1268 Vaccination data reporting expired #1269

HenrZu · 2025-04-28T13:49:36Z

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 · 2025-04-28T14:18:27Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 97.22%. Comparing base (672cbc1) to head (f3860b6).
Report is 3 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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annawendler

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?

cpp/memilio/io/epi_data.h

cpp/tests/test_odesecirts.cpp

annawendler · 2025-05-14T10:20:34Z

cpp/tests/test_odesecirvvs.cpp

@@ -666,14 +661,14 @@ TEST(TestOdeSECIRVVS, read_data)

    auto read_result1 = mio::osecirvvs::read_input_data_county(model1, {2020, 12, 01}, {1002},
                                                               std::vector<double>(size_t(num_age_groups), 1.0), 1.0,
-                                                               TEST_GERMANY_PYDATA_DIR, 10);
+                                                               TEST_GERMANY_PYDATA_DIR, 30);


Why did you change this?

I initially wanted to write a comment regarding this here :D
The vaccination data for the tests is completely synthetic and starts on 1 October. If we only look 10 days in the future, then is_vaccination_data_available would return false and no vaccination data would be set. If I set this to 30, then the vaccination data is set because it then returns true ;)
that might be a bit confusing, but it would solve the problem for now. I will adjust the synthetic data in a future pull request to make this more realistic.

cpp/tests/test_odesecirvvs.cpp

Co-authored-by: annawendler <[email protected]>

HenrZu · 2025-05-21T09:11:16Z

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.

HenrZu · 2025-05-21T09:31:18Z

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;

vaccination data data restriction, rm for divi data

9932b75

move into if makro

2a6ea57

HenrZu linked an issue Apr 28, 2025 that may be closed by this pull request

Vaccination data is outdated since july 2024 #1268

Open

2 tasks

HenrZu requested a review from annawendler April 29, 2025 07:21

HenrZu changed the title ~~1268 Vaccination data is outdated~~ 1268 Vaccination data reporting expired Apr 29, 2025

annawendler requested changes May 14, 2025

View reviewed changes

HenrZu and others added 2 commits May 21, 2025 08:27

Apply suggestions from code review

6562ec3

Co-authored-by: annawendler <[email protected]>

add doc for function is_vaccination_data_available

5e2aff1

check if data is partially avail and log info

f3860b6

HenrZu requested a review from annawendler May 21, 2025 11:58

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