[R] Multiple comparisons for a two-factor ANCOVA

Dieter Menne dieter.menne at menne-biomed.de
Mon Mar 15 09:46:27 CET 2010

Eric Scott-3 wrote:
> I'm trying to do an ANCOVA with two factors (clipping treatment with two
> levels, and plot with 4 levels) and a covariate (stem diameter).  The
> response variable is fruit number.  The minimal adequate model looks like
> this:
> model3<-lm(fruit~clip + plot + st.dia + clip:plot)
> I'd like to get some multiple comparisons like the ones from TukeyHSD,
> but...

To quote glht:
The mcp function must be used with care when defining parameters of interest
in two-way ANOVA or ANCOVA models. Here, the definition of treatment
differences (such as Tukey's all-pair comparisons or Dunnett's comparison
with a control) might be problem specific. Because it is impossible to
determine the parameters of interest automatically in this case, mcp in
multcomp version 1.0-0 and higher generates comparisons for the main effects
only, ignoring covariates and interactions (older versions automatically
averaged over interaction terms). A warning is given. We refer to Hsu
(1996), Chapter 7, and Searle (1971), Chapter 7.3, for further discussions
and examples on this issue. 

Too bad there is no example (Hi, Torsten.... it would be nice).

A thread coming close is in:



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