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Barplot with "Independent" Lines Y axis

Without seeing a reproducible example we cannot be sure, but my guess is that you are letting twoord.plot set the limits and the function does not remove missing values, if you specify rylim and or lylim arguments specifically, then it should not run into the problem you are seeing (I hope).

If that does not work, then send a small reproducible example (the dput command is great for the data part) which will help us find the problem.