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!