treeDbalance (version 1.2.0)

enum2depthwise: Change the node enumeration of trees in phylo(3D) format

Description

enum2depthwise - Changes the enumeration of the nodes of a tree to a depthwise (top-down) enumeration that complies with the phylo format's requirements.
The input tree must have its nodes enumerated with 1,...,|V| (with |V| being the total number of nodes). enum2depthwise changes the node enumeration s.t. it fulfills the other enumeration requirements of the phylo format like:
- leaves are enumerated with 1,...,n, (with n being the number of leaves)
- the root has number n+1,
- and the rule for inner nodes: descendants have higher numbers than their ancestors.
The edge enumeration and order remains untouched. The function works for phylo as well as phylo3D objects and possible extensions like 'node.ancs', 'node.descs', etc. remain intact.

enum2cladewise - Changes the enumeration of the nodes of a tree to a cladewise enumeration (i.e. starting from the root we follow the rule: Go to left child; if that doesn't exist or was already visited go to the right child) that complies with the phylo format's requirements.
The input tree must have its nodes enumerated with 1,...,|V| (with |V| being the total number of nodes). enum2depthwise changes the node enumeration s.t. it fulfills the other enumeration requirements of the phylo format like:
- leaves are enumerated with 1,...,n, (with n being the number of leaves)
- the root has number n+1,
- and the rule for inner nodes: descendants have higher numbers than their ancestors.
The edge enumeration and order remains untouched. The function works for phylo as well as phylo3D objects and possible extensions like 'node.ancs', 'node.descs', etc. remain intact.

enum2_1toV - Changes the enumeration of the nodes of a tree such that they are enumerated with 1,...,|V| (with |V| being the total number of nodes). Then enum2cladewise or enum2depthwise can be used to switch to a specific enumeration. The edge enumeration and order remains untouched.
The input tree must have its nodes enumerated, i.e. the 'edge' attribute must be a numeric matrix (with no missing values). Note that the attribute 'node.coords' is allowed, but then the old node enumeration must point to the correct coordinates. All other rows of the coordinate matrix will be ignored and deleted.

Usage

enum2depthwise(tree)
enum2cladewise(tree)
enum2_1toV(tree_bad_enum)

Value

enum2depthwise(tree) Tree in (extended) phylo(3D) format as before but with node enumeration conforming to the phylo format standard.

enum2cladewise(tree) Tree in (extended) phylo(3D) format as before but with node enumeration conforming to the phylo format standard.

enum2_1toV(tree) Tree in format as before but with nodes enumerated from 1 to |V|.

Arguments

tree

A rooted tree in (extended) phylo(3D) format (no special node enumeration required, except that nodes are numbered from 1 to |V| = the total number of nodes). There must be at least 2 nodes, i.e. one edge.

tree_bad_enum

A rooted tree in a a rough phylo(3D) format (no special node enumeration required). There must be at least 2 nodes, i.e. one edge.

Author

Sophie Kersting

Examples

tree <- treeDbalance::example3Dtrees$bean21
# Visualize enumeration: plotPhylo3D(tree, show_node_enum = TRUE)
tree_depthwise <- enum2depthwise(tree)
# Visualize: addPhylo3D(tree_depthwise, offset=c(2,0,0), show_node_enum = TRUE)
tree_cladewise <- enum2cladewise(tree)
# Visualize: addPhylo3D(tree_cladewise, offset=c(4,0,0), show_node_enum = TRUE)
bad_tree <- list(
  edge = matrix(c(1, 13, 1, -7, 13, 4), byrow = TRUE, ncol = 2),
  tip.label = c("", ""), Nnode = 2
)
better_tree <- enum2_1toV(bad_tree)
better_tree$edge
bad_3Dtree <- list(
  edge = matrix(c(1, 2, 1, 5, 2, 4), byrow = TRUE, ncol = 2),
  tip.label = c("", ""), Nnode = 2,
  node.coord = matrix(c(
    1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4,
    5, 5, 5, 6, 6, 6
  ), byrow = TRUE, ncol = 3),
  edge.weight = c(1, 1, 1)
)
better_3Dtree <- enum2_1toV(bad_3Dtree)
better_3Dtree$edge
better_3Dtree$node.coord