Hello. I have the following distance matrix between 8 points: [1,] 0.000000 3.162278 7.280110 8.544004 7.071068 9.899495 6.403124 8.062258 [2,] 3.162278 0.000000 5.000000 6.403124 4.472136 8.944272 6.082763 8.062258 [3,] 7.280110 5.000000 0.000000 1.414214 1.000000 5.000000 4.242641 5.830952 [4,] 8.544004 6.403124 1.414214 0.000000 2.236068 4.123106 4.472136 5.656854 [5,] 7.071068 4.472136 1.000000 2.236068 0.000000 6.000000 5.000000 6.708204 [6,] 9.899495 8.944272 5.000000 4.123106 6.000000 0.000000 3.605551 3.000000 [7,] 6.403124 6.082763 4.242641 4.472136 5.000000 3.605551 0.000000 2.000000 [8,] 8.062258 8.062258 5.830952 5.656854 6.708204 3.000000 2.000000 0.000000
I want to apply the cluster algorithm using single linkage procedure. The metric is the euclidean metric. In order to do this, I do: aux=agnes(xMatrix, diss = inherits(xMatrix,"dist"),metric="euclidean",method="single") Next, I do plot(aux) because I want to view the dendogram. My question is about the graph of the dendogram. What means the number "height" that appears on the left hand of it? My assumption was it was the distance between clusters but I was wrong because the distance matrices between the clusters are the following: Join clusters {3} and {5} (distance=1) New matrix distance: [1,] 0.000000 3.162278 7.071068 8.544004 9.899495 6.403124 8.062258 [2,] 3.162278 0.000000 4.472136 6.403124 8.944272 6.082763 8.062258 [3,] 7.071068 4.472136 0.000000 1.414214 5.000000 4.242641 5.830952 [4,] 8.544004 6.403124 1.414214 0.000000 4.123106 4.472136 5.656854 [5,] 9.899495 8.944272 5.000000 4.123106 0.000000 3.605551 3.000000 [6,] 6.403124 6.082763 4.242641 4.472136 3.605551 0.000000 2.000000 [7,] 8.062258 8.062258 5.830952 5.656854 3.000000 2.000000 0.000000 Join clusters {3,5} and {4} (distance=1.414214). New matrix distance: [1,] 0.000000 3.162278 7.071068 9.899495 6.403124 8.062258 [2,] 3.162278 0.000000 4.472136 8.944272 6.082763 8.062258 [3,] 7.071068 4.472136 0.000000 4.123106 4.242641 5.656854 [4,] 9.899495 8.944272 4.123106 0.000000 3.605551 3.000000 [5,] 6.403124 6.082763 4.242641 3.605551 0.000000 2.000000 [6,] 8.062258 8.062258 5.656854 3.000000 2.000000 0.000000 Join clusters {7} and {8} (distance = 2). New matrix distance: [1,] 0.000000 3.162278 7.071068 9.899495 6.403124 [2,] 3.162278 0.000000 4.472136 8.944272 6.082763 [3,] 7.071068 4.472136 0.000000 4.123106 4.242641 [4,] 9.899495 8.944272 4.123106 0.000000 3.000000 [5,] 6.403124 6.082763 4.242641 3.000000 0.000000 etc... but in the graph of the dendogram, it appears the following numbers when it joins the clusters: cluster {3} and {5}: more or less 2.3 cluster {3,5} and {4}: more or less 3 cluster {7} and {8}: more or less 4.75. As you can see, these numbers are distint from the distance between clusters (1, 1.414214 and 2). So, can somebody say me what do these numbers represent? Thanks in advance, Arnau. ______________________________________________ R-help@stat.math.ethz.ch 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.