Design plan for new architecture

[jamesmbaazam]

Towards interoperability

• S3 class (transmission.chain): for handling transmission chains Version number #32:
  • Objects of this class will have attributes to store key simulation metadata (value for infinite from chain_sim(), stat = length/size specified, out.type = if tree = TRUE, 'chain.tree', else, 'chain.notree').
• Methods:
  • Constructor {make_transmission_chain}: function to create a transmission_chain object; Initiates data/output storage and retrieval/subsetting (inherit from data.frame/tibble).
  • Validator {is.transmission.chain}: function to confirm if an object is a transmission.chain object else throw error.
  • Output {print.transmission.chain}: function to format and pretty print transmission_chain objects, depending on whether they are of type "tree" or "notree".
  • Summary {summary.transmission_chain}: function to calculate the following summaries: number of chains, min and max chain length/size, average chain length/size, and others as may be required. This will depend on whether an object is of type "tree" or "notree".
  • Plotting {plot.transmission_chain}: function to plot transmission chains in different ways:
    - trees/chains plotted as a network Refactor chain_sim()  #13
    - cluster sizes per onset date (if specified by user) as barplots Add lifecycle badge #9

Utils

• helper functions for passing whole linelists to bpmodels and with tagged columns using linelist package.
• helper functions for decomposing case count time series into linelists with tagged columns (not aware of packages for achieving this).

Dependencies

This new architecture might require the following dependencies:

Simulations and post-processing

• epicontacts: for visualization methods
• projections: for summary, print, and visualization methods
• linelist
• incidence2

Package backend

• cli for printing messages/errors/warnings and for other user-facing features
• checkmate for input validation

[jamesmbaazam]

Closing this as it is now provided as a vignette here: https://epiverse-trace.github.io/epichains/articles/design-principles.html.