From wdunlap at tibco.com  Thu Apr 21 16:59:37 2016
From: wdunlap at tibco.com (William Dunlap)
Date: Thu, 21 Apr 2016 07:59:37 -0700
Subject: [Rd] "cophenetic" function for objects of class "dendrogram"
In-Reply-To: <VI1PR01MB138950829C65980A4FF9CC01F56E0@VI1PR01MB1389.eurprd01.prod.exchangelabs.com>
References: <VI1PR01MB138950829C65980A4FF9CC01F56E0@VI1PR01MB1389.eurprd01.prod.exchangelabs.com>
Message-ID: <CAF8bMcahx7fiNhmTjW7Qpnrgoi5UbXepBce8PYtRk_ms76upfw@mail.gmail.com>

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 Fern?ndez 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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>
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>

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