Stoner stochastic graphing overhaul

[weshinsley]

A pretty horrible PR really with a lot of churn to achieve some specific things. It might be best to just review the finished stochastic_file and stochastic_graph files (and maybe read the vignette) - and not treat this as a diff, as it's so messy,

Anywyay - it achieves the following, which kind of had to come in one go, or something else would break...

• stochastic_file has a new command stone_stochastic_make_meta which makes a meta.csv in the root of the stochastic files (\wpia-hn2.hpc.dide.ic.ac.uk\vimc_stochastics), giving meta-data about the groups, diseases, touchstones, scenarios, outcomes and countries, so we know what we've got at a glance, rather than having to do a nasty trawl.

• stochastic_explorer (the shiny app) uses the meta file instead of having to do exactly that nasty trawl, which saves about 20 seconds on startup, and makes everything a bit less sluggish generally. Some churn in utils.R with how it finds the info.

• stochastic_graph can now produce two graphs at once with the same y-axis scale, in order to compare estimates in different touchstones, or by different modellin groups (keeping all other selections the same) - with the additional possibility of being able to plot the difference (often called impact) between two scenarios. This also was quite a churny update.

• stochastic_graph can also plot with age as the x-axis, and filter which years to reduce - as well as plotting by time on the x-axis, and choosing which ages to reduce. Basically this is all flexed up.

• All the above is available from the shiny app....

• And written up in the vignette.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 100.00%. Comparing base (4d10598) to head (ac7cbb7).
⚠️ Report is 7 commits behind head on master.

Additional details and impacted files

@@             Coverage Diff             @@
##           master       #37      +/-   ##
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+ Coverage   98.01%   100.00%   +1.98%     
===========================================
  Files          23        22       -1     
  Lines        2568      2640      +72     
===========================================
+ Hits         2517      2640     +123     
+ Misses         51         0      -51     

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