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The R Book by Michael J. Crawley

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Multiple Comparisons

When comparing the means for the levels of a factor in an analysis of variance, a simple comparison using multiple t tests will inflate the probability of declaring a significant difference when there is none. This because the intervals are calculated with a given coverage probability for each interval but the interpretation of the coverage is usually with respect to the entire family of intervals (i.e. for the factor as a whole).

If you follow the protocol of model simplification recommended in this book, then issues of multiple comparisons will not arise very often. An occasional significant t test amongst a bunch of non-significant interaction terms is not likely to survive a deletion test (see p. 325). Again, if you have factors with large numbers of levels you might consider using mixed-effects models rather than ANOVA (i.e. treating the factors as random effects rather than fixed effects; see p. 627).

John Tukey introduced intervals based on the range of the sample means rather than the individual differences; nowadays, these are called Tukey's honest significant differences. The intervals returned by the TukeyHSD function are based on Studentized range statistics. Technically the intervals constructed in this way would only apply to balanced designs where the same number of observations is made at each level of the factor. This function incorporates an adjustment for sample size that produces sensible intervals for mildly unbalanced designs.

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