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ivanalaman

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Trouble with unbalanced design

First, congratulations for the good job, I really like your package.
I think I found an issue while working with unbalanced cases. As we know, for those cases we have to calculate a variance estimation of the contrast estimation on the msd calculations. This can lead to a problem, because a mean can differ from the immediate lower one, but not from the second lower one, because its error estimation may be greater.
I will try to explain better:

Browse[5]> m.tmp
       7        6        7        5 
5.389086 4.935529 4.868243 4.862371 

Browse[5]> msd
            MELOID/P MELOID/PS MELOID/V21 MELOID/TG
MELOID/P   0.0000000 0.5012896  0.4816234 0.5275920
MELOID/PS  0.5012896 0.0000000  0.5012896 0.5456037
MELOID/V21 0.4816234 0.5012896  0.0000000 0.5275920
MELOID/TG  0.5275920 0.5456037  0.5275920 0.0000000

Browse[5]> difm
            MELOID/P  MELOID/PS  MELOID/V21   MELOID/TG
MELOID/P   0.0000000 0.45355714 0.520842857 0.526714286
MELOID/PS  0.4535571 0.00000000 0.067285714 0.073157143
MELOID/V21 0.5208429 0.06728571 0.000000000 0.005871429
MELOID/TG  0.5267143 0.07315714 0.005871429 0.000000000

Browse[5]> dif
           MELOID/P MELOID/PS MELOID/V21 MELOID/TG
MELOID/P      FALSE     FALSE       TRUE     FALSE
MELOID/PS     FALSE     FALSE      FALSE     FALSE
MELOID/V21     TRUE     FALSE      FALSE     FALSE
MELOID/TG     FALSE     FALSE      FALSE     FALSE

As you can see, we have a F F T F, where we expected to have a F F T T, since the values are sorted decreasingly. This happens because the error estimation is greater, and may be expected behavior but is leading to an infinite loop.

Thanks in advance

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