R: Fast hierarchical, agglomerative clustering routines for R...

fastcluster {fastcluster} | R Documentation

## Fast hierarchical, agglomerative clustering routines for R and Python

### Description

The fastcluster package provides efficient algorithms for hierarchical, agglomerative clustering. In addition to the R interface, there is also a Python interface to the underlying C++ library, to be found in the source distribution.

### Details

The function `hclust` provides clustering when the input is a dissimilarity matrix. A dissimilarity matrix can be computed from vector data by `dist`. The `hclust` function can be used as a drop-in replacement for existing routines: `stats::hclust` and `flashClust::hclust` alias `flashClust::flashClust`. Once the fastcluster library is loaded at the beginning of the code, every program that uses hierarchical clustering can benefit immediately and effortlessly from the performance gain

When the package is loaded, it overwrites the function `hclust` with the new code.

The function `hclust.vector` provides memory-saving routines when the input is vector data.

Further information:

- R documentation pages: `hclust`, `hclust.vector`

- A comprehensive User's manual: fastcluster.pdf. Get this from the R command line with `vignette('fastcluster')`.

- JSS paper: https://www.jstatsoft.org/v53/i09/.

- See the author's home page for a performance comparison: http://danifold.net/fastcluster.html.

### Author(s)

Daniel Müllner

### References

http://danifold.net/fastcluster.html

### See Also

`hclust`, `hclust.vector`

### Examples

    # Taken and modified from stats::hclust
    #
    # hclust(...)        # new method
    # hclust.vector(...) # new method
    # stats::hclust(...) # old method

    require(fastcluster)
    require(graphics)

    hc <- hclust(dist(USArrests), "ave")
    plot(hc)
    plot(hc, hang = -1)

    ## Do the same with centroid clustering and squared Euclidean distance,
    ## cut the tree into ten clusters and reconstruct the upper part of the
    ## tree from the cluster centers.
    hc <- hclust.vector(USArrests, "cen")
    # squared Euclidean distances
    hc$height <- hc$height^2
    memb <- cutree(hc, k = 10)
    cent <- NULL
    for(k in 1:10){
      cent <- rbind(cent, colMeans(USArrests[memb == k, , drop = FALSE]))
    }
    hc1 <- hclust.vector(cent, method = "cen", members = table(memb))
    # squared Euclidean distances
    hc1$height <- hc1$height^2
    opar <- par(mfrow = c(1, 2))
    plot(hc,  labels = FALSE, hang = -1, main = "Original Tree")
    plot(hc1, labels = FALSE, hang = -1, main = "Re-start from 10 clusters")
    par(opar)

[Package fastcluster version 1.1.25 Index]