dendextend: count_terminal_nodes – R documentation

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count_terminal_nodes

Counts the number of terminal nodes (merging 0 nodes!)

Description

This function counts the number of "practical" terminal nodes (nodes which are not leaves, but has 0 height to them are considered "terminal" nodes). If the tree is standard, that would simply be the number of leaves (only the leaves will have height 0). However, in cases where the tree has several nodes (before the leaves) with 0 height, the count_terminal_nodes counts such nodes as terminal nodes

The function is recursive in that it either returns 1 if it reached a terminal node (either a leaf or a 0 height node), else: it will count the number of terminal nodes in each of its sub-nodes, sum them up, and return them.

Usage

count_terminal_nodes(dend_node, ...)

Arguments

`dend_node`	a dendrogram object for which to count its number of terminal nodes (leaves or 0 height nodes).
`...`	not used

Value

The number of terminal nodes (excluding the leaves of nodes of height 0)

Examples

# define dendrogram object to play with:
hc <- hclust(dist(USArrests[1:3, ]), "ave")
dend <- as.dendrogram(hc)

###
# Trivial case
count_terminal_nodes(dend) # 3 terminal nodes
length(labels(dend)) # 3 - the same number
plot(dend,
  main = "This is considered a tree \n with THREE terminal nodes (leaves)"
)

###
# NON-Trivial case
str(dend)
attr(dend[[2]], "height") <- 0
count_terminal_nodes(dend) # 2 terminal nodes, why? see this plot:
plot(dend,
  main = "This is considered a tree \n with TWO terminal nodes only"
)
# while we have 3 leaves, in practice we have only 2 terminal nodes
# (this is a feature, not a bug.)

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