[R-sig-genetics] R & Arlequin (little OT?)

[Vojtěch Zeisek]

Hello,
the point is, that Arlequin produces XML file containing all results. Results 
are in form of tables. There is set of Arlequin's R scripts, which should be 
able to parse this XML and produce graphics. But I'm not able to get it to 
work... :-( Never mind, I asked just in case someone would have experience 
with it.
All the best,
Vojtěch

Dne St 20. března 2013 10:10:18, Jombart, Thibaut napsal(a):
> Hello,
> 
> I'm not sure if you're trying to export data, or merely results of some
> analyses. For data, the best may be to export to a format such as GENETIX,
> FStat, or Genepop, and then import the data in R (see import2genind in
> adegenet). For results, it is probably easiest to export everything to a
> text file and then read it from R. I have never used Arlequin, but I
> suspect these are standard features.
> 
> Best
> Thibaut
> ________________________________________
> From: r-sig-genetics-bounces at r-project.org
> [r-sig-genetics-bounces at r-project.org] on behalf of Vojtěch Zeisek
> [vojtech.zeisek at opensuse.org] Sent: 20 March 2013 09:23
> To: mailinglist R
> Subject: [R-sig-genetics] R & Arlequin (little OT?)
> 
> Hello,
> I hope this is not too much off-topic for this list. I'm using Arlequin 3.5
> http://cmpg.unibe.ch/software/arlequin35/ (actually, Linux version of
> Arlecore) and I'd like to parse Arelquin's output through R as described in
> the manual, but I get error about missing function
> xmlTreeParse, so nothing is computed:
> 
> source("/home/vojta/bin/arlecore_linux/Rfunctions/rParsingSettings.r")
> Error in library(XML, lib.loc = paste(substr(sourcePath, 0,
> nchar(sourcePath) -  :
>   no library trees found in 'lib.loc'
> Error in library(XML, lib.loc = paste(substr(sourcePath, 0,
> nchar(sourcePath) -  :
>   no library trees found in 'lib.loc'
> Error in parseArlequin(infile, outfiles, sourcePath) :
>   could not find function "xmlTreeParse"
> 
> So it seems the xmlTreeParse is missing. Or am I doing something very wrong?
> Does anyone have any experience with this? :-)
> All the best,
> Vojtěch
-- 
Vojtěch Zeisek

Komunita openSUSE GNU/Linuxu
Community of the openSUSE GNU/Linux

http://www.opensuse.org/
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