skygrowth: Phylodynamic inference with nonparametric growth rate models
In mrc-ide/skygrowth: Phylodynamic inference with nonparametric growth rate models

This package provides methods for inferring effective population size for time-scaled phylogenies using Bayesian MCMC and maximum a posteriori.

The main functions of the package are:

phylo.mapma and phylo.bnpma provide maximum and a posteriori methods respectively for inferring effective population size through time given a dated genealogy.
phylo.mapma.covars and phylo.bnpma.covars allow you to include a data.frame with time-varying covariates which may improve the inference. Covariates should be included if they are likely to be associated with the growth rate of effective population size.

Erik M Volz and Xavier Didelot Maintainer Erik M Volz erik.volz@gmail.com

Erik M Volz and Xavier Didelot, Manuscript in prepration.

https://github.com/mrc-ide/skygrowth

mrc-ide/skygrowth documentation built on May 19, 2020, 5:10 p.m.