Ebola vignette clean-up

[athowes]

The Ebola vignette PR (#52) got really big. There are a few comments left to go over but I recommend we merge a rougher version of the vignette, then I'll pick these up in a new issue. One reason for that is that I'm finding it a bit unweildy with such a large comment history.

• Issue 48: Ebola vignette #52 (comment) Should we use bf(mu ~ 1, sigma ~ 1) or just leave as default. I prefer writing it out, Sam prefers leaving it as default.
• Issue 48: Ebola vignette #52 (comment) Should we have facet specific x-axis for the plot showing the data. I prefer no, Katie prefers yes. (Moved to Extensions for Ebola vignette #285)
• Issue 48: Ebola vignette #52 (comment) Could we simplify ptime and ptime_daily. See Refactor of observe_process #291 also. (Moved to Extensions for Ebola vignette #285)
• Issue 48: Ebola vignette #52 (comment) Better explainations of what is happening in the PMF and PDF prediction generation. From my perspective, I understand them as being predictions of something. Why this is exactly what you want for policy purposes I understand less. For example, why do you want to predict what you would observe with censoring for the PMF, rather than what you would observe without censoring and then discretise that? I somewhat get it but not all the way (and if I'm confused then readers will be also I think). This relates to the "going around in circles"-esque discussion on the initial vignette and follow-up issue e.g. Is there an issue with using a histogram to plot continuous data? #67 (Moved to Extensions for Ebola vignette #285)
• Issue 48: Ebola vignette #52 (comment) Possible reordering of sections. I'm open to this. Also would fit into "possible regrouping of plots". Right now I've grouped all models for a particular plot type
• Issue 48: Ebola vignette #52 (comment) Need to make sure it's consistent in use of :: in text the first time a function is introduced and then not using :: in code. Also using () to get automatic pkgdown links

Other things I notice

• Title has ` failing to render properly
• Maths is failing to render properly e.g. (x \sim \mathcal{N}(\mu, \sigma)). (Moved to Make sure maths renders correctly in vignettes #333)
• Calling head(obs_prep) twice
• I don't like that I have to call sex = case_when over and over -- way to fix this?
• Figure 2.3 panel C is too small / needs sorting
• Figure 2.4 panel C also too small / needs sorting

[athowes]

@seabbs that's fair regarding this being 6 issues vs 1 issue. I don't have enough personal experience to have preference yet but I can see the appeal of 6 issues. It was easier for me initially to do 1 issue and it felt like "I just want to get this gone" hence where we are.

[seabbs]

I think I would track this with a meta-issue but assign each as individual issues to give the option of splitting into their own PRs

[athowes]

Should we use bf(mu ~ 1, sigma ~ 1) or just leave as default. I prefer writing it out, Sam prefers leaving it as default.

@seabbs can we leave this as it is for the time being? We are likely making changes to the formula interface anyway soon.