Set of 100 mutation based 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(). We then change the edge
lengths from time-based to mutation-based by drawing from a poisson
distribution with mean equal to edge length (in units of time) multiplied
by the mutation rate, nu, which is drawn from a uniform distribution between
10 and 20 mutations per year.
Usage
data(exampleMutTrees)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
edgematrix. Units are mutations.- 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.framecontaining 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::exampleMutTrees[[1]],
direction = "downwards", show.tip.label = FALSE
)
