[R] RAxML using R

[Ista Zahn]

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.luigi at 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 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.
>>
>>
>
> ______________________________________________
> 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.