Thanks for all the replies!

Steve: I don't know whether my suggestion is a good one. I'm quite new to programming, have absolutely no experience and this was the only one I could think of. :-) I'm not sure whether I'm able to put your tips into practice, unfortunately I had no time for much reading today but I'll dive into it tomorrow.

David: To be honest I don't understand your code yet, but the result is not equivalent to the original matrix since the row sums don't match, isn't it? Or is it intended like this? I'll try to ask Google (or rather RSeek) tomorrow to understand your code. :-)

Ted: Wow, that's heavy reading. In fact the matrices that I need to compare are incidence matrices so I suppose it's exactly the thing I need, but I don't know if I have the basics knowledge to understand this paper within the next months.

Gabor: To sort the matrices in the same way and then to compare them element by element was my intent, too. I don't understand your code yet, but it seems similar to David's proposal, at least the results seem to be the same.

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