[R] Multiple comparisons for a two-factor ANCOVA

[Dieter Menne]

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:

http://markmail.org/message/rhdohxlrt3cpsdpx

Dieter

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