> I would like to obtain for each factor of my anova model the
> "response variable vs factor" plot with means and 95% Tukey HSD
> intervals.
I believe you are asking for the multiple comparisons plots from the
multcomp package. The example below is an extension of one of the
examples in ?glht:
library(multcomp)
### multiple comparison procedures
### set up a one-way ANOVA
amod <- aov(breaks ~ tension, data = warpbreaks)
### set up all-pair comparisons for factor `tension'
### using a symbolic description (`type' argument
### to `contrMat()')
warp.mca <- glht(amod, linfct = mcp(tension = "Tukey"))
confint(warp.mca)
plot(warp.mca)
You asked about the level means themselves, rather than the pairwise
comparisons above. That is done with
warp.pairwise <- glht(amod, linfct = mcp(tension = "Means"))
confint(warp.pairwise)
plot(warp.pairwise)
I recommend the MMC (Mean-mean Multiple Comparison) plot that includes
both sets of information, pairwise comparisons and individual means, and
also allows arbitrary contrasts.
library(HH)
warp.mmc <- glht.mmc(amod, linfct = mcp(tension = "Tukey"))
warp.mmc
plot(warp.mmc)
See the help files
?glht
?mmc
for more details. Both glht and glht.mmc extend to multi-way designs.
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