phydynR: phydynR

In emvolz-phylodynamics/phydynR: Model-based coalescent simulation and likelihood for phylodynamic inference

phydynR

Description

This package provides functions for defining infectious diseae models or ecological process models in terms of ODEs or SDEs; functions for simulating trees conditional on process models; and functions for computing likelihoods of trees conditional on a process model.. Phylodynamic inference and simulation in R.

Details

This package provides an interface to building demographic process models (ODEs or SDEs) and simulating genealogies based on these models. Low level functions can be used to construct more complex models. A structured coalescent likelihood allows for inference of model parameters provided a time-scaled genealogy.

Maintainer

Erik Volz <[e-mail]>

Author(s)

Erik Volz

References

1. Volz, Erik M. Complex population dynamics and the coalescent under neutrality. Genetics 190.1 (2012): 187-201.

2. Volz, Erik M., Katia Koelle, and Trevor Bedford. Viral phylodynamics. PLoS Comput Biol 9.3 (2013): e1002947.

Examples

See the README for common usage and examples.

emvolz-phylodynamics/phydynR documentation built on July 28, 2023, 6:06 a.m.