RAxML using R

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RAxML using R

Luigi
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

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Re: RAxML using R

Rui Barradas
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
>
> ______________________________________________
> [hidden email] 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.

______________________________________________
[hidden email] 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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Re: RAxML using R

Luigi
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
>>
>> ______________________________________________
>> [hidden email] 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.
>

______________________________________________
[hidden email] 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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Re: 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
<[hidden email]> 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
>>>
>>> ______________________________________________
>>> [hidden email] 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.
>>
>>
>
> ______________________________________________
> [hidden email] 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.

______________________________________________
[hidden email] 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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Re: RAxML using R

Luigi
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
> <[hidden email]> 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
>>>>
>>>> ______________________________________________
>>>> [hidden email] 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.
>>>
>> ______________________________________________
>> [hidden email] 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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______________________________________________
[hidden email] 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.