There is a function to create arlequin files in the package strataG. If this is what you are looking for, try
Edit : have you tried a simple search on RDocumentation ? There are a few functions to work with arlequin files.
Release of new R functions for R package ver 3.01 here. The zip file contains a directory called Rfunctions, which needs to replace the Rfunctions directory located in your Arlequin home directory. If you have already installed Arlequin and update your R package to ver 3.01 (latest version in June 2013), then this update is necessary to be able to produce graphics in your xml files
Maybe this is what you are looking for?
You are either looking for arlecore or for generating R-plots of different results in XML file using Rcmd. (in the latter look for chapter 7.8 XML output file)