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).