R Packages

covidseir: Bayesian SEIR Modelling for Multivariate COVID-19 Case Data

A R software package capable of estimating a Bayesian SEIR model using daily COVID-19 case counts. Package was developed by Sean Anderson based on two papers (Estimating the impact of COVID-19 control measures using a Bayesian model of physical distancing and How much leeway is there to relax COVID-19 control measures?).

TransPhylo: Reconstruction of transmission trees using genomic data

A software package that can reconstruct infectious disease transmission using genomic data. TransPhylo now allows users to specify their own epidemiological prior on the transmission trees.

treenomial: Comparing tree polynomials

An R package that provides functionality for creation and comparison of polynomials that uniquely describe trees.

phyloTop: Calculating Topological Properties of Phylogenies

Tools for calculating and viewing topological properties of phylogenetic trees. 


treespace: Statistical Exploration of Landscapes of Phylogenetic Trees

Tools for the exploration of distributions of phylogenetic trees. This package includes a 'shiny' interface which can be started from R using treespaceServer().

transcluster: Inferring and viewing transmission clusters

A package for inferring and viewing transmission clusters from sequence alignments and sample dates.


Compare tree shapes using integer labels: an R package.


transnp: Transmission inference using SNP data

Takes SNP alignments for clusters, together with sampling dates and some assumptions, and models transmission events and times.

cr0eso: R0 estimation in multiple outbreaks using a hierarchical SEIR model

cr0eso fits a Bayesian hierarchical SEIR (susceptible, exposed, infected, recovered) model to a collection of outbreak data from different facilities.