[R] lda() called with data=subset() command

[Prof Brian Ripley]

I presume is lda from the uncredited package MASS and you ignored the
advice to ask the maintainer?

The short answer is `don't ignore the warning', and set up a proper data 
frame with just the groups you actually want.

As a quick fix, look in lda.default and alter the line that looks like

        cl <- factor(max.col(dist), levels=seq(along=lev1), labels=lev1)

to be exactly like that.  (You will need fixInNamespace to do so.)


On Mon, 5 Jan 2004, Christoph Lehmann wrote:

> Hi
> I have a data.frame with a grouping variable having the levels 
> 
> C, 
> mild AD, 
> mod AD, 
> O and 
> S
> 
> since I want to compute a lda only for the two groups 'C' and 'mod AD' I
> call lda with data=subset(mydata.pca,GROUP == 'mod AD' | GROUP == 'C')
> 
> 
> my.lda <- lda(GROUP ~ Comp.1 + Comp.2 + Comp.3 + Comp.4+  Comp.5 +
> Comp.6 + Comp.7 + Comp.8  , data=subset(mydata.pca,GROUP == 'mod AD' |
> GROUP == 'C'), CV = TRUE)
> 
> this results in the warning "group(s) mild AD O S are empty in:
> lda.default(x, grouping, ...)" of course...
> 
> my.lda$class now shows 
> 
>  [1] C       C       C       C       C       C       C       C       C
> [10] C       C       C       C       C       C       C       C       C
> [19] C       C       C       mild AD mild AD mild AD mild AD mild AD
> mild AD
> [28] mild AD C       mild AD mild AD mild AD C       C       mild AD
> mild AD
> [37] mild AD mild AD
> Levels: C mild AD mod AD O S
> 
> it seems it just took the second level (mild AD) for the second class,
> even though the second level was not used for the lda computation (only
> the first level (C) and the third level (mod AD)
> 
> what shall I do to resolve this (little) problem?
> 
> thanks for a  hint
> 
> christoph
> 

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595