[R] hvcluster() with distance method from vegdist(), package = vegan

Jari Oksanen jari.oksanen at oulu.fi
Wed Feb 3 14:02:32 CET 2010

Kay Cichini <Kay.Cichini <at> uibk.ac.at> writes:

> hello,
> i'd be happy if someone could provide help with the following problem:
> i have a dist.matrix that comes from vegdist() function of the vegan
> package. the used method = "horn" is not accepted as argument in
> hvcluster(...,dist.method="..."). 
> is there a way to incorporate the method "horn" in hvcluster()?
(This concerns function pvclust in the pvclust package, like probably was
intended in the message.)

No, there is no way of incorporating vegan::vegdist() methods in
pvclust::pvclust(). At least not according to the documentation of pvclust which
clearly says that the first argument is a data structure (not a 'dist' object),
and dissimilarities are found either with the internal pvclust methods or using
dist() function of the base R. Neither vegan function nor input of
dissimiliraties are allowed in pvclust(). You must edit pvclust() to make it
work with your choice of dissimilarity methods and other dissimilarity functions.

Best wishes, Jari Oksanen

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