A mathematical approach to double words, conditional logic and the missing pages

[asteckley]

I simply assigned a mathematical label ('1' or '0') to the text blocks depending on whether they actually contained a doublet or not. 
During the 1,000 permutations, the algorithm randomly shuffled only these mathematical labels, forcing the model to look for a syntactic rule on fake targets while the underlying text remained perfectly intact.

Sorry -- I just saw this part of your previous answers.  If I understand what you did correctly, then your violin result is probably not surprising at all. 

In any randomly selected document (of which the VMS is one such document), you can form a bar chart of logistic regression coefficients where all the words can be ordered from whatever the highest value is to whatever the lowest value is. In the case of the VMS you got a range of 0.933 down to -0.665. (Again, from that chart, there is no clustering apparent -- just a continual trend from some positive value down to some negative value andmore or less centered on zero.) The only question is whether that range that is spread across the value zero is larger than expected by chance or smaller.  (Determining that would require you going one step further to perform a statistical test of significance on the range or variance of the coefficients.)  

By randomly assigning the mathematical label on the text blocks, you come up with a different set of coefficients, but the range of those coefficients is not necessarily any different than in the subject case. (That's what the statistical test of significance would determine.)

It is important to understand just how you came up with the "predictive accuracy" in your violin chart.  Is it the predictive accuracy of your top triggers (and bottom inhibitors), or some averaging of the accuracies of all the words as predictors, or what? If you are considering, for example, the predictive accuracy of just the most powerful trigger plus that of the most powerful inhibitor, then finding the "Actual Voynich Data" located in the extreme tail might be meaningful because your randomization technique is then testing if the VMS case is indeed unusual or not.

Regards,
--Andrew