The function TukeyHSD( ) is applied to the output of an ANOVA (aov(lm(log(con)~trt,vetjoh)) to create a set of confidence intervals on the differences between the means using the specified family-wise probability of coverage. The default provides 95% confidence intervals.
The intervals are based on the Studentized range statistic using Tukey's 'Honest Significant Difference' method. A P-value is also given for each difference.
The method is designed for where there are the same number of observations made at each level of the factor. However, it incorporates an adjustment for sample size that produces sensible intervals for mildly unbalanced designs.