Re: [R] e1071 question: what's the definition of performance in t une.* functions?

From: Tae-Hoon Chung <thchung_at_tgen.org>
Date: Wed 14 Jul 2004 - 02:46:20 EST

Thank you Andy.

It seems like this can be the reason for the confusion. I never thought that there can be this kind of catches for using tune.* functions.
For the record, I actually emailed to Dr. Friedrich Leisch the author of this library.
When I get some reply, I will post it also.

Regards,
TH

On Jul 12, 2004, at 6:40 PM, Liaw, Andy wrote:

> Looking at the body of tune(), it has:
>
> ...
> repeat.errors[reps] <- if (is.factor(true.y))
> 1 - classAgreement(table(pred, true.y))
> else crossprod(pred - true.y)/length(pred)
> ...
>
> where classAgreement() is a function defined inside tune() that
> computes the
> fraction of correctly predicted cases. So it looks like tune() and
> friends
> are returning error rates as fractions, not percentages.
>
> You're right that the fraction shouldn't be larger than 1. Did you
> make
> sure that tune() sees the data as classification, not regression
> (i.e., did
> you make sure that the class labels given to tune.*() are factor)?
>
> HTH,
> Andy

Tae-Hoon Chung, Ph.D

Post-doctoral Research Fellow
Molecular Diagnostics and Target Validation Division Translational Genomics Research Institute 1275 W Washington St, Tempe AZ 85281 USA Phone: 602-343-8724



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