[R] RAxML using R

[Luigi Marongiu]

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.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.


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