[R] anova vs aov commands for anova with repeated measures

Bill.Venables at csiro.au Bill.Venables at csiro.au
Sat Jan 8 04:01:41 CET 2011

lm() and aov() are not fully equivalent.  They both fit linear models, but they use different algorighms, and this allows aov, for example, to handle some simple multistratum models.  The algorithm used by lm does not allow this, but it has other advantages for simpler models.

If you want to fit a multistratum model, such as a repeated measures model, you need to use aov.

When it comes to finding the residuals, you have to be explicit about which residuals you mean, too.  You get residuals for each stratum in a multistratum model.  Using plain old resid() will not work as that function can only be used when there is only one kind of residuals vector defined.  (it could me made to do something sensible, but that's another issue.  Right now, it doesn't.)

The function proj() can be used on a fitted model object to obtain the projections, at each stratum, on to the subspaces defined by the terms in the model, and includes the residuals (the projection onto the orthogonal complement of the model space in R^n) as the final column of the matrix of projections.  These are easy to dig out and you can analyse away.

See ?proj for an example of its use, but you will need to dig out the appropriate column yourself.

From: r-help-bounces at r-project.org [r-help-bounces at r-project.org] On Behalf Of Frodo Jedi [frodo.jedi at yahoo.com]
Sent: 08 January 2011 01:51
To: r-help at r-project.org
Subject: [R] anova vs aov commands for anova with repeated measures

Dear all,
I need to understand a thing in the beheaviour of the two functions aov and
anova in the following case
involving an analysis of ANOVA with repeated measures:

If I use the folowing command I don´t get any problem:

>aov1 = aov(response ~ stimulus*condition + Error(subject/(stimulus*condition)),
> summary(aov1)

Instead if I try to fit the same model for the regression I get an error:
> fit1<- lm(response ~ stimulus*condition + Error(subject/(stimulus*condition)),
Error in eval(expr, envir, enclos) : could not find function "Error"

so I cannot run the command anova(fit1) afterwards.

I want to use fit1<- lm(response ~ stimulus*condition +
Error(subject/(stimulus*condition)), data=scrd)

because I want to analyse the residuals in order to check normality, and see if
the anova assumption of normality
still holds.

Could you please help me in understanding how to do this?

Thanks in advance

Best regards

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