tpq/propr

Extracting connected components from `propr` objects

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Greetings. I've been reading the reference manual to find a built-in method for cluster-extraction, but I haven't found anything useful. Basically, I need a way to transform a propr object into a list of vectors, wherein each vector is a connected component/cluster. Am I missing something? Right now I'm thinking about using getAdj to extract an adjacency matrix and extract connected components myself.

tpq commented

G'day,

For maximum control of the clustering procedure, I recommend pulling the propr matrix straight from the object. You can then cluster on this using any method you like. For big objects, I've had luck with the fastcluster package on CRAN.

library(propr)
data(iris)
pr <- propr(iris[,1:4])
pr@matrix

@tpq Thanks for responding. I went with applying MCL to the adjacency matrix to remove weak connections prior to clustering, but I get the general point.