Function reference • Dune

Dune algorithm The core Dune function and associated functions
`Dune()`	Dune
`ARIs()`	ARI Matrix
Tracking Functions to track how objects evolve as merging occurs
`ARIImp()`	ARI improvement
`clusterConversion()`	clusterConversion
`functionTracking()`	Track the evolution of a function along merging
`intermediateMat()`	Find the clustering matrix that we would get if we stopped the ARI merging early
Static visualization Functions to plot the results and many other tools to compare clusterings.
`ARItrend()`	ARI improvement plot
`ConfusionPlot()`	Plot confusion matrix
`plotARIs()`	Plot an heatmap of the ARI matrix
`plotPrePost()`	Plot the reduction in cluster size for an ARI merging with `Dune`
Dynamic visualization Functions to plot the results and many other tools to compare clusterings in a dynamic format.
`ARIEvolution()`	Plot the evolution of the pairwise ARIs as merging happens
`ConfusionEvolution()`	Plot the evolution of the ConfusionPlot as merging happens
Data The datasets used in examples
`clusMat`	A clustering matrix used to demonstrate the ari-merging process.
`nuclei`	Cluster labels for a subset of the allen Smart-Seq nuclei dataset
Utilitise Functions used internally for Dune
`.adjustedRandIndex()`	adjustedRandIndex
`whenToStop()`	When to Stop

Reference