I am having what I think is a strange problem with applying TukeyHSD to
an aov fit with error strata.
TukeyHSD is supposed to take "A fitted model object, usually an
'aov'
fit." aov (with error strata) is supposed to generate an object of type
aovlist, which is a list of objects of type aov. But I can't seem to
feed components of my aovlist to TukeyHSD. I guess I wouldn't expect to
be able to use the error strata, but I did expect to be able to use the
final stratum.
I have posted a complete example, which I hope explains why I am
confused, below. Any help will be appreciated.
Jonathan Dushoff
----------------------------------------------------------------------
> morley$Expt = factor(morley$Expt)
> morley$Run = factor(morley$Run)
>
> mod = aov(Speed~Expt+Run, data=morley)
> class(mod)
[1] "aov" "lm">
> TukeyHSD(mod)$Expt
diff lwr upr
2-1 -53.0 -117.91627 11.916268
3-1 -64.0 -128.91627 0.916268
4-1 -88.5 -153.41627 -23.583732
5-1 -77.5 -142.41627 -12.583732
3-2 -11.0 -75.91627 53.916268
4-2 -35.5 -100.41627 29.416268
5-2 -24.5 -89.41627 40.416268
4-3 -24.5 -89.41627 40.416268
5-3 -13.5 -78.41627 51.416268
5-4 11.0 -53.91627 75.916268>
> errmod = aov(Speed~Expt+Error(Run), data=morley)
> names(errmod)
[1] "(Intercept)" "Run"
"Within"> basemod = errmod$W
>
> class(basemod)
[1] "aov" "lm"> TukeyHSD(basemod)
Error in sort(unique.default(x), na.last = TRUE) :
'x' must be atomic
