Vignette on parameter uncertainty

epiverse-trace / epidemics

A library of published compartmental epidemic models, and classes to represent demographic structure, non-pharmaceutical interventions, and vaccination regimes, to compose epidemic scenarios.

https://epiverse-trace.github.io/epidemics/

Other

8 stars 2 forks source link

Vignette on parameter uncertainty #131

Closed pratikunterwegs closed 10 months ago

pratikunterwegs commented 11 months ago

This PR is related to #20 and adds a vignette initially authored by @adamkucharski showing how to use {EpiEstim} to generate an $R$ estimate, and how to run multiple iterations of epidemic_default_*() for different $R$ values.

This PR is scheduled be merged after #128.

pratikunterwegs commented 11 months ago

Hi @adamkucharski - I've drafted this PR from your branch on $R_0$ uncertainty, are you happy for me to get it passing checks and merge it, or would you like to continue developing it? No rush either way.

adamkucharski commented 11 months ago

Thanks. One thing that would be useful to add is a plot of outcomes in the final section of the vignette, e.g. showing the trajectories of cases from the output_samples array across different sampled R0 values (didn't have time on the day to find neatest way of wrangling into ggplot!)

pratikunterwegs commented 11 months ago

Thanks. One thing that would be useful to add is a plot of outcomes in the final section of the vignette, e.g. showing the trajectories of cases from the output_samples array across different sampled R0 values (didn't have time on the day to find neatest way of wrangling into ggplot!)

Thanks, can definitely do! Will tag you again once it's complete.

github-actions[bot] commented 10 months ago

This pull request:

Adds 16 new dependencies (direct and indirect)
Adds 2 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

(cc @Bisaloo for workflow monitoring)

github-actions[bot] commented 10 months ago

This pull request:

Adds 16 new dependencies (direct and indirect)
Adds 2 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

(cc @Bisaloo for workflow monitoring)

github-actions[bot] commented 10 months ago

This pull request:

Adds 16 new dependencies (direct and indirect)
Adds 2 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

(cc @Bisaloo for workflow monitoring)

pratikunterwegs commented 10 months ago

This is looking very nice – good starting example that should open doors for a lot of useful scenario analysis work. Only a couple of minor comments.

Great, thanks for the feedback, merging this now.