n.bouget wrote:
Hi,
I want to know which distance is using in the function kmeans
and if we can change this distance. Indeed, in the function pam, we can put a distance matrix in
parameter (by the line "pam<-pam(dist(matrixdata),k=7)" ) but
we can't do it in the function kmeans, we have to put the
matrix of data directly ...
Thanks in advance,
Nicolas BOUGET
One solution is to transform the data in a way, that the euclidean distance of the transformed values represents some other distance of the original values. This works at least for the Mahalanobis-Distance, when one applies a multivariate technique to a PCA transformed and re-scaled matrix, but I don't know if there are transformations for some other distance measures.
Thomas P.
Other solutions from an ecological paper are:
Chord distance Chi square metric Chi square distance Hellinger Distance Distance between species profiles
All these can be seen as Euclidean distances of some transformation of the data.
The paper "Ecologically meaningful transformations for ordination of species data" Pierre Legendre, and Eugene D. Gallagher (2001) Oecologia Vol. 129, Issue 2, 271-280, explains the concept and how to do the transformations.
An R example is given in the help file of decostand() in Jari Oksanen's vegan library for two of the transformations mentioned above.
Gav
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