Kay Cichini
2010-Feb-02 12:22 UTC
[R] hvcluster() with distance method from vegdist(), package = vegan
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()? thanks in advance! yours, kay -- View this message in context: http://n4.nabble.com/hvcluster-with-distance-method-from-vegdist-package-vegan-tp1459859p1459859.html Sent from the R help mailing list archive at Nabble.com.
Kay Cichini
2010-Feb-02 12:27 UTC
[R] hvcluster() with distance method from vegdist(), package = vegan
sorry, it should say pvclust(), of course... -- View this message in context: http://n4.nabble.com/hvcluster-with-distance-method-from-vegdist-package-vegan-tp1459859p1459865.html Sent from the R help mailing list archive at Nabble.com.
Jari Oksanen
2010-Feb-03 13:02 UTC
[R] hvcluster() with distance method from vegdist(), package = vegan
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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