Thanks. I had a look at that and it says:
Partitioning Clustering:
Function kmeans() from package stats provides several algorithms for computing partitions with respect to Euclidean distance.
Hence why I am using a euclidean distance matrix. Why is this incorrect?
Gabor Grothendieck wrote:
There are many clustering functions in R and R packages and some
take distance objects whereas others do not. You likely read about
hclust or some different clustering function. See ?kmeans for the
kmeans function and also look at the CRAN Task View on clustering for
other clustering functions:
http://cran.r-project.org/src/contrib/Views/
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