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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.
treetop
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.