That tool creates a lineup with Jason Kendall leading off, instead of batting ninth. The lineups differ, depending on which projection tool you use:
With Thomas, using ZiPS: Kendall Johnson Chavez Bradley Thomas Crosby Swisher Kotsay Ellis
With Thomas, using Marcel: Kendall Bradley Thomas Chavez Johnson Swisher Crosby Ellis Kotsay
With Payton, using ZiPS: Kendall Johnson Chavez Bradley Crosby Swisher Kotsay Payton Ellis
With Payton, using Marcel: Kendall Johnson Chavez Bradley Swisher Crosby Payton Ellis Kotsay
I don't know about that. I still kinda like the idea of Ellis batting leadoff instead of Kendall that came out of the last tool. But the rest of the lineup looks a little better.
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Along those lines, Cyril Morong made some corrections to his DH-only stats. That changes the "ideal" lineup under the corrected AL numbers to the following:
With Thomas: Ellis Thomas Chavez Johnson Swisher Kotsay Crosby Bradley Kendall
With Payton: Ellis Chavez Johnson Bradley Swisher Payton Crosby Kotsay Kendall
I don't think Thomas batting second is likely to happen. Nor Bradley batting eighth.
For what it's worth, I'd probably write a Thomas lineup like this:
Ellis Johnson Bradley Chavez Thomas Crosby Swisher Kotsay Kendall
which keeps the left-right thing through the top of the order.
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And then late this afternoon, David Pinto emailed me that he had translated my Perl script to Python, and made an online tool for creating lineups. Now you all kinds of choices for your lineup generation. Enjoy.