README.md
In xhtai/clusterTruster: Benchmarking Minimax Linkage

clusterTruster

This is a package to benchmark linkages in hierarchical clustering. Please see our paper on arXiv for more detailed examples: https://arxiv.org/abs/1906.03336. The authors of the paper and this package are Xiao Hui Tai (https://xhtai.github.io/) and Kayla Frisoli (http://stat.cmu.edu/~kfrisoli/).

You can install clusterTruster from GitHub with:

devtools::install_github("xhtai/clusterTruster", build_vignettes = TRUE)
library(clusterTruster)

The package contains a vignette with code to reproduce the results in our paper. To view the vignette, you would have had to install the package with the option build_vignettes = TRUE. You can then view the vignette using

vignette("reproducePaperResults", package = "clusterTruster")

We can analyze the iris data set as follows. We first center and scale the four features, “Sepal.Length”, “Sepal.Width”, “Petal.Length”, “Petal.Width”, and generate the l2 distance between all pairs. We then use various linkage methods to generate all associated evaluation metrics.

myPairwise <- clusterTruster::genPairwise(iris, 5)
iris[, 1:4] <- scale(iris[, 1:4])
myPairwise <-
  clusterTruster::genSimDiff(iris, 1:4, myPairwise, 1:2, "l2dist")

Note that the following code could take a while to run.

outMetrics_iris_single <- clusterTruster::getMetrics(
  myPairwise,
  pairColNums = 1:2,
  matchColNum = 3,
  distSimCol = "l2dist",
  linkage = "single"
)
outMetrics_iris_complete <- clusterTruster::getMetrics(
  myPairwise,
  pairColNums = 1:2,
  matchColNum = 3,
  distSimCol = "l2dist",
  linkage = "complete"
)
outMetrics_iris_average <- clusterTruster::getMetrics(
  myPairwise,
  pairColNums = 1:2,
  matchColNum = 3,
  distSimCol = "l2dist",
  linkage = "average"
)
outMetrics_iris_centroid <- clusterTruster::getMetrics(
  myPairwise,
  pairColNums = 1:2,
  matchColNum = 3,
  distSimCol = "l2dist",
  linkage = "centroid"
)
outMetrics_iris_minimax <- clusterTruster::getMetrics(
  myPairwise,
  pairColNums = 1:2,
  matchColNum = 3,
  distSimCol = "l2dist",
  linkage = "minimax"
)

Plotting linkage method results for iris

To compare single, complete, and average:

clusterTruster::plotResultsGG_base(
  single = outMetrics_iris_single,
  complete = outMetrics_iris_complete,
  average = outMetrics_iris_average,
  correlation = FALSE,
  write_plot = FALSE,
  plot_type = c("all", "minimax", "misclass", "pr")
)

To compare all:

clusterTruster::plotResultsGG_base(
  single = outMetrics_iris_single,
  complete = outMetrics_iris_complete,
  average = outMetrics_iris_average,
  centroid = outMetrics_iris_centroid,
  minimax = outMetrics_iris_minimax,
  correlation = FALSE,
  write_plot = FALSE,
  plot_type = c("all", "minimax", "misclass", "pr")
)