[R] se.contrasts.

Peter Ho peter at esb.ucp.pt
Tue Feb 29 19:48:05 CET 2000

Dear R users,

Firstly, I would like to congratulate the R core team in bringing out R
1.0.0 and all who have helped in developing it.
I have been having problems with using se.contrasts and would be pleased
if someone help.

I have been doing a repeated measures ANOVA using aov using a split plot
design for a single variable, color. The aov results were as follows:

> summary(aov(CD2~cont + Error(cont:rpl)+times+cont:times, color))

Error: cont:rpl
                  Df         Sum Sq         Mean Sq         F
value         Pr(>F)
cont             6         8.6214          1.4369
6.8651            0.2841
Residuals      1         0.2093          0.2093

Error: Within
                   Df         Sum Sq         Mean Sq         F
value        Pr(>F)
times           7         53.133               7.590
1053.32         4.886e-10 ***
cont:times    42        86.030               2.048
284.24         2.149e-08 ***
Residuals       7          0.050               0.007
Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1

I then used model.tables to get the effects and standard errors , which
gave me this:

> model.tables(cd.aov2, "effects", se=T)
Standard error information not returned as design is unbalanced.
Standard errors can be obtained through se.contrast.
........... followed by the table of effects

However, whatever I do I cannot calculate se.contrast.

In the above test the factor cont has 7 levels (1,2,3,4,5,6,7,7) , rpl
is the replication, and times has 8 levels.
I want to test if there is a significant difference between the

(1) if there is a difference between cont (1,2,3) between times (6,7,8)
(2) if there is a difference between cont (4,5,6) between times (6,7,8)

essentially these are the main contrast I am interested in, as a
treatment is applied between times 6 and 7 at 3 levels within
cont(1,2,3) and cont(4,5,6).
Interaction effects between cont with times can be seem by plotting
effects, but I suppose this isn't enough to show significant
differences, isn't it?

I would be grateful if someone could suggests how I might calculate the
contrasts using se.contrasts.
As there are also different contrasts.ie. helmert,treatments, etc. This
confuses me even more.

Also I mentioned in the beginning of the text that I did the ANOVA for a
single variable.  I infact measured 13 variables and wanted do
originally try a repeated measures MANOVA, but did not know how to do
this. Any suggestions here would also be grateful. Cons and Pros of
univariate and multivariate approach.
I have looked at  the growth and rmutil, which the author J Lindsey
suggested could be used, but as I had no experience using them, again I
did not know what to do. Has anyone tried this approach?



Peter Ho
Escola Superior de Biotecnologia
Universidade Católica Portuguesa
Rua Dr. António Bernardino de Almeida
Porto 4200-072

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