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.