Yes, the output from a summary of lm does include the uninteresting test.  Partly at least due to a legacy from when we used to compute a lot of these things by hand.  Certain layouts and sequences of calculations were developed to make the hand calculations easier.  When we first started having computers do all the calculations, we kept the same layout because it was familiar (and since we might not trust the computer, it made it easier to see that all the steps had still been taken).

It is best to stay away from putting to much interpretation into those tests (except under certain circumstances that used to be more common).  But if you are going to look at the results, read them from the bottom up: if the overall F-test is not significant, then don't bother looking at the t-tests, if an interaction is significant, don't look at the subinteractions or main effects, etc.

There are some really good posts, webpages, and books by Venables and Harrell (and others) that discuss this in more detail, but the main point is that you get the best information by thinking in terms of full and reduced models and comparing the models  (what you were trying to do to start this thread).  There are exceptions, but make sure you understand the rule before worrying about the exceptions.

--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.snow@imail.org
801.408.8111

From: paul@gribblelab.org [mailto:paul@gribblelab.org] On Behalf Of Paul Gribble
Sent: Friday, February 27, 2009 12:10 PM
To: Greg Snow
Cc: r-help@r-project.org
Subject: Re: [R] testing two-factor anova effects using model comparison approach with lm() and anova()

Thanks Greg - that makes sense... that the test of the main effect of A is uninteresting if the AxB interaction is in the model

- but isn't that exactly what appears in the usual anova(fullmodel) output? A test of the main effect of A, a test of the main effect of B, and then a test of the interaction AxB?

Is it simply the case that the lm() function was designed so as to circumvent the uninteresting test, even if the user asks for it? (which would be fine by me - I just want to understand what's happening when I use it).

-Paul
On Fri, Feb 27, 2009 at 1:30 PM, Greg Snow <Greg.Snow@imail.org<mailto:Greg.Snow@imail.org>> wrote:
Notice the degrees of freedom as well in the different models.

With factors A and B, the 2 models:

A + B + A:B

And

A + A:B

Are actually the same overall model, just different parameterizations (you can also see this by using x=TRUE in the call to lm and looking at the x matrix used).

Testing if the main effect A should be in the model given that the interaction is in the model does not make sense in most cases, therefore the notation gives a different parameterization rather than the generally uninteresting test.

--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.snow@imail.org<mailto:greg.snow@imail.org>
801.408.8111


> -----Original Message-----
> From: r-help-bounces@r-project.org<mailto:r-help-bounces@r-project.org> [mailto:r-help-bounces@r-<mailto:r-help-bounces@r->
> project.org<http://project.org>] On Behalf Of Paul Gribble
> Sent: Friday, February 27, 2009 11:01 AM
> To: r-help@r-project.org<mailto:r-help@r-project.org>
> Subject: [R] testing two-factor anova effects using model comparison
> approach with lm() and anova()
>
> I wonder if someone could explain the behavior of the anova() and lm()
> functions in the following situation:
>
> I have a standard 3x2 factorial design, factorA has 3 levels, factorB
> has 2
> levels, they are fully crossed. I have a dependent variable DV.
>
> Of course I can do the following to get the usual anova table:
>
> > anova(lm(DV~factorA+factorB+factorA:factorB))
> Analysis of Variance Table
>
> Response: DV
>                 Df  Sum Sq Mean Sq F value   Pr(>F)
> factorA          2  7.4667  3.7333  4.9778 0.015546 *
> factorB          1  2.1333  2.1333  2.8444 0.104648
> factorA:factorB  2  9.8667  4.9333  6.5778 0.005275 **
> Residuals       24 18.0000  0.7500
>
> This is perfectly satisfactory for my situation, but as a pedagogical
> exercise, I wanted to demonstrate the model comparison approach to
> analysis
> of variance by using anova() to compare a full model that contains all
> effects, to restricted models that contain all effects save for the
> effect
> of interest.
>
> The test of the interaction effect seems to be as I expected:
>
> > fullmodel<-lm(DV~factorA+factorB+factorA:factorB)
> > restmodel<-lm(DV~factorA+factorB)
> > anova(fullmodel,restmodel)
> Analysis of Variance Table
>
> Model 1: DV ~ factorA + factorB + factorA:factorB
> Model 2: DV ~ factorA + factorB
>   Res.Df     RSS Df Sum of Sq      F   Pr(>F)
> 1     24 18.0000
> 2     26 27.8667 -2   -9.8667 6.5778 0.005275 **
>
> As you can see the value of F (6.5778) is the same as in the anova
> table
> above. All is well.
>
> However, if I try to test a main effect, e.g. factorA, by testing the
> full
> model against a restricted model that doesn't contain the main effect
> factorA, I get something strange:
>
> > restmodel<-lm(DV~factorB+factorA:factorB)
> > anova(fullmodel,restmodel)
> Analysis of Variance Table
>
> Model 1: DV ~ factorA + factorB + factorA:factorB
> Model 2: DV ~ factorB + factorA:factorB
>   Res.Df RSS Df Sum of Sq F Pr(>F)
> 1     24  18
> 2     24  18  0         0
>
> upon inspection of each model I see that the Residuals are identical,
> which
> is not what I was expecting:
>
> > anova(fullmodel)
> Analysis of Variance Table
>
> Response: DV
>                 Df  Sum Sq Mean Sq F value   Pr(>F)
> factorA          2  7.4667  3.7333  4.9778 0.015546 *
> factorB          1  2.1333  2.1333  2.8444 0.104648
> factorA:factorB  2  9.8667  4.9333  6.5778 0.005275 **
> Residuals       24 18.0000  0.7500
>
> This looks fine, but then the restricted model is where things are not
> as I
> expected:
>
> > anova(restmodel)
> Analysis of Variance Table
>
> Response: DV
>                 Df  Sum Sq Mean Sq F value   Pr(>F)
> factorB          1  2.1333  2.1333  2.8444 0.104648
> factorB:factorA  4 17.3333  4.3333  5.7778 0.002104 **
> Residuals       24 18.0000  0.7500
>
> I was expecting the Residuals in the restricted model (the one not
> containing main effect of factorA) to be larger than in the full model
> containing all three effects. In other words, the variance accounted
> for by
> the main effect factorA should be added to the Residuals. Instead, it
> looks
> like the variance accounted for by the main effect of factorA is being
> soaked up by the factorA:factorB interaction term. Strangely, the
> degrees of
> freedom are also affected.
>
> I must be misunderstanding something here. Can someone point out what
> is
> happening?
>
> Thanks,
>
> -Paul
>
> --
> Paul L. Gribble, Ph.D.
> Associate Professor
> Dept. Psychology
> The University of Western Ontario
> London, Ontario
> Canada N6A 5C2
> Tel. +1 519 661 2111 x82237
> Fax. +1 519 661 3961
> pgribble@uwo.ca<mailto:pgribble@uwo.ca>
> http://gribblelab.org
>
>       [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org<mailto:R-help@r-project.org> mailing list
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> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> and provide commented, minimal, self-contained, reproducible code.



--
Paul L. Gribble, Ph.D.
Associate Professor
Dept. Psychology
The University of Western Ontario
London, Ontario
Canada N6A 5C2
Tel. +1 519 661 2111 x82237
Fax. +1 519 661 3961
pgribble@uwo.ca<mailto:pgribble@uwo.ca>
http://gribblelab.org

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