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@BigPimpinNYC: If we included set 3s and encores, Sleeping Monkey -> Tweezer Reprise ranks #5 with an astounding 13 shows (just under Mike's Song -> Simple and the same 4 seen at the top of the graph in the article). Nice observation!
@pikepredator: "(FWIW I don't fully understand the Implication column, 73% for BOABH and Zero?) Did you control for the frequency of the songs?" BOABH was played in 4% of shows (about 11 shows probably) and 73% of those shows (8 shows?) contained "Character Zero". This list was generated by picking the implications with the best % in the second column with at least 4% in the third column. You rarely see high second column percentages if the third column is high (ie. the song implying the other is frequently played). I didn't think it was necessary to control for anything. Likely the most prediction power will be when you hear a fairly rare (but not so rare that it is barely played) song which almost always comes with another more common song. The more common songs tended to have several second column percentage implications in the 30% range but, like you said, this is expected and maybe not so interesting.
@ucpete: Thanks for providing a musician's prospective. I don't have this knowledge so these ideas would not have occurred to me.
Another interesting little fact to leave you with: Tweezer always has a Tweezer Reprise. 92% of the time they are done in the same show and 8% of the time Tweezer is played in one show and Tweezer Reprise is saved for a future show which doesn't have a Tweezer.