Add vignette on superspreading pipeline

[joshwlambert]

Issue #1 proposed having a vignette which included:

1. Read in and tidy data
2. Fit negative binomial model with {fitdistrplus}
3. Apply summary metrics from {superspreading}
4. Simulate with {bpmodels} with negative binomial parameters

Instead a vignette focussing on fitting distributions (#15) was added.

Here I reissue a request to write a vignette which covers the pipeline from initial data wrangling, to parameter estimation, to superspreading metrics and simulating with either {bpmodels} or {epichains}.

[adamkucharski]

Agree, would be useful to have a full data-to-fitting-to-scenario pipeline illustrated (although the fitting distribution vignette is a nice stand-alone). Perhaps could also integrate with {ringbp} as @jamesmbaazam develops those options?

[jamesmbaazam]

{epichains} is currently unstable/experimental to be used here. {bpmodels} provides a stable interface for this via chain_sim().

[joshwlambert]

I'll use {bpmodels} for now with the aim to convert to using {epichains} once stable.

I'll track progress on epiverse-trace/epichains#6 and once there is a working version I can incorporate into {superspreading}.

@jamesmbaazam this could be a good topic of collaboration/cross-pillar work. Let me know if want to collaborate on this development.

[joshwlambert]

Note: reproducing figure 1B from Ebola Superspreading using {bpmodels} for simulation would be a good fit for this vignette.

[jamesmbaazam]

@joshwlambert I'm happy to work on this with you as these two projects are quite intertwined.

[joshwlambert]

Removing from v0.2.0 release as it needs to be reviewed whether such a pipeline is within the scope of the {superspreading} package. Possibly more suitable to case studies.