How to do a Tukey HSD test with the Anova command (car package)

Question

I'm dealing with an unbalanced design/sample and originally learned aov(). I know now that for my ANOVA tests I need to use the Type III Sum of Squares which involves using fitting using lm() rather than using aov().

The problem is getting post-hoc tests (specifically Tukey's HSD) using lm(). All the research I've done has said that using simint in the multcomp package would work, but now that it's updated that command seems to not be available. It also seems to rely upon going through aov() to calculate.

Essentially all of the Tukey HSD tests I've found for R assume that you use aov() for the comparison rather than lm(). To get the Type III Sum of Squares I need for the unbalanced design I have to use:

mod<-lm(Snavg~StudentEthnicity*StudentGender)

Anova(mod, type="III")

How do I use a Tukey HSD test with my mod using lm()? Or conversely, calculate my ANOVA using Type III and still be able to run a Tukey HSD test?

Thanks!

Answer 1

Try HSD.test in agricolae

library(agricolae)
data(sweetpotato)
model<-lm(yield~virus, data=sweetpotato)
comparison <- HSD.test(model,"virus", group=TRUE,
main="Yield of sweetpotato\nDealt with different virus")

Output

Study: Yield of sweetpotato
Dealt with different virus

HSD Test for yield 

Mean Square Error:  22.48917 

virus,  means

      yield  std.err replication
cc 24.40000 2.084067           3
fc 12.86667 1.246774           3
ff 36.33333 4.233727           3
oo 36.90000 2.482606           3

alpha: 0.05 ; Df Error: 8 
Critical Value of Studentized Range: 4.52881 

Honestly Significant Difference: 12.39967 

Means with the same letter are not significantly different.

Groups, Treatments and means
a        oo      36.9 
ab       ff      36.33333 
 bc      cc      24.4 
  c      fc      12.86667