exampleUltraTrees: Example ultrametric tree data

In cloneRate: Estimate Growth Rates from Phylogenetic Trees

Example ultrametric tree data

Description

Set of 100 time-based ultrametric trees reconstructed from the distribution of a sample of n=100 tips. All trees have a net growth rate of 1 with birth rates between 1 and 2 (sampled from a uniform distribution). Death rates are equal to the chosen birth rate minus 1. Tree reconstruction uses the exact distribution of coalescence times described in "The coalescent of a sample from a binary branching process", Lambert A., Theor. Pop. Bio. 2018. Tree construction and formatting uses ape R package ape::rcoal().

Usage

data(exampleUltraTrees)

Format

A list of objects of class phylo

edge

A matrix of edge connections which reconstruct the tree.

edge.length

A numeric vector of the branch lengths of the connections in edge matrix. Units are years.

tip.label

A character vector containing the (arbitrary in this case) labels for the 100 tips/samples of the tree.

Nnode

Integer number of internal nodes of the tree

params

data.frame containing info on the params used to generate the tree

See ape package for details on class phylo objects.

References

This data set was created for the cloneRate package using coalescent theory approaches described in "The coalescent of a sample from a binary branching process", Lambert A., Theor. Pop. Bio. 2018.

Examples

# Plot first of 100 trees
ape::plot.phylo(cloneRate::exampleUltraTrees[[1]],
  direction = "downwards", show.tip.label = FALSE
)

cloneRate documentation built on Sept. 22, 2023, 5:09 p.m.