"cophenetic" function for objects of class "dendrogram"
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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