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1268 Vaccination data reporting expired#1269

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HenrZu merged 5 commits intomainfrom
1268-Vaccination-data-is-outdated-since-july-2024
May 30, 2025
Merged

1268 Vaccination data reporting expired#1269
HenrZu merged 5 commits intomainfrom
1268-Vaccination-data-is-outdated-since-july-2024

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@HenrZu HenrZu commented Apr 28, 2025 •
edited by annawendler
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Changes and Information

Please briefly list the changes (main added features, changed items, or corrected bugs) made:

  • Since vaccination data is no longer reported since July 24, we dont need it to init the model for days after.
  • DIVI data has continued to be reported. Therefore, we can enable the usage for days after July 24 again.

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codecov bot commented Apr 28, 2025 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 97.22%. Comparing base (672cbc1) to head (f3860b6).
Report is 6 commits behind head on main.

Additional details and impacted files 
@@           Coverage Diff           @@
##             main    #1269   +/-   ##
=======================================
  Coverage   97.21%   97.22%           
=======================================
  Files         156      156           
  Lines       14674    14709   +35     
=======================================
+ Hits        14266    14301   +35     
  Misses        408      408

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@HenrZu HenrZu linked an issue Apr 28, 2025 that may be closed by this pull request
Vaccination data is outdated since july 2024 #1268
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@HenrZu HenrZu requested a review from annawendler April 29, 2025 07:21
@HenrZu HenrZu changed the title 1268 Vaccination data is outdated 1268 Vaccination data reporting expired Apr 29, 2025
annawendler
annawendler requested changes May 14, 2025
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@annawendler annawendler left a comment •
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The code looks good and is consistent in itself. I was wondering why you chose to implement the functionality to set the vacc data to zero in this set_vacc_data() function and not the other one. When you implement it like this it is unclear to me what happens if the simulation interval is only partially contained in the vacc dates. Here https://github.com/SciCompMod/memilio/blob/main/cpp/models/ode_secirts/parameters_io.h#L866 you are already mentioning that for the dates after the end of vacc_data you set the values to 0 but I don't findwhere this is actually done. Also I don't understand why you don't throw a similar warning for the respective min_date, can you explain?

Comment thread cpp/memilio/io/epi_data.h
Comment thread cpp/tests/test_odesecirts.cpp Outdated
Comment thread cpp/tests/test_odesecirvvs.cpp
Comment thread cpp/tests/test_odesecirvvs.cpp Outdated
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HenrZu commented May 21, 2025 •
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I was wondering why you chose to implement the functionality to set the vacc data to zero in this set_vacc_data() function and not the other one.

Because the other function requires the vaccination data. So, if the data is not available, we dont need to read in the vaccination data.

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HenrZu commented May 21, 2025

Here https://github.com/SciCompMod/memilio/blob/main/cpp/models/ode_secirts/parameters_io.h#L866 you are already mentioning that for the dates after the end of vacc_data you set the values to 0 but I don't findwhere this is actually done

in the secirvvs model, if data in future is not avialable, we do some linear continuation based on the last entries. If the Simulation
is starting before vaccinations are available, they are set to Zero.

In the secirts model, we set all vaccinations to Zero, before and after the vaccination data is avail.
Here

memilio/cpp/models/ode_secirts/parameters_io.h

Line 901 in 2a6ea57

if (date_df == offset_full_date) {

we only set if data is avail. For Dates after, we go in the else loop. FOr all Dates before, we have already initialized it with Zero in

memilio/cpp/models/ode_secirts/parameters_io.h

Line 852 in 2a6ea57

model[i].parameters.template get<DailyPartialVaccinations<FP>>()[{g, d}] = 0.0;

@HenrZu HenrZu requested a review from annawendler May 21, 2025 11:58
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annawendler reviewed May 30, 2025
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Thank you for the clarifications! :) Can you link the corresponding issue in the PR? Otherwise everything is fine.

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annawendler approved these changes May 30, 2025
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I oversaw that the issue was already linked

@HenrZu HenrZu merged commit 3252cf5 into main May 30, 2025
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@HenrZu HenrZu deleted the 1268-Vaccination-data-is-outdated-since-july-2024 branch May 30, 2025 09:48
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Vaccination data is outdated since july 2024

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