Register Seriation Methods from Package DendSer
Register the DendSer dendrogram seriation method and the ARc criterion (Earle and Hurley, 2015).
register_DendSer()
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.
Michael Hahsler based on code by Catherine B. Hurley and Denise Earle
D. Earle, C. B. Hurley (2015): Advances in dendrogram seriation for application to visualization. Journal of Computational and Graphical Statistics, 24(1), 1–25.
## 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)
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