I am a biology student investigating a new method of creating a dichotomous identification key. I have created a dendrogram using data I have collected from a survey on how people rate how similar pictures of plant leaves are. I used ward's method to link the clusters. In the resulting dendrogram, I have a y-axis that ranges between 0 and about 50. I know that this axis represents at which the objects are joined in a cluster, thus how far they are from other objects, but I was wondering what exactly does the numeric value represent?

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#### Best Answer

I'm going to, ahem, go out on a limb here, ahem, and guess that you built your tree via the `hclust`

function in base R with `method = "ward.D2"`

, which is Ward's original method. If you type `?hclust`

and look for `height`

in the `value`

(output) section, it says "The clustering height: that is, the value of the criterion associated with the clustering method for the particular agglomeration." In this case, Ward's criterion is the total within-cluster error sum of squares, which increases as you go up the tree and make the clusters bigger.

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