R: Global Comparison of two (or more) dendrograms

all.equal.dendrogram {dendextend} | R Documentation

## 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)

[Package dendextend version 1.8.0 Index]