Linux Shell with some kind of interface. Best regards Luigi On 29/12/14 11:18, Rui Barradas wrote:> Hello, > > 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. >