R devel - Apr 2016 - "cophenetic" function for objects of class "dendrogram"

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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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
>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
	[[alternative HTML version deleted]]

Note that cophenetic.default (which works on the output of hclust(dist(X)))
uses the
row names of X as labels.  as.dendrogram.hclust does not retain those row
names
so cophenetic.dendrogram cannot use them (so it orders them based on the
topology of the dendrogram).

Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Thu, Apr 21, 2016 at 7:59 AM, William Dunlap <wdunlap at tibco.com>
wrote:
> 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
>>
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
>
	[[alternative HTML version deleted]]