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Are you just trying to display the results as a compact letter display? Where, means sharing a letter are not significantly different. If so, this can be accomplished with the multcompLetters functio …

It may be helpful if you leave the levels of f1 as 0 and 1 and change the levels of f2 to a and b. As you have the data set up, to answer the question in simplified notation, $f1 is like 1:(1&0) - 0(1 …

(Partially from comments.) There is no indication in the results of the Tukey HSD test that group A is different than the other groups. The p values for each comparison are greater than 0.24. [e.g. …

As to the use of emmeans here, this is really a programming question. The code just needs to be updated a little: A = rep(c("I","II","III"), each=5) Y = c(1,2,3,4,5,3,4,5,6,7,9,10,11,12,13) m1 = lm(Y …

My best advice is, if by "medical paper" you mean something that will be published and valuable for others, that you consult someone a little better versed in analyzing experiments. It's absolutely …

Your concern in 1) is correct. The p-value results do not match those in the compact letter display. Without having the original data and code, it's not known how this happened. It's possible that …

The data are arranged in complete block design. Because the values between any two groups are paired, Tukey's HSD test isn't appropriate. Instead you want to use something like a paired t test or ot …

In glht, "tukey" doesn't refer to Tukey's HSD. It just means "do all pairwise comparisons". By default, ghlt uses a "single-step" correction method, but other correction methods could be used. As far …

The simple answer is that Tukey's HSD isn't a test of overlapping plots. If it were, we would just look at the plots and not worry about conducting the HSD test. Note also that LFa and LK have overla …

Tukey HSD, Dunn-Sidak correction, and Dunn test are all different things, and aren't really alternatives to one another. Tukey HSD is a method to compare among means of multiple groups, as would be c …

There's probably no need to apologize. Despite the large amount of educational material free on the web for learning statistics in R, the vast majority don't address situations that users of other pa …

I'll try to answer one piece of the question. There is an established protocol for distinguishing similar groups from dissimilar groups which results in a compact letter display. A series of pairwis …