Hi Alberto,
Everyone in this thread are correct.
I'll just mention that if your goal was to calculate the cophenetic
correlation between dendrograms, the function cor_cophenetic from the
dendextend package can help with that (as well as other functions such as
cor_bakers_gamma tanglegram and others. See the bioinformatics paper for
more: http://bioinformatics.oxfordjournals.org/content/31/22/3718 ).
As you can see from dendextend:::cor_cophenetic.default it deals with
properly ordering the distance matrices.
With regards,
Tal
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On Thu, Apr 21, 2016 at 7:38 PM, William Dunlap via R-devel <
r-devel@r-project.org> wrote:
> 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 <wdun...@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 Fernández Sabater <
> > alberto.fernan...@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@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>
> >
> >
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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