Dear Michael,
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. Apologies, I am brand new to R and this mailing list. Will try to be more concise. Here is my data a NEW verion of my data: Curvature Diameter Quality 1 2.95 6.63 Passed 2 2.53 7.79 Passed 3 3.57 5.65 Passed 4 3.16 5.47 Passed 5 2.58 4.46 NotPassed 6 2.16 6.22 NotPassed 7 3.27 3.52 NotPassed What I am trying to get from the candisc method is a 1 dimensional scatterplot that separates my two groups Passed and NotPassed On this data I do a "do.mod <- lm(cbind(Diameter, Curvature) ~ Quality, data=do)" >do.mod produces Coefficients: Diameter Curvature (Intercept) 4.7333 2.6700 QualityPassed 1.6517 0.3825 I then run the "candisc" method: "do.can <- candisc(do.mod, data=do)" this produces: Canonical Discriminant Analysis for Quality: CanRsq Eigenvalue Difference Percent Cumulative 1 0.91354 10.566 100 100 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 0.086 52.831 1 5 0.0007706 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 What "I think" I would like to plot is the discriminant function of each sample 1-7. Here is an example of what I am trying to do with candisc. http://people.revoledu.com/kardi/tutorial/LDA/Numerical%20Example.html Thanks On Thu, Dec 11, 2008 at 3:36 PM, Michael Friendly <frien...@yorku.ca> wrote: > 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 >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> >> > > -- > 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 > Toronto, ONT M3J 1P3 CANADA > > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.