This is the first CRAN release of {epichains}.
as_is = TRUE setting in vignette YAML headers to avoid partial incompatibility with incoming pkgdown versions.We are excited to announce the first minor release of {epichains}.
{epichains} re-implements {bpmodels}, focusing on a unified simulation framework using branching processes to simulate transmission chains data. The framework incorporates susceptible depletion and pre-existing immunity and provides dedicated data structures for handling and analysing transmission chains in both tabular and vector formats. The goal is to provide seamless interoperability with other packages within the Epiverse-TRACE Initiative and the broader epidemiological tool ecosystem.
{epichains} (Contributor documentation).simulate_chains(): Simulate independent transmission chains from a specified number of initial cases, incorporating susceptible depletion and pre-existing immunity.simulate_chain_stats(): Generate a vector of chain sizes or lengths from a specified number of initial cases, incorporating susceptible depletion and pre-existing immunity.likelihood(): Estimate the (log)likelihood of transmission chain sizes or lengths, with support for numeric vectors or <epichains> and <epichains_summary> objects.summary(): Extract vectors of chain sizes or lengths from <epichains> objects.aggregate(): Generate case time series by aggregating by generation or time of infection.plot(): Visualize individual transmission chains filtered by their id.