tree utility function

Functions for describing relationships among phylogenetic nodes.

Usage

Ancestors(x, node, type = c("all", "parent"))

allDescendants(x)

Children(x, node)

Descendants(x, node, type = c("tips", "children", "all"))

Siblings(x, node, include.self = FALSE)

mrca.phylo(x, node = NULL, full = FALSE)

Arguments

x: a tree (a phylo object).
node: an integer or character vector (or scalar) corresponding to a node ID
type: specify whether to return just direct children / parents or all
include.self: whether to include self in list of siblings
full: a logical indicating whether to return the MRCAs among all tips and nodes (if TRUE); the default is to return only the MRCAs among tips.

Value

a vector or a list containing the indices of the nodes.

Details

These functions are inspired by treewalk in phylobase package, but work on the S3 phylo objects. The nodes are the indices as given in edge matrix of an phylo object. From taxon labels these indices can be easily derived matching against the tip.label argument of an phylo object, see example below. All the functions allow node to be either a scalar or vector. mrca is a faster version of the mrca in ape, in phangorn only because of dependencies. If the argument node is missing the function is evaluated for all nodes.

Functions

allDescendants(): list all the descendant nodes of each node

Examples


tree <- rtree(10)
plot(tree, show.tip.label = FALSE)
nodelabels()
tiplabels()

Ancestors(tree, 1:3, "all")
#> [[1]]
#> [1] 14 13 12 11
#> 
#> [[2]]
#> [1] 15 14 13 12 11
#> 
#> [[3]]
#> [1] 15 14 13 12 11
#> 
Children(tree, 11)
#> [1] 12 18
Descendants(tree, 11, "tips")
#> [[1]]
#>  [1]  1  2  3  4  5  6  7  8  9 10
#> 
Siblings(tree, 3)
#> [1] 2
# Siblings of all nodes
Siblings(tree)
#> [[1]]
#> [1] 15
#> 
#> [[2]]
#> [1] 3
#> 
#> [[3]]
#> [1] 2
#> 
#> [[4]]
#> [1] 14
#> 
#> [[5]]
#> [1] 6
#> 
#> [[6]]
#> [1] 5
#> 
#> [[7]]
#> [1] 17
#> 
#> [[8]]
#> [1] 19
#> 
#> [[9]]
#> [1] 10
#> 
#> [[10]]
#> [1] 9
#> 
#> [[11]]
#> NULL
#> 
#> [[12]]
#> [1] 18
#> 
#> [[13]]
#> [1] 16
#> 
#> [[14]]
#> [1] 4
#> 
#> [[15]]
#> [1] 1
#> 
#> [[16]]
#> [1] 13
#> 
#> [[17]]
#> [1] 7
#> 
#> [[18]]
#> [1] 12
#> 
#> [[19]]
#> [1] 8
#> 
mrca.phylo(tree, 1:3)
#> [1] 14
mrca.phylo(tree, match(c("t1", "t2", "t3"), tree$tip))
#> [1] 11
mrca.phylo(tree)
#>     t4 t6 t1 t5 t7 t9 t2 t10 t8 t3
#> t4   1 14 14 13 12 12 12  11 11 11
#> t6  14  2 15 13 12 12 12  11 11 11
#> t1  14 15  3 13 12 12 12  11 11 11
#> t5  13 13 13  4 12 12 12  11 11 11
#> t7  12 12 12 12  5 17 16  11 11 11
#> t9  12 12 12 12 17  6 16  11 11 11
#> t2  12 12 12 12 16 16  7  11 11 11
#> t10 11 11 11 11 11 11 11   8 18 18
#> t8  11 11 11 11 11 11 11  18  9 19
#> t3  11 11 11 11 11 11 11  18 19 10
# same as mrca(tree), but faster for large trees