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epiverse-trace / finalsize

R package to calculate the final size of an SIR epidemic in populations with heterogeneity in social contacts and disease susceptibility
https://epiverse-trace.github.io/finalsize/
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Simplify "Get started" vignette #143

Closed pratikunterwegs closed 1 year ago

pratikunterwegs commented 1 year ago

This PR fixes #142 and also simplifies the "Get started" vignette (finalsize.Rmd), to show an example without age-stratified social contact patterns, and with a single population-wide susceptibility to infection.

This is likely to provide an easier entry point for users than the previous contents, which are now moved to their own vignette, "Modelling heterogeneous social contacts".

This PR also:

  1. Uses an $R_0$ value of 1.5 (pandemic influenza) in all cases,
  2. Adds links to earlier vignettes where required,
  3. Adds an example showing how heterogeneous susceptibility can be modelled without also including heterogeneous social contacts.
  4. Fixes #116 again by editing the Readme.
pratikunterwegs commented 1 year ago

Thanks for taking a look @avallecam - I've edited the vignette and the Readme, and will merge this into main if that's okay with you.

Once this is merged into main, there will be a discrepancy between main and your fork branch (from which a PR is open, #144. The way to get the fork branch up to date would be to rebase it on upstream/main after fetch-ing the upstream, and then force-pushing your fork branch. I can help with this if needed.

avallecam commented 1 year ago

sorry for the delayed reply on this! this was ok for me 👍 thanks for the PR update details, will get in touch after finishing the suggestion edits