Hi, @David: Thanks for the explanation why this does not work. This of course makes theoretically sense.
However in a recent discussion ( http://stats.stackexchange.com/questions/107448/spatial-distance-between-cluster-means ) it was stated that "the 'reversals problem' of centroid method is not a serious reason to deactivate the option of 'tree cut'". Instead a warning message should be provided rather than a deactivation. So does anyone know how a tree that was created with "centroid" can still be cut at a specific height? I tried the package "dynamicTreeCut", but this also relies on cutree and consequently raises an error when used for cutting "centroid" trees. Does anyone know a work around and can provide a minimum working example? /Johannes On Wed, Jul 9, 2014 at 4:58 PM, David L Carlson <dcarl...@tamu.edu> wrote: > To cut the tree, the clustering algorithm must produce consistently > increasing height values with no reversals. You used one of the two options > in hclust that does not do this. Note the following from the hclust manual > page: > > "Note however, that methods "median" and "centroid" are not leading to a > monotone distance measure, or equivalently the resulting dendrograms can > have so called inversions (which are hard to interpret)." > > The cutree manual page: > > "Cutting trees at a given height is only possible for ultrametric trees > (with monotone clustering heights)." > > Use a different method (but not median). > > ------------------------------------- > David L Carlson > Department of Anthropology > Texas A&M University > College Station, TX 77840-4352 > > -----Original Message----- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] > On Behalf Of Johannes Radinger > Sent: Wednesday, July 9, 2014 7:07 AM > To: R help > Subject: [R] Cutting hierarchical cluster tree at specific height fails > > Hi, > > I'd like to cut a hierachical cluster tree calculated with hclust at a > specific height. > However ever get following error message: > "Error in cutree(hc, h = 60) : > the 'height' component of 'tree' is not sorted (increasingly)" > > > Here is a working example to show that when specifing a height in cutree() > the code fails. In contrast, specifying the number of clusters in cutree() > works. > What is the exact problem and how can I solve it? > > x <- c(rnorm(100,50,10),rnorm(100,200,25),rnorm(100,80,15)) > y <- c(rnorm(100,50,10),rnorm(100,200,25),rnorm(100,150,25)) > df <- data.frame(x,y) > plot(df) > > hc <- hclust(dist(df,method = "euclidean"), method="centroid") > plot(hc) > > df$memb <- cutree(hc, h = 60) # this does not work > df$memb <- cutree(hc, k = 3) # this works! > > plot(df$x,df$y,col=df$memb) > > > Thank you for your hints! > > Best regards, > Johannes > > [[alternative HTML version deleted]] > > ______________________________________________ > 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. > [[alternative HTML version deleted]] ______________________________________________ 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.
