register_DendSer: Register Seriation Methods from Package DendSer

In mhahsler/seriation: Infrastructure for Ordering Objects Using Seriation

Register Seriation Methods from Package DendSer

Description

Register the DendSer dendrogram seriation method and the ARc criterion (Earle and Hurley, 2015) for use with seriate().

Usage

register_DendSer()

Details

Registers the method "DendSer" for seriate. DendSer is a fast heuristic for reordering dendrograms developed by Earle and Hurley (2015) able to use different criteria.

control for seriate() with method "DendSer" accepts the following parameters:

• "h" or "method": A dendrogram or a method for hierarchical clustering (see hclust). Default: complete-link.

• "criterion": A seriation criterion to optimize (see list_criterion_methods("dist"). Default: "BAR" (Banded anti-Robinson from with 20% band width).

• "verbose": a logical; print progress information?

• "DendSer_args": additional arguments for DendSer::DendSer().

For convenience, the following methods (for different cost functions) are also provided:

• "DendSer_ARc" (anti-robinson form),

• "DendSer_BAR" (banded anti-Robinson form),

• "DendSer_LPL" (lazy path length),

• "DendSer_PL" (path length).

Note: Package DendSer needs to be installed.

Value

Nothing.

Author(s)

Michael Hahsler based on code by Catherine B. Hurley and Denise Earle

References

D. Earle, C. B. Hurley (2015): Advances in dendrogram seriation for application to visualization. Journal of Computational and Graphical Statistics, 24(1), 1–25.

See Also

DendSer::DendSer()

Other seriation: register_GA(), register_optics(), register_smacof(), register_tsne(), register_umap(), registry_for_seriaiton_methods, seriate(), seriate_best()

Examples

## Not run: 
register_DendSer()
get_seriation_method("dist", "DendSer")

d <- dist(random.robinson(20, pre=TRUE))

## use Banded AR form with default clustering (complete-link)
o <- seriate(d, "DendSer_BAR")
pimage(d, o)

## use different hclust method (Ward) and AR as the cost function for
## dendrogram reordering
o <- seriate(d, "DendSer", control = list(method = "ward.D2", criterion = "AR"))
pimage(d, o)

## End(Not run)

mhahsler/seriation documentation built on April 24, 2024, 10:08 p.m.