Re: [R] Jaccard dissimilarity matrix for PCA

2010-12-28 Thread Flabbergaster
This sounds like something I could use.. I'm kind of new with R, meaning I've having some minor troubles all the time... Say I have a range of binary(0,1) variables X1 to Xn, with missing data for different cases. At the moment my data is a binary indicator matrix; rows representing the i individu

Re: [R] Jaccard dissimilarity matrix for PCA

2010-12-28 Thread Christian Hennig
jaccard in package prabclus computes a Jaccard matrix for you. By the way, if you want to do hierarchical clustering, it doesn't seem to be a good idea to me to run PCA first. Why not cluster the dissimilarity matrix directly without information loss by PCA? (I should not make too general stat

Re: [R] Jaccard dissimilarity matrix for PCA

2010-12-28 Thread David L Lorenz
Jacob, You might have a look at the vegan package. It might compute the Jaccard distance and it might have some other toolsa that you might be interested in. Dave From: Flabbergaster To: r-help@r-project.org Date: 12/28/2010 08:26 AM Subject: [R] Jaccard dissimilarity matrix for PCA Sent

Re: [R] Jaccard dissimilarity matrix for PCA

2010-12-28 Thread Marcelo Luiz de Laia
Flabbergaster gmail.com> writes: > My problem is, that I don't know how to compute the jaccard dissimilarity > matrix in R? Which package to use, and so on... http://rss.acs.unt.edu/Rdoc/library/arules/html/dissimilarity.html http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/vegdist.html

[R] Jaccard dissimilarity matrix for PCA

2010-12-28 Thread Flabbergaster
Hi I have a large dataset, containing a wide range of binary variables. I would like first of all to compute a jaccard matrix, then do a PCA on this matrix, so that I finally can do a hierarchical clustering on the principal components. My problem is, that I don't know how to compute the jaccard