evaluate_corpus is the function to look at, it is called an number of times in main for the various corpora that we are evaluating. Also note the output of analysis and the code inside of analysis. These are the spots that are relevant for the analysis and printing of graphs @Zach and @Youssef.
This project is very much a WIP. Not to be taken as an example of my work for recruiting. We are developing a framework for evaluating the Voynich Manuscript from a new perspective.