1075 Let persons die from hospital (non ICU) in the ABM

[khoanguyen-dev]

Changes and Information

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

• Add the possibility for a person to go from InfectedCritical to Dead in Infection.
• Add a parameter SevereToDead and put similar inputs as CriticalToDead.
• Add a relevant test in test_abm_model.

If need be, add additional information and what the reviewer should look out for in particular:

• See draw_infection_course_forward() and draw_infection_course_backward() in infection.cpp
• See parameter SevereToDead in parameters.h, abm.cpp and abm_braunschweig.cpp
• See TEST(TestModel, personCanDieInHospital) in test_abm_model.cpp

Merge Request - Guideline Checklist

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Checks by code author

• Every addressed issue is linked (use the "Closes #ISSUE" keyword below)

• New code adheres to coding guidelines

• No large data files have been added (files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)

• Tests are added for new functionality and a local test run was successful (with and without OpenMP)

• Appropriate documentation for new functionality has been added (Doxygen in the code and Markdown files if necessary)

• Proper attention to licenses, especially no new third-party software with conflicting license has been added

• (For ABM development) Checked benchmark results and ran and posted a local test above from before and after development to ensure performance is monitored.

• Branch Main:

Run on (8 X 24.0805 MHz CPU s)
CPU Caches:
L1 Data 64 KiB (x8)
L1 Instruction 128 KiB (x8)
L2 Unified 4096 KiB (x2)
Load Average: 4.99, 5.66, 5.30

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Benchmark Time CPU Iterations

abm_benchmark/abm_benchmark_50k 1377 ms 1359 ms 1
abm_benchmark/abm_benchmark_100k 2748 ms 2721 ms 1
abm_benchmark/abm_benchmark_200k 5580 ms 5519 ms 1

• New branch:

Run on (8 X 24.0875 MHz CPU s)
CPU Caches:
L1 Data 64 KiB (x8)
L1 Instruction 128 KiB (x8)
L2 Unified 4096 KiB (x2)
Load Average: 4.66, 4.20, 4.72

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Benchmark Time CPU Iterations

abm_benchmark/abm_benchmark_50k 1330 ms 1324 ms 1
abm_benchmark/abm_benchmark_100k 3187 ms 2794 ms 1
abm_benchmark/abm_benchmark_200k 5882 ms 5484 ms 1

Checks by code reviewer(s)

• Corresponding issue(s) is/are linked and addressed
• Code is clean of development artifacts (no deactivated or commented code lines, no debugging printouts, etc.)
• Appropriate unit tests have been added, CI passes, code coverage and performance is acceptable (did not decrease)
• No large data files added in the whole history of commits(files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)
• On merge, add 2-5 lines with the changes (main added features, changed items, or corrected bugs) to the merge-commit-message. This can be taken from the briefly-list-the-changes above (best case) or the separate commit messages (worst case).

Closes #1075

[codecov]

Codecov Report

Attention: Patch coverage is 83.33333% with 3 lines in your changes missing coverage. Please review.

Project coverage is 96.96%. Comparing base (3a06d82) to head (1b97796).

Files with missing lines	Patch %	Lines
cpp/models/abm/parameters.h	62.50%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1100      +/-   ##
==========================================
- Coverage   96.98%   96.96%   -0.03%     
==========================================
  Files         142      142              
  Lines       11874    11889      +15     
==========================================
+ Hits        11516    11528      +12     
- Misses        358      361       +3     

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[DavidKerkmann]

Thank you, not much to add, only a couple of suggestions.

[DavidKerkmann]

To improve the codeline coverage, you could add a test where the other option in draw_backwards is checked.

[reneSchm]

Then this should be called Exactly(n_persons * 3) times. Can you test and add this (or change the description)?

[DavidKerkmann]

It is called more often than that: 5 times in drawing the viral load, 1 time per person in the infection draw_backwards, so that the persons came from Critical to Dead, four times in each person for the random_workgroups etc. and maybe more times in the evolve functions. Perhaps we can change the mocking to only affect calls in the infection draw_backwards? That would also help at other places.
There are also other instances in this test file one could change it. Not really part of this issue, but what do you think we should do? This seems to be part of #1067 .

[reneSchm]

Perhaps we can change the mocking to only affect calls in the infection draw_backwards?

That is quite difficult to do, it would probably be easier (and a cleaner solution) to write the test such that only draw_backwards uses RNG in the first place.

This seems to be part of 1067 .

I am fine with adding the names of the other tests (with the necessary context) to that issue. We do not need to fix everything here, but at least we have to write down what needs fixing.