Hello Sebastian,
Thank you so much! It kind of worked. I was able to generated .graphml files with the appropriate file names, but when I went to open each file, the contents were all identical e.g. the friendship network had the same nodes/edges as the publication network (which I know isn't the case with the data set).
It seems so strange to me because when I make .net files and open them in Gephi, they save/look correctly. I know I'm very close it's just a little off. Any other ideas?
Thank you,
Hannah