tpoisot
commented
10 years ago As the goal of this paper is not to compare measures of modularity (this has been done by Thébault in 2012, cited in main text), the important piece of information is indeed to compare the Q/Qr relationship for different modularity optimisation methods, as one previous referee required. I added an explanation of this point.
So as not to over-report minute details, the raw results are linked to the paperm and so the exact number of networks with negative values of Qr' can be retrieved.
I have changed the reporting of statistical analyses so that it is homogeneous throughout the whole text.
Adressed in aab53f8
As said above, this is not connected to the rest of the paper. Of course it improves the paper to consider alternative methods for module assignment. However, this paragraph has several shortcomings. First, restricting this analysis to the unipartite networks makes it hard to compare to the other results. Second, it remains unclear why this focuses on the correlation between Q and Q'R. The modularity of the partition returned by each method would be compared more directly by comparing the values of Q or Q'R between methods. At the moment, for judging the three methods the reader is just left at guessing that “several” negative values (for methods walktrap and edge-betweenness) are more than “less than 8%” (method spinglass). Third, it looks like an inconsistent ad-hoc addition: citations for the methods and the igraph library (package) are missing, the methods are not mentioned before or described and correlation coefficients are called r here but rho above.