Hello, Perhaps, you should chose another toy example closer to the reality. Cases with exactly same distance rarely occur "in the field". You should, at least, add some random error:
datamatrix <- matrix(c(2,2,2.5,2,1.5,2,2,1.5,2,2.5, 6,2,6.5,2,5.5,2,6,1.5,6,2.5, 4,4,4.5,4,3.5,4,4,3.5,4,4.5) + rnorm(30, sd = 0.1), ncol = 2, byrow = TRUE) distmatrix <- dist(datamatrix, method = "manhattan") hc <- hclust(distmatrix, method = "single") dendro <- as.dendrogram(hc) plot(dendro) #Now, I want to impose an order: weights <- c(2.0, 2.0, 2.0, 2.0, 2.0, 6.0, 6.0, 6.0, 6.0, 6.0, 4.0, 4.0, 4.0, 4.0, 4.0) ddd <- reorder(dendro, weights, agglo.FUN=mean) plot(ddd) unlist(ddd) # [1] 4 2 3 1 5 13 14 15 11 12 10 7 9 6 8 unlist(dendro) # [1] 10 7 9 6 8 13 14 15 11 12 4 2 3 1 5 Best, Philippe Grosjean ..............................................<°}))><........ ) ) ) ) ) ( ( ( ( ( Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( ( Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .............................................................. Thomas Walter wrote: > Hi! > > I am trying to reorder a dendrogram via reorder.dendrogram. However, I > observed some problems with this, and I will illustrate them with an > example. > > Take the following clustering problem: > > datamatrix <- matrix(c(2,2,2.5,2,1.5,2,2,1.5,2,2.5, > 6,2,6.5,2,5.5,2,6,1.5,6,2.5, 4,4,4.5,4,3.5,4,4,3.5,4,4.5), ncol=2, > byrow=TRUE) > distmatrix <- dist(datamatrix, method="manhattan") > hc <- hclust(distmatrix, method="single") > dendro <- as.dendrogram(hc) > > The datamatrix contains three equidistant (for manhattan distance) > clusters, each of which contains 5 points. > Now, I want to impose an order: > > weights <- c(2.0, 2.0, 2.0, 2.0, 2.0, 6.0, 6.0, 6.0, 6.0, 6.0, 4.0, 4.0, > 4.0, 4.0, 4.0) > ddd <- reorder(dendro, weights, agglo.FUN=mean) > > but if you compare the order of ddd with dendro, you see no change: > > unlist(ddd) > [1] 15 14 13 11 12 5 4 3 1 2 10 9 8 6 7 > > unlist(dendro) > [1] 15 14 13 11 12 5 4 3 1 2 10 9 8 6 7 > > I would have expected something like: > 5 4 3 1 2 15 14 13 11 12 10 9 8 6 7 > > or something of the sort. (I still do not know, if the order should be > ascending or descending, but in the obtained result, it is neither nor). > I do not see, where my mistake is ... > > Thanks for your advice! > > Thomas. > > ______________________________________________ > 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. > ______________________________________________ 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.
