R: Register Seriation Methods from Package DendSer

register_DendSer {seriation} | R Documentation

## Register Seriation Methods from Package DendSer

### Description

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

### 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"`

  print progress information.

`"DendSer_args"`

  additional arguments for `DendSer`.

For convenience the following methods (for differnt cost functions) are also provided: `"DendSer_ARc"` (anti-robinson form), `"DendSer_BAR"` (banded anti-Robinson form), `"DendSer_LS"` (leaf seriation), `"DendSer_PL"` (path length).

Note: Package DendSer needs to be installed.

### 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

`seriate`, `DendSer` in DendSer.

### Examples

    ## Not run:
    register_DendSer()
    list_seriation_methods("dist")

    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)

[Package seriation version 1.2-8 Index]