mlesky : Maximum likelihood phylodynamic inference

This package performs inference of past population size dynamics from a dated phylogeny using a maximum likelihood approach. The main features are as follows:

• Three different phylodynamic models are implemented (skygrid, skygrowth and skykappa)
• A novel cross-validation approach is used for selecting the smoothing parameter
• The resolution of the grid can be selected using AIC or BIC
• Covariate data can be included into the analysis to quantify association
• Multiple phylogenies can be analysed simultaneously that share the same demographic function

For a complete description of the statistical methodology underpinning this package, see our paper:

Model design for nonparametric phylodynamic inference and applications to pathogen surveillance
Xavier Didelot, Vinicius Franceschi, Simon D. W Frost, Ann Dennis, Erik M Volz
Virus Evolution, Volume 9, Issue 1, 2023, vead028, https://doi.org/10.1093/ve/vead028

Installation

In R, install the devtools package and run

devtools::install_github('emvolz-phylodynamics/mlesky')

Documentation

See the vignettes in the R package for examples of how to use mlesky.