Of course, manually checking the number of clusters that are cut at a specific height (e.g. by abline()) is one possibility. However, this only makes sense for single trees, but is not a feasible approach for multiple model runs when hundreds of trees are built with many cluster branches.
Thus, I'd be nice if somebody knows a more programatic approach or another package that allows cutting "centroid"-trees. /Johannes On Fri, Jul 11, 2014 at 4:19 PM, David L Carlson <dcarl...@tamu.edu> wrote: > The easiest workaround is the one you included in your original posting. > Specify k= and not h=. Examine the dendrogram and decide how many clusters > are at the level you want. You could add guidelines to the dendrogram with > abline() to make it easier to see the number of clusters at various heights. > > > > plot(hc) > > abline(h=c(20, 40, 60, 80, 100, 120), lty=3) > > > > David C > > > > *From:* Johannes Radinger [mailto:johannesradin...@gmail.com] > *Sent:* Friday, July 11, 2014 3:24 AM > *To:* David L Carlson; R help > *Subject:* Re: [R] Cutting hierarchical cluster tree at specific height > fails > > > > 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.
