Hello, In the documentation for agnes in the package 'cluster', it says that NAs are allowed, and sure enough it works for a small example like :
> m <- matrix(c( 1, 1, 1, 2, 1, NA, 1, 1, 1, 2, 2, 2), nrow = 3, byrow = TRUE) > agnes(m) Call: agnes(x = m) Agglomerative coefficient: 0.1614168 Order of objects: [1] 1 2 3 Height (summary): Min. 1st Qu. Median Mean 3rd Qu. Max. 1.155 1.247 1.339 1.339 1.431 1.524 Available components: [1] "order" "height" "ac" "merge" "diss" "call" "method" "data" But I have a large matrix (23371 rows, 50 columns) with some NAs in it and it runs for about a minute, then gives an error : > agnes(iMatrix) Error in agnes(iMatrix) : No clustering performed, NA-values in the dissimilarity matrix. I've also tried getting rid of rows with all NAs in them, and it still gave me the same error. Is this a bug in agnes() ? It doesn't seem to fulfil the claim made by its documentation. The matrix I'm using can be obtained here : http://129.94.136.7/file_dump/dario/iMatrix.obj -------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia ______________________________________________ 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.