I tried to use TukeyHSD(my_anova$aov) but it gives an error:
Error in UseMethod("TukeyHSD") :
no applicable method for 'TukeyHSD' applied to an object of class "c('aovlist', 'listof')"
Google says that there is no way to post hoc with ‘aovlist’. But maybe you have any idea about post hoc with ezANOVA output.
Example:
require(ez)
data(ANT)
rt_anova = ezANOVA(data = ANT[ANT$error==0,], dv = rt, wid = subnum, within = cue,return_aov = TRUE)
Try to use multcomp:
require(multcomp)
glht(my_anova$aov, linfct = mcp(cue = "Tukey"))
Error in model.matrix.aovlist(model) :
‘glht’ does not support objects of class ‘aovlist’
Error in factor_contrasts(model) :
no ‘model.matrix’ method for ‘model’ found!
Try to use lme:
require(nlme)
lme_velocity = lme(rt ~ cue, data=ANT[ANT$error==0,], random = ~1|subnum)
Error in .Call("La_chol", as.matrix(x), PACKAGE = "base") :
Incorrect number of arguments (1), expecting 2 for 'La_chol'
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: i386-w64-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=Russian_Russia.1251 LC_CTYPE=Russian_Russia.1251 LC_MONETARY=Russian_Russia.1251 LC_NUMERIC=C LC_TIME=Russian_Russia.1251
attached base packages:
[1] splines stats graphics grDevices utils datasets methods base
other attached packages:
[1] nlme_3.1-108 multcomp_1.2-15 survival_2.37-2 mvtnorm_0.9-9994 ez_4.1-1 stringr_0.6.2 scales_0.2.3 reshape2_1.2.2 plyr_1.8 memoise_0.1
[11] mgcv_1.7-22 lme4_0.999999-0 Matrix_1.0-10 lattice_0.20-13 ggplot2_0.9.3 car_2.0-15 nnet_7.3-5 MASS_7.3-23
loaded via a namespace (and not attached):
[1] colorspace_1.2-1 dichromat_2.0-0 digest_0.6.2 grid_2.15.0 gtable_0.1.2 labeling_0.1 munsell_0.4 proto_0.3-10 RColorBrewer_1.0-5
[10] stats4_2.15.0 tools_2.15.0
It’s not that it’s ezANOVA output but that it’s a repeated measures ANOVA. The class ‘aovlist’ is typically for that. TukeyHSD is for independent designs. See this question and related links there.