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

Please check our git workflow. Use the draft feature if the Pull Request is not yet ready to review.

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

---

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

---

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

All modified and coverable lines are covered by tests ✅

Project coverage is 96.97%. Comparing base (339768e) to head (a338810).
Report is 5 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1100      +/-   ##
==========================================
- Coverage   96.98%   96.97%   -0.02%     
==========================================
  Files         148      148              
  Lines       13783    13798      +15     
==========================================
+ Hits        13368    13381      +13     
- Misses        415      417       +2     

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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]

Looks good, this has some nice improvements to documentation and testing.