[Rd] "cophenetic" function for objects of class "dendrogram"

[William Dunlap]

I think the results differ only in the order of the labels.  The following
function
puts the labels in a standard order and then the results are the same:

  canonicalize.dist <- function (distObject)
  {
      o <- order(labels(distObject))
      as.matrix(distObject)[o, o, drop = FALSE]
  }
  identical(canonicalize.dist(d2), canonicalize.dist(d3))
  [1] TRUE




Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Thu, Apr 21, 2016 at 2:37 AM, Alberto Fernández Sabater <
alberto.fernandez at urv.cat> wrote:

> Hello,
>
>
> I have been using the "cophenetic" function for objects of class
> "dendrogram" and I have realised that it gives different results when it is
> used with objects of class "hclust". For instance, running the first
> example in the help file of the "cophenetic" function,
>
>
> d1 <- dist(USArrests)
>
> hc <- hclust(d1, "ave")
>
> d2 <- cophenetic(hc)
>
> cor(d1, d2)  # 0.7659
>
>
> the result given is different to the one obtained using an object of class
> "dendrogram",
>
>
> dendro <- as.dendrogram(hc)
>
> d3 <- cophenetic(dendro)
>
> cor(d1, d3)  # 0.0151
>
>
> I think that it would be desirable to obtain the same result with all the
> "cophenetic" methods, irrespectively of the class of the object used. If
> this is not possible, users could be warned in the help file.
>
>
> Thanks,
>
> Alberto Fernandez
>
>
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