Configuration sizes in a tree

Finds the sizes of configurations in the tree.

nConfig(tree, maxClade = NULL)

Arguments

tree

a tree of class phylo or phylo4. The tree should be binary and rooted; if not it will be coerced into a binary rooted tree using multi2di, if possible.

maxClade

an integer between 1 and the number of tips (the default), specifying the maximum clade size of interest.

Value

A list with 2 entries:

• cladeSizes is a vector giving the size of the clade descending at each node:tips all have the value 1, internal nodes have their number of tip descendants.

• numClades is a vector where numClades[[i]] is the number of clades of size i in the tree. All clade sizes are calculated, but the output can be restricted using maxClade to just those of size up to 'maxClade'.

Author

Michelle Kendall michelle.louise.kendall@gmail.com

Examples

## Configuration sizes on a random tree with 10 tips:
tree <- rtree(10)
plot(tree)
nodelabels()

nConfig(tree)
#> $cladeSizes
#>     t3     t8    t10     t9     t5     t6     t7     t4     t1     t2 node11 
#>      1      1      1      1      1      1      1      1      1      1     10 
#> node12 node13 node14 node15 node16 node17 node18 node19 
#>      5      3      2      2      5      4      2      2 
#> 
#> $numClades
#>  1  2  3  4  5  6  7  8  9 10 
#> 10  4  1  1  2  0  0  0  0  1 
#>