---------- Forwarded message ---------- From: Vivek Ayer <vivek.a...@gmail.com> Date: Fri, May 7, 2010 at 10:17 AM Subject: Re: [R] custom metric for dist for use with hclust/kmeans To: Greg Snow <greg.s...@imail.org>
Hi Greg, The pam function is exactly what I needed. I can now create my own distance matrix, run as.dist on it and pass it into pam. Thanks a lot! Vivek On Thu, May 6, 2010 at 12:42 PM, Greg Snow <greg.s...@imail.org> wrote: > The pam function in the cluster package accepts either raw data or a > dissimilarity matrix and does the same idea as kmeans. The daisy function > has more options for creating the dissimilarity matrix, if what you want is > not in there, you could still use it as a model for creating your own > function. You could also use the outer function and as.dist to create the > distance matrix. > > -- > Gregory (Greg) L. Snow Ph.D. > Statistical Data Center > Intermountain Healthcare > greg.s...@imail.org > 801.408.8111 > > >> -----Original Message----- >> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- >> project.org] On Behalf Of Vivek Ayer >> Sent: Thursday, May 06, 2010 9:56 AM >> To: r-help@r-project.org >> Subject: Re: [R] custom metric for dist for use with hclust/kmeans >> >> Bump...no insights on defining custom metrics. Guess I'll give the >> other languages a shot. >> >> Vivek >> >> On Wed, May 5, 2010 at 10:13 AM, Vivek Ayer <vivek.a...@gmail.com> >> wrote: >> > Hi guys, >> > >> > I've been using the kmeans and hclust functions for some time now and >> > was wondering if I could specify a custom metric when passing my data >> > frame into hclust as a distance matrix. Actually, kmeans doesn't even >> > take a distance matrix; it takes the data frame directly. I was >> > wondering if there's a way or if there's a package that lets you >> > create distance matrices from non-standard metrics, e.g., >> > KL-divergence (which is not really one), but metrics used often in >> > information theory. I'm assuming kmeans just assumes the euclidean >> > metric, but it would be nice to customize that as well. Is stuff out >> > there, or would I have create my own? >> > >> > Thanks, >> > Vivek >> > >> >> ______________________________________________ >> 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. > ______________________________________________ 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.
