[R] candisc plotting

[Michael Friendly]

Dear Pete,

You haven't told us what your data is, and we can only surmise -- not 
very helpful for you and annoying for those who try to help.

Pete Shepard wrote:
> Hello,
> 
> I have a file with two dependent variables (three and five) and one
> independent variable. I do  i.mod <- lm(cbind(three, five) ~ species,
> data=i.txt) and get the following output:
> 
> 
> Coefficients:
>              three   five
> (Intercept)   9.949   9.586
> species      -1.166  -1.156
 From this, it seems that species is numeric variable, not a factor.
If so, canonical discriminant analysis in not appropriate, so
all following bets are off.

That's likely why you end up with only one canonical dimension.


> I do a" i.can<-candisc(i.mod,data=i):
Is data=i the same as data=i.txt?
> 
> and get the following output:
> 
> Canonical Discriminant Analysis for species:
> 
>     CanRsq Eigenvalue Difference Percent Cumulative
> 1 0.096506    0.10681                100        100
> 
> Test of H0: The canonical correlations in the
> current row and all that follow are zero
> LR test stat approx F num Df den Df   Pr(> F)
> 1        0.903   63.875      1    598 6.859e-15 ***
> ---
> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> 
> this is different than the output I get with SAS:
What was your SAS code? Was the data the same?
> 
>          Eigenvalue Difference Proportion Cumulative      Ratio     F Value
> Num DF Den DF Pr > F
> 
>        1     0.1068                1.0000     1.0000 0.90349416
> 31.88      2    597 <.0001


> 
> I am also wondering how to plot the can1*can1 like it is done in SAS.
> 
> proc plot;
>     plot can1*can1=species;
>     format species spechar.;
>     title2 'Plot of Constits_vs_cassettes';
>  run;
> 
If you want to compare plots for canonical analysis in SAS and R,
see my macros, canplot and hecan at
http://www.math.yorku.ca/SCS/sasmac/

But in general, if all you have is 1 canonical dimension, a dotplot or
boxplot of the canonical scores would be more useful than a scatterplot 
plot of can1 * can1.

The plot method for candisc objects in the candisc package has some
code to handle the 1 can-D case.

hope this helps
-Michael
> Thanks
> 
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> 
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-- 
Michael Friendly     Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University      Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street    http://www.math.yorku.ca/SCS/friendly.html
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