README.md

In phoscheit/LambdaSkyline: Demographic Analysis of Multifurcating Phylogenies

LambdaSkyline

The LambdaSkyline package provides functions to manipulate multifurcating trees (as ape phylo objects) and compute their skyline plot (originally introduced by Pybus et al.), using Lambda-coalescents (specifically, Beta(2-alpha,alpha)-coalescents) as model. The package also provides functions for simulating trees under the Beta-coalescent, using the results in (Schweinsberg 2003).

Installation

To install LambdaSkyline, make sure the devtools library is installed, then type the following commands:

library(devtools)
devtools::install_github("phoscheit/LambdaSkyline")

Usage

The main function provided by the package is skyline.multi(), which extends the skyline functions present in ape to enable the computation of skyline plots based on Lambda-coalescents, specifically Beta(2-alpha,alpha)-coalescents. The function takes a phylo tree as input, as well as the alpha parameter between 0 and 2, and returns the skyline plot as a skyline object (which can then be plotted using ape's plot.skyline function).

Strictly bifurcating trees have zero likelihood under any Beta(2-alpha,alpha)-coalescent model with 0 < alpha < 2. Such trees, especially containing branches with zero length, can be converted into multifurcating trees by the di2multi.cons() function, which collapses branches shorter than a given length.

The function betacoal.maxlik() performs maximum-likelihood estimation of the alpha parameter on a given multifurcating tree.

phoscheit/LambdaSkyline documentation built on May 3, 2019, 8:36 p.m.