Add heterogeneous contacts R function and vignette

[joshwlambert]

This PR addresses and closes #55, by adding one new function calc_network_R() and one new vignette heterogeneous_network_outbreaks.Rmd.

The new function calculates both the unadjusted and adjusted reproduction number, see #55 for explanation. The vignette gives two use cases of the function from the epidemiological literature. The references.json file is updated to include new references cited in the vignette.

The {scales} package is added as a suggested dependency to handle plot axes labelling.

Tests and documentation is added for calc_network_R().

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Notes for draft

@adamkucharski please check the function is working as you expected and that the function documentation is correctly describing the method.

@sbfnk I cannot reproduce the values from Endo et al. (2022) for the second figure in the new vignette. I've read through the main text and supplementary material for the values used. It also looks like the calculation to produce Fig 2A from that paper differs from calc_network_R(). Please let me know if I should update the values input into the function and whether some numerical differences given different formulations are expected.

The new vignette is best viewed by running pkgdown::build_site().

[adamkucharski]

Thanks, I've suggested a few edits to the markdown, which hopefully also explains the difference in assumptions with the Endo et al analysis.

[joshwlambert]

@adamkucharski thanks for the updates. I have now made this PR live and will merge the changes at the start of next week. This PR will be the last of the changes for the next version release (v0.2.0).

[joshwlambert]

Closing and reopening the PR to trigger workflows after GHA commit.