Re: [R] RAxML using R
Dear Ista, that sos package is certainly something, didn't know there was one! It turned out that ips is written by the same person who wrote phyloch, so the latter must have been an alpha version of the former. The raxml function worked from ips worked fine -- just a matter of defining the parameters now -- and the installation was smooth, although I had to pre-install the ubuntu package |libxml2-dev|. Thank you for your help, Luigi On 29/12/14 15:07, Ista Zahn wrote: Let's step back for a moment and look at the larger picture. There are real advantages to using packages on CRAN, including convenient installation, updates, etc., so let's see if we can find a package on cran that does what we want: install.packages(sos) library(sos) findFn(raxml) This suggests that the ips package does what we want, so let's install it and test it out: install.packages(ips) library(ips) example(raxml) If for some reason this does not do what you want, and you really need to install packages outside the standard R package repositories, the devtools package will make this easier: library(devtools) nstall_url(http://www.christophheibl.de/phyloch_1.5-5.tar.gz;) library(phyloch) example(raxml) HTH, Ista On Mon, Dec 29, 2014 at 9:23 AM, Luigi Marongiu marongiu.lu...@gmail.com wrote: 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@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. __ R-help@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. [[alternative HTML version deleted]] __ R-help@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.
Re: [R] RAxML using R
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@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. __ R-help@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.
Re: [R] RAxML using R
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@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. __ R-help@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.
Re: [R] RAxML using R
Let's step back for a moment and look at the larger picture. There are real advantages to using packages on CRAN, including convenient installation, updates, etc., so let's see if we can find a package on cran that does what we want: install.packages(sos) library(sos) findFn(raxml) This suggests that the ips package does what we want, so let's install it and test it out: install.packages(ips) library(ips) example(raxml) If for some reason this does not do what you want, and you really need to install packages outside the standard R package repositories, the devtools package will make this easier: library(devtools) nstall_url(http://www.christophheibl.de/phyloch_1.5-5.tar.gz;) library(phyloch) example(raxml) HTH, Ista On Mon, Dec 29, 2014 at 9:23 AM, Luigi Marongiu marongiu.lu...@gmail.com wrote: 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@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. __ R-help@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. __ R-help@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.
