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Split and Disbanded: Add delta, improve vaccination rollout, reduce testing morale#125

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roecla wants to merge 54 commits intomainfrom
add-delta
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Split and Disbanded: Add delta, improve vaccination rollout, reduce testing morale#125
roecla wants to merge 54 commits intomainfrom
add-delta

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@roecla roecla commented Aug 27, 2021 •
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**THIS PR HAS BEEN SPLIT INTO SEVERAL OTHERS: #126 #127 #128 #129 #130 #131 #132 **

  • adjust vaccination priority and roll out to fit the share of 12 to 17 year olds that are vaccinated:

simulated_vs_empirical_rates_by_age_group.pdf

  • extrapolate vaccination rates by using the average over the last four weeks

verify_ever_vaccinated.pdf

  • calibrate the other multiplier and vacation contacts to fit the increase from July onwards
  • calibrate the rapid test reduction when incidences are low

roecla added 30 commits August 17, 2021 11:07
@roecla
Adjust to new RKI format.
81adcbb
@roecla
Update to require pytask >= 1.0.0.
d34cb13
@roecla
Add summer baseline scenario simulation.
849deaf
@roecla
Add Delta's transmissibility factor.
e804e91
@roecla
Add Delta shares to virus strain info.
ace2ef0
@roecla
Add delta hopefully everywhere in the pipeline.
0cc341f
@roecla
Extend share known cases at 31% until end of 2021.
f2f4f57
@roecla
Update COSMO's empirical frequency of rapid tests until July. Extend …
8096edf 
…the share of tests going to symptomatic individuals until end of the year.
@roecla
Add vaccination shares by age group. Improve extrapolation by using t…
cc4aaeb 
…he mean of the last four weeks. Add fall vacations of 2021.
@roecla
Increase infection probabilities because delta leads to a downscaling…
523cf62 
… of all infection probs in sid.
@roecla
Fix typo in transmissibility.
7d09623
@roecla
Plot empirical equivalents for the summer plots.
19f7673
@roecla
Have different vaccination refuser shares for youths and adults.
33add57
@roecla
Implement vaccines for youths and removal of vaccination priorities i…
a7f048b 
…n the summer.
@roecla
Reduce Delta import.
cd99d37
@roecla
Create a plot comparing vaccination rates by age group as reported by…
314757d 
… the RKI.
@roecla
Update dates to have longer spring.
93bf323
@roecla
Set higher other multiplier in the summer.
6699bef
@roecla
Lower but longer inflow of Delta.
e667c25
@roecla
Implement that fully vaccinated individuals do not do preemptive rapi…
00ad100 
…d tests.
@roecla
Extend combined scenario to September and don't run summer scenario t…
dd1b1ca 
…o save time.
@roecla
Introduce later and longer to better fit Delta's expansion in Germany.
3e337d4
@roecla
Change plot time frame.
27ecad8
@roecla
Reduce other contact rapid tests when the incidence is low.
05aa160
@roecla
Make other contact rapid test demand reduction random and add random …
b5f9ebd 
…reduction for work contacts when incidences are low.
@roecla
Increase other multiplier and vacation contacts in summer 2021.
9a40872
@roecla
Extract floats for the low incidence values and not Series.
dc14d2b
@roecla
Only plot currently relevant scenario comparison plots and move other…
b7302e8 
…s to separate .py file. Change spring dates to end on April 1 such that all parameters to calibrate only take effect in the summer dates.
@roecla
Don't raise an error when the spring baseline scenario is not plotted.
968fe01
@roecla
Remove table script that was never used.
226c5d2
@roecla roecla changed the title Add delta, improve vaccination rollout, Add delta, improve vaccination rollout, reduce testing morale Aug 31, 2021
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roecla added 18 commits August 31, 2021 18:58
@roecla
Reduce length of Delta imports. Implement initial states path at the …
bf9c008 
…gridsearch level.
@roecla
Running version of calibrate summer params with actually using the in…
acd284d 
…itial states path.
@roecla
Show plots in the notebook. Save calibration figures in the figures f…
12df85a 
…older.
@roecla
Plot difference between simulated and empirical official case numbers.
2fe7b12
@roecla
Further improvements to the calibrate_summer_params notebook.
563202a
@roecla
Remove accidentally saved results.
6336213
@roecla
Set Delta's infectiousness to 2.3.
fe49cbd
@roecla
Merge branch 'add-delta' of https://github.com/covid-19-impact-lab/si…
22a73d2 
…d-germany into add-delta
@roecla
Set Delta to 2.0.
91d004d
@roecla
Adjust plot start and end times.
184cb34
@roecla
Split changes into several PRs 1: Put changes for delta into separate…
04b99bd 
… PR.
@roecla
Undo some changes that have been moved to prep-for-longer-simulation.
9272641
@roecla
More undoing of things that are now on the just-add-delta branch.
a7a6a13
@roecla
Finish undoing changes for preparation for longer simulation and addi…
faabe7a 
…ng delta.
@roecla
More undoing of things that were moved to other PRs.
a563fcd
@roecla
Remove and reset files that are moved to the add-empirical-vaccinatio…
c43795e 
…ns-by-age-group PR.
@roecla
Move rapid test changes to separate PR.
4ba0b49
@roecla
Reset the broken infection probs since they are set in the only-add-d…
a0a3eb3 
…elta PR.
@roecla roecla changed the title Add delta, improve vaccination rollout, reduce testing morale Being disbanded: Add delta, improve vaccination rollout, reduce testing morale Sep 3, 2021
@roecla roecla changed the title Being disbanded: Add delta, improve vaccination rollout, reduce testing morale Split and Disbanded: Add delta, improve vaccination rollout, reduce testing morale Sep 5, 2021
@roecla roecla closed this Sep 5, 2021
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@roecla