Movatterモバイル変換

epichains 0.1.1

This is the first CRAN release of{epichains}.

Package

• Removed theas_is = TRUE setting in vignette YAMLheaders to avoid partial incompatibility with incoming pkgdownversions.

epichains 0.1.0

We are excited to announce the first minor release of{epichains}.

{epichains} re-implements{bpmodels},focusing on a unified simulation framework using branching processes tosimulate transmission chains data. The framework incorporatessusceptible depletion and pre-existing immunity and provides dedicateddata structures for handling and analysing transmission chains in bothtabular and vector formats. The goal is to provide seamlessinteroperability with other packages within the Epiverse-TRACEInitiative and the broader epidemiological tool ecosystem.

New Features

Documentation

• Dedicated Website: Explore all features anddocumentation on theepichainswebsite.
• Help: Each function comes with extensivedocumentation. We welcome your feedback and suggestions forimprovements.
• Vignettes: This release comes with five detailedvignettes:
  • Getting Started: A quick guide to the keyfunctions.
  • Modelling Disease Control Interventions: Learn howto model various intervention strategies.
  • Projecting Infectious Disease Incidence: A casestudy on projecting COVID-19 incidence.
  • Literature: A curation of literature on branchingprocess applications in epidemiology.
  • Theoretical Background: A deep dive into thetheoretical background of the functions in the package (Contributordocumentation).
  • Design principles: The design principles of{epichains} (Contributor documentation).

Simulation

• simulate_chains(): Simulateindependent transmission chains from a specified number of initialcases, incorporating susceptible depletion and pre-existingimmunity.
• simulate_chain_stats(): Generate avector of chain sizes or lengths from a specified number of initialcases, incorporating susceptible depletion and pre-existingimmunity.

Inference

• likelihood(): Estimate the(log)likelihood of transmission chain sizes or lengths, with support fornumeric vectors or<epichains> and<epichains_summary> objects.

Transmission Chain DataManipulation

• summary(): Extract vectors of chainsizes or lengths from<epichains> objects.
• aggregate(): Generate case time seriesby aggregating by generation or time of infection.
• plot(): Visualize individualtransmission chains filtered by their id.