I came across the following paper by Ahti Pietarinen:
https://www.researchgate.net/publication/271419583_Two_Papers_on_Existential_Graphs_by_Charles_Peirce

In that article, Ahti includes and comments on two papers.
The first is "a paper prepared and read for the National
Academy of Sciences, Washington DC, 16–18 April 1906."

In this one, he uses the notation I claimed was his final
preferred notation:  shading the negative areas and leaving
the positive areas unshaded.

In the second paper from 1911, Peirce also used shading for the
negative areas and white for the positive areas.  But he wrote
"It is needless to say that the process of making a black surface
with a diagram in white upon it is insufferably inconvenient. For
that reason in practice one substitutes Fig. 9 or Fig. 10 in place
of Fig. 8."

This is further evidence that Peirce preferred shading for
distinguishing negative areas.

With computer graphics today, it's easy to generate the shading.
But if you're drawing EGs by hand (on paper, blackboard, or
whiteboard), Peirce recommended the version without shading.

John
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