Solved – Post Hoc test for between subject factor in a repeated measures ANOVA in R

post-hocrrepeated measurestukey-hsd-test

I have done an experiment of how different animal species affect nutrient fluxes in sediments. I had a number of experimental units (sediment boxes) to which different animal species were added. I then measured nutrient fluxes in these units. Each unit was measured five times. I have used the ezANOVA package for R to do a repeated measures ANOVA with two factors (between subjects factor “Species” and within subject factor “Time”).
Here's an example of my input:

> ezANOVA(data=NoP_3_5,dv=.(AcPO4),wid=.(Subject),within=.(Time),between=.(Species),return_aov=T)
$ANOVA
    Effect DFn DFd           F            p p<.05        ges
2      Species   2   6 10.60384830 1.072453e-02     * 0.50875722
3         Time   2  12 27.88590570 3.081718e-05     * 0.76667542
4 Species:Time   4  12  0.08093179 9.867291e-01       0.01871588

$`Mauchly's Test for Sphericity`
        Effect         W           p p<.05
3         Time 0.1439855 0.007866779     *
4 Species:Time 0.1439855 0.007866779     *

$`Sphericity Corrections`
        Effect       GGe       p[GG] p[GG]<.05       HFe       p[HF] p[HF]<.05
3         Time 0.5387889 0.001349263         * 0.5630403 0.001103048         *
4 Species:Time 0.5387889 0.933492515           0.5630403 0.939138882          

$aov

Call:
aov(formula = formula(aov_formula), data = data)

Grand Mean: -0.004276663 

Stratum 1: Subject

Terms:
                     Species    Residuals
Sum of Squares  0.0004410742 0.0001247870
Deg. of Freedom            2            6

Residual standard error: 0.004560464 
Estimated effects may be unbalanced

Stratum 2: Subject:Time

Terms:
                        Time Species:Time    Residuals
Sum of Squares  0.0013994206 0.0000081229 0.0003011028
Deg. of Freedom            2            4           12

Residual standard error: 0.005009181 
Estimated effects may be unbalanced

I want to use the $aov output to do a Tukey HSD post hoc test of the between factor ("Species"). However, it does not work:

mod <- ezANOVA(data=NoP_3_5,dv=.(AcPO4),wid=.(Subject),within=.(Time),between=.(Species),return_aov=T)
    > TukeyHSD(mod$aov)
Error in UseMethod("TukeyHSD") : 
  no applicable method for 'TukeyHSD' applied to an object of class "c('aovlist', 'listof')"

I have also tried to use the aov-command directly:

> mod2 <- aov(AcPO4~(Species)+Error(Subject/Time)+(Species),data=NoP_3_5)
> TukeyHSD(mod2)
Error in UseMethod("TukeyHSD") : 
  no applicable method for 'TukeyHSD' applied to an object of class "c('aovlist', 'listof')"

I have tried to use lme() to specify the anova-model with the aim to produce something that TukeyHSD() will accept without success.

Any help would be greatly appreciated!

Best Answer

In R when you have any ANOVA (other than simple one-factor), you have to provide to TukeyHSD the variables to have intervals calculated. 

summary(cc<-aov(weight~as.factor(Diet)+as.factor(Chick),data=ChickWeight))
TukeyHSD(cc,"as.factor(Diet)",data=ChickWeight)

Use ?TukeyHSD to get the detailed help.

Related Question