R: Number of trees one SPR step away

N1Spr {TreeTools} | R Documentation

## Number of trees one SPR step away

### Description

`N1Spr()` calculates the number of trees one subtree prune-and-regraft operation away from a binary input tree using the formula given by Allen and Steel (2001); `IC1Spr()` calculates the information content of trees at this distance: i.e. the entropy corresponding to the proportion of all possible n-tip trees whose SPR distance is at most one from a specified tree.

### Usage

    N1Spr(n)

    IC1Spr(n)

### Arguments

`n` | Integer vector specifying the number of tips in a tree.

### Value

`N1Spr()` returns an integer vector denoting the number of trees one SPR rearrangement away from the input tree..

`IC1Spr()` returns an numeric vector giving the phylogenetic information content of trees 0 or 1 SPR rearrangement from an n-leaf tree, in bits.

### References

Allen BL, Steel MA (2001). “Subtree transfer operations and their induced metrics on evolutionary trees.” Annals of Combinatorics, 5(1), 1–15. doi: 10.1007/s00026-001-8006-8.

### Examples

    N1Spr(4:6)
    IC1Spr(5)

[Package TreeTools version 1.2.0 Index]