[phylocom-user] using R for running phylocom.comstruct

Steven Kembel steve.kembel at gmail.com
Tue May 12 09:14:03 PDT 2009


Hi Simon,

First, what does the data object 'a' look like - is it a data.frame  
with species in columns and samples in rows?

Second, for those scripts to work the phylocom executable needs to be  
in your path or in the R working directory.

Third, are you running those commands on a Windows system? Statements  
like "system("cp -f phylo phylo.tmp")" get executed at the command  
line and "cp" (copy) won't work on Windows. Do you have access to a  
system running Mac OS or Linux? Otherwise you could try changing "cp"  
to "copy" throughout the R code. I don't have access to a computer  
running Windows to test this.

If you're using R with phylocom my suggestion would be to install the  
picante package, which contains several scripts for getting data in  
phylocom format in and out of R. Try the commands 'readsample' and  
'writesample' to read/write a community matrix from phylocom format to  
R. You could then analyze the resulting file using phylocom.

Cheers,
Steve

On May 12, 2009, at 5:09 AM, Simon Blanchet wrote:

> Dear all,
>
> Me again...We are trying to use the R scripts to run  
> phylocom.comstruct.
> Unfortunately, the following error message appears (I used the  
> example files):
>
> > phylocom.comstruct(a)
> Error in read.table("comstruct.tmp", header = T, row.names = 1, skip  
> = 1,  :
>  no lines available in input
> In addition: Warning message:
> In system("cp -f phylo phylo.tmp") : cp not found
>
> Some of my colleagues tried to help me but we were unable to debug...
>
> Do you have any ideas to fix the problem?
>
> Many thanks again,
>
> All the best,
>
> Simon
> -- 
> Simon Blanchet (PhD)
> Post-doctorate (Brosse's lab)
> University Paul Sabatier - Toulouse III
> 118 Rte de Narbonne
> 31062 Toulouse Cedex4
> France
> Tel: 05 61 55 67 47
> Email: blanchet at cict.fr
> Website: http://simon.blanchet1.free.fr
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