get_all_distances_to_root {castor} R Documentation

## Get distances of all tips and nodes to the root.

### Description

Given a rooted phylogenetic tree, calculate the phylogenetic distance (cumulative branch length) of the root to each tip and node.

### Usage

```get_all_distances_to_root(tree, as_edge_count=FALSE)
```

### Arguments

 `tree` A rooted tree of class "phylo". The root is assumed to be the unique node with no incoming edge. `as_edge_count` Logical, specifying whether distances should be counted in number of edges, rather than cumulative edge length. This is the same as if all edges had length 1.

### Details

If `tree\$edge.length` is missing, then every edge in the tree is assumed to be of length 1. The tree may include multi-furcations as well as mono-furcations (i.e. nodes with only one child). The asymptotic average time complexity of this function is O(Nedges), where Nedges is the number of edges in the tree.

### Value

A numeric vector of size Ntips+Nnodes, with the i-th element being the distance (cumulative branch length) of the i-th tip or node to the root. Tips are indexed 1,..,Ntips and nodes are indexed (Ntips+1),..,(Ntips+Nnodes).

### Author(s)

Stilianos Louca

`get_pairwise_distances`

### Examples

```# generate a random tree
Ntips = 1000
tree = generate_random_tree(list(birth_rate_intercept=1,
death_rate_intercept=0.5),
max_tips=Ntips)\$tree

# calculate distances to root
all_distances = get_all_distances_to_root(tree)

# extract distances of nodes to root
node_distances = all_distances[(Ntips+1):(Ntips+tree\$Nnode)]

# plot histogram of distances (across all nodes)
hist(node_distances, xlab="distance to root", ylab="# nodes", prob=FALSE);
```

[Package castor version 1.7.0 Index]