Why and how the text could be Bavarian

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The high value for  p can be explained simply by the fact that  p at the start of a line is very much a language B phenomenon. Moreover also language B pages ( typically quires 13 and 20 ) have longer lines. So it should not surprise you to see a correlation between frequency of  p start lines and line length.

Because of the language and writing and text differences between the sections I believe you would get more meaningful results if you were to perform your analysis separately for each of the main work groups

Herbal A1
Herbal B2
Pharma A1
Quire 13
Quire 20