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

[Jombart, Thibaut]

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

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