bootstrap: bootstrap

In sgibb/bootstrap: Simple Bootstrapping for Hierarchical Clustering

Description

This function provides bootstrapping for hierarchical clustering (hclust objects).

Usage

  bootstrap(x, fun, n = 1000L,
    mc.cores = getOption("mc.cores", 2L))

Arguments

x	matrix, rows: individuals, columns: observations
fun	function which creates the individual hclust object
n	integer, number of bootstrap replicates
mc.cores	integer, number of processes to run in parallel

Value

numeric vector with frequencies of each node

References

Felsenstein, Joseph. Confidence limits on phylogenies: an approach using the bootstrap. Evolution (1985): 783-791.

Efron, Bradley, Elizabeth Halloran, and Susan Holmes. Bootstrap confidence levels for phylogenetic trees. Proceedings of the National Academy of Sciences 93.23 (1996): 13429-13429.

See Also

dist, link{hclust}

Examples

## hclust example
createHclustObject <- function(x)hclust(dist(x), "ave")

## bootstrap
b <- bootstrap(USArrests, fun=createHclustObject, n=100L)

## plot
hc <- createHclustObject(USArrests)
plot(hc)

## draw bootstrap values to corresponding node
bootlabels.hclust(hc, b, col="blue")

sgibb/bootstrap documentation built on May 29, 2019, 8:04 p.m.