An analytic tool (TranStat) is available to analyze data from outbreaks of acute infectious disease to test for the presence of human-to-human transmission (or animal-to-animal in veterinary settings) and to estimate epidemiologic characteristics of the disease.


Software for the analysis and visualization of deep mutational scanning data:  


Sequential Monte Carlo Approximate Bayesian Computation with Partial Least Squares parameter estimator:

pomp:  statistical inference for partially-observed Markov processes

pomp provides a very general realization of nonlinear partially-observed Markov processes (AKA nonlinear stochastic dynamical systems). These are a generalization of linear state-space and hidden Markov models to nonlinear, non-Gaussian processes in either discrete or continuous time.


Software for phylogenetics using deep mutational scanning:


R package for statistical inference on panel partially observed Markov processes (alpha release version).