Proposed Manuscript Chronology

[Jorge_Stolfi]

Furthermore, the clusters only appear isolated because the voids are in areas where the missing bifolios would naturally slot. They are between pharma, and f58. F58 is known to be missing 3 bifolio. The missing quires, the foliation would put them exactly in the voids. There is an obvious linear sequence in the data here.

I will address the "Guttman horseshoe" issue in a latter post.  Here I must disagree with the above statement.

The "voids" are not significant because they are determined by the outliers, ignoring the bulk of the points.  That is not how one infers whether a set of data points is "clustered" or "continuous".

A more reliable way to tell whether a set of points on the plane is "clustered" is to replace each point by a roundish fuzzy smudge and add the smudges.  Make the smudges just big enough for most of them to overlap their neighbors. 

Then, if the points come from a simple distribution -- like a 2D Gaussian -- you should see a single dark smudge surrounded by a few scattered small smudges, like this:
   
If you instead see something like this
   
you should realize that a single 2D Gaussian distribution is not an adequate model for the data.  A better model would be: a point can be any of three classes, and each class has its own 2D Gaussian distribution, with its own centroid and principal vectors.

You claim that the data points extracted from the VMS pages fit instead a model where, instead of N discrete classes, there is a 2D probability distribution D(t) that depends on a single parameter t, such that for each fixed t you get (say) a 2D Gaussian with centroid C(t), but C(t) varies continuously and smoothly along some curved path as the points are generated.  

If that were the case, the procedure above should give an image like this:
   
But, even without actually building the image, we can see that this is not what we would get.  Each major section would produce a concentrated lump, much like the second image above.  

So the page statistics do not suggest or support that (1) there is an intrinsic order of the pages or (2) there is a gradual transition between pages of different sections.

They do not suggest or support claim (1) even within each section. 

If you arrange the books of a library in a single row, sorted by height, you will get a fairly smooth variation of height from one end to the other.  That of course does not imply that those books are the product of a single process with a continuously varying parameter.   That conclusion is unwarranted even if you do that for each shelf separately.

All the best, --stolfi