[R] LDA in R: how to extract full equation, especially constant term

Frank Gibbons fgibbons at hms.harvard.edu
Fri Aug 22 00:35:15 CEST 2003


Having dipped my toe into R a few times over the last year or two, in the 
last few weeks I've been using it more and more; I'm now a thorough 
convert. I've just joined the list, because although it's great, I do have 
this problem...

I'm using linear discriminant analysis for binary classification, and am 
happy with the classification performance using predict(). What I'd like to 
do now is extract the equation for this classifier, for use elsewhere (in 
Perl/Python code).

I know that I can get the means and scaling factors from the predict() 
object, but I'm having trouble computing the constant term. From reading 
Venables & Ripley and Hastie/Tibshirani/Friedman, I know the priors play 
a  role in adjusting the "cut-point" from zero (for equally sized classes), 
based on the relative sizes of the two classes. But when I try to do the 
computation, I don't get a value that agrees with that returned by predict().

I've seen a post about this problem in the past, but it was never really 
answered by anyone who was familiar with R/S-PLUS. Can anyone help me with 
this? I guess I'm really wondering how R is computing the constant term in 
its discriminant function.


-Frank Gibbons

PhD, Computational Biologist,
Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA.
Tel: 617-432-3555       Fax: 
617-432-3557       http://llama.med.harvard.edu/~fgibbons

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