Le vendredi 12 octobre 2012 à 11:33 -0700, Christopher R. Dolanc a écrit : > That command gives me the same result. Do you see that R is not listing > the plot numbers? Just all the numbers between 1 and 137, 138 and 310, > etc. It's like it has reordered the dendrogram, so that everything > occurs chronologically. > > Instead, I would expect something like this: > > [1] > 3, 15, 48, 134, 136, 213, 299, ..... > > [2] > 44, 67, 177, ..... Yeah, but that's a problem with your data or your dist function, not with hclust() and cutree().
As always, it's good to try to find the minimal example that reproduces the problem. Start from examples provided by ?cutree: hc <- hclust(dist(USArrests)) cutree(hc, k=2) Alabama Alaska Arizona Arkansas California 1 1 1 2 1 Colorado Connecticut Delaware Florida Georgia 2 2 1 1 2 etc. Here you see the cluster numbers are not in sequence, and my command shows groups correctly: split(rownames(USArrests), cutree(hc, 2)) $`1` [1] "Alabama" "Alaska" "Arizona" "California" etc. $`2` [1] "Arkansas" "Colorado" "Connecticut" "Georgia" [5] "Hawaii" "Idaho" "Indiana" "Iowa" etc. So either your data is already ordered, or you have a problem with your distance function. One guess: you have included the "Plot" column in the call to vegdist(). I don't know this function, but it seems to work like dist(), which means passing the plot id is plain wrong. Indeed, if I use VTM.Dist<-vegdist(VTM.Matrix[,-1]) VTM.HClust<- hclust(VTM.Dist, method="ward") VTM.8groups<- cutree(VTM.HClust, 8) the result is not ordered as before. Lesson: try with simple, standard data when complex data sets don't work, and compare results. My two cents ______________________________________________ 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.