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dendextend

DendSer.dendrogram

Tries to run DendSer on a dendrogram

Description

Implements dendrogram seriation. The function tries to turn the dend into hclust, on which it runs DendSer.

Also, if a distance matrix is missing, it will try to use the cophenetic distance.

Usage

DendSer.dendrogram(dend, ser_weight, ...)

Arguments

dend

An object of class dendrogram
ser_weight

Used by cost function to evaluate ordering. For cost=costLS, this is a vector of object weights. Otherwise is a dist or symmetric matrix. passed to DendSer. If it is missing, the cophenetic distance is used instead.
...

parameters passed to DendSer

Value

Numeric vector giving an optimal dendrogram order

See Also

Examples

## Not run: 
library(DendSer) # already used from within the function
hc <- hclust(dist(USArrests[1:4, ]), "ave")
dend <- as.dendrogram(hc)
DendSer.dendrogram(dend)

## End(Not run)
dendextend

Extending 'dendrogram' Functionality in R

v1.15.1
GPL-2 | GPL-3
Authors
Tal Galili [aut, cre, cph] (https://www.r-statistics.com), Yoav Benjamini [ths], Gavin Simpson [ctb], Gregory Jefferis [aut, ctb] (imported code from his dendroextras package), Marco Gallotta [ctb] (a.k.a: marcog), Johan Renaudie [ctb] (https://github.com/plannapus), The R Core Team [ctb] (Thanks for the Infastructure, and code in the examples), Kurt Hornik [ctb], Uwe Ligges [ctb], Andrej-Nikolai Spiess [ctb], Steve Horvath [ctb], Peter Langfelder [ctb], skullkey [ctb], Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram), Andrie de Vries [ctb] (ggdendro author), Zuguang Gu [ctb] (circlize author), Cath [ctb] (https://github.com/CathG), John Ma [ctb] (https://github.com/JohnMCMa), Krzysiek G [ctb] (https://github.com/storaged), Manuela Hummel [ctb] (https://github.com/hummelma), Chase Clark [ctb] (https://github.com/chasemc), Lucas Graybuck [ctb] (https://github.com/hypercompetent), jdetribol [ctb] (https://github.com/jdetribol), Ben Ho [ctb] (https://github.com/SplitInf), Samuel Perreault [ctb] (https://github.com/samperochkin), Christian Hennig [ctb] (http://www.homepages.ucl.ac.uk/~ucakche/), David Bradley [ctb] (https://github.com/DBradley27), Houyun Huang [ctb] (https://github.com/houyunhuang)
Initial release
2021-05-08

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