How can I classify post-hoc test results in R?

Question

I am trying to understand how to work with ANOVAs and post-hoc tests in R. So far, I have used aov() and TukeyHSD() to analyse my data. Example:

uni2.anova <- aov(Sum_Uni ~ Micro, data= uni2)

uni2.anova

Call:
aov(formula = Sum_Uni ~ Micro, data = uni2)

Terms:
                    Micro  Residuals
Sum of Squares  0.04917262 0.00602925
Deg. of Freedom         15         48

Residual standard error: 0.01120756 
Estimated effects may be unbalanced

My problem is, now I have a huge list of pairwise comparisons but cannot do anything with it:

 TukeyHSD(uni2.anova)
 Tukey multiple comparisons of means
   95% family-wise confidence level

Fit: aov(formula = Sum_Uni ~ Micro, data = uni2)

$Micro
                               diff          lwr           upr     p adj
Act_Glu2-Act_Ala2     -0.0180017863 -0.046632157  0.0106285840 0.6448524
Ana_Ala2-Act_Ala2     -0.0250134285 -0.053643799  0.0036169417 0.1493629
NegI_Ala2-Act_Ala2     0.0702274527  0.041597082  0.0988578230 0.0000000

This dataset has 40 rows... Idealy, I would like to get a dataset that looks something like this:

• Act_Glu2 : a
• Act_Ala2 : a
• NegI_Ala2: b...

I hope you get the point. So far, I have found nothing comparable online... I also tried to select only significant pairs in the file resulting from TukeyHSD, but the file does not "acknowlegde" that it is made up of rows & columns, making selecting impossible...

Maybe there is something fundamentally wrong with my approach?

Answer 1

I think the OP wants the letters to get a view of the comparisons.

library(multcompView)
multcompLetters(extract_p(TukeyHSD(uni2.anova)))

That will get you the letters.

You can also use the multcomp package

library(multcomp)
cld(glht(uni2.anova, linct = mcp(Micro = "Tukey")))

I hope this is what you need.

Answer 2

The results from the TukeyHSD are a list. Use str to look at the structure. In your case you'll see that it's a list of one item and that item is basically a matrix. So, to extract the first column you'll want to save the TukeyHSD result

hsd <- TukeyHSD(uni2.anova)

If you look at str(hsd) you can that you can then get at bits...

hsd$Micro[,1]

That will give you the column of your differences. You should be able to extract what you want now.