all.equal.dendrogram: Global Comparison of two (or more) dendrograms

In dendextend: Extending 'dendrogram' Functionality in R

Global Comparison of two (or more) dendrograms

Description

This function makes a global comparison of two or more dendrograms trees.

The function can get two dendlist objects and compare them using all.equal.list. If a dendlist is in only "target" (and not "current"), it will go through the dendlist and compare all of the dendrograms within it to one another.

Usage

## S3 method for class 'equal.dendrogram'
all(
  target,
  current,
  use.edge.length = TRUE,
  use.tip.label.order = FALSE,
  use.tip.label = TRUE,
  use.topology = TRUE,
  tolerance = .Machine$double.eps^0.5,
  scale = NULL,
  ...
)

Arguments

target	an object of type dendrogram or dendlist
current	an object of type dendrogram
use.edge.length	logical (TRUE). If to check branches' heights.
use.tip.label.order	logical (FALSE). If to check labels are in the same and in identical order
use.tip.label	logical (TRUE). If to check that labels are the same (regardless of order)
use.topology	logical (TRUE). If to check teh existence of distinct edges
tolerance	the numeric tolerance used to compare the branch lengths.
scale	a positive number (NULL as default), comparison of branch height is made after scaling (i.e., dividing) them by this number.
...	Ignored.

Value

Either TRUE (NULL for attr.all.equal) or a vector of mode "character" describing the differences between target and current.

See Also

all.equal, all.equal.phylo, identical

Examples

## Not run: 

set.seed(23235)
ss <- sample(1:150, 10)
dend1 <- iris[ss, -5] %>%
  dist() %>%
  hclust("com") %>%
  as.dendrogram()
dend2 <- iris[ss, -5] %>%
  dist() %>%
  hclust("single") %>%
  as.dendrogram()
dend3 <- iris[ss, -5] %>%
  dist() %>%
  hclust("ave") %>%
  as.dendrogram()
dend4 <- iris[ss, -5] %>%
  dist() %>%
  hclust("centroid") %>%
  as.dendrogram()
#    cutree(dend1)

all.equal(dend1, dend1)
all.equal(dend1, dend2)
all.equal(dend1, dend2, use.edge.length = FALSE)
all.equal(dend1, dend2, use.edge.length = FALSE, use.topology = FALSE)

all.equal(dend2, dend4, use.edge.length = TRUE)
all.equal(dend2, dend4, use.edge.length = FALSE)

all.equal(dendlist(dend1, dend2, dend3, dend4))
all.equal(dendlist(dend1, dend2, dend3, dend4), use.edge.length = FALSE)
all.equal(dendlist(dend1, dend1, dend1))

## End(Not run)

dendextend documentation built on Oct. 13, 2024, 1:06 a.m.