epichains update

[avallecam]

modifications after epichains update

• [x] (1) index_cases to n_chains

  • we can simulate multiple chains within the 1 simulation

• [x] (2) we need to replace chain_id to simulation_id when using purrr

  • we make multiple simulations, instead of simulating multiple chains!
  • simulate_chains() simulate 1 chain or more
  • when we iterate simulate_chains(), we make multiple simulations of 1 chain or more

• [x] (3) update output column names

# A tibble: 28 × 6
   chain infector infectee generation  time simulation_id
   <int>    <dbl>    <dbl>      <int> <dbl>         <int>

[jamesmbaazam]

Hey Andree, I was coming here to point this out after the v0.1.0 release. I would be happy to support if you need any help.

plotting <epichains> objects

I also want to point out that you can now plot the <epichains> objects using {epicontacts}. There is a snippet of code in this issue https://github.com/epiverse-trace/epichains/issues/255 and a section in the Getting Started vignette. Note that if you don't want to go the route of subsetting the longest chain, you can simulate an outbreak with 1 case (n_chains) and create an <epicontacts> object directly from the resulting <epichains> object. If you want a big enough network, use the default pop = Inf and set a high stat_max. Please let me know if you need any help with this.