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Refactor time until death calculations#160

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yiwen-h merged 5 commits intomainfrom
151_153_refactor-time-until-death-calculations
Jan 19, 2026
Merged

Refactor time until death calculations#160
yiwen-h merged 5 commits intomainfrom
151_153_refactor-time-until-death-calculations

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@yiwen-h yiwen-h commented Jan 19, 2026 •
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Closes #151
Closes #153

Have compared model results with validation run prior to code changes and they are exactly the same (with exception of mortality in year sim_duration + 1 - previously we were truncating time to death, now we do not). This is mostly just rearranging things to make them clearer.

For example, in config instead of relying on developers remembering that the first value in the list is the shape and the second value is the scale, we are now very explicit about naming what the values are.

before:

"initialisation": {
    "not_listed": {
        "early": {
            1: [0.926963321, 2127.231053] }}}

after:

"initialisation": {
    "not_listed": {
        "early": {
            1: {"shape": 0.926963321, "scale": 2127.231053},

@yiwen-h yiwen-h requested a review from morganle-48 as a code owner January 19, 2026 15:44
@yiwen-h yiwen-h self-assigned this Jan 19, 2026
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codecov bot commented Jan 19, 2026 •
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Codecov Report

❌ Patch coverage is 87.09677% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.81%. Comparing base (6f1ac91) to head (201e46b).
⚠️ Report is 6 commits behind head on main.

Files with missing lines Patch % Lines
renal_capacity_model/process_outputs.py 0.00% 2 Missing ⚠️
renal_capacity_model/main.py 0.00% 1 Missing ⚠️
renal_capacity_model/model.py 96.00% 0 Missing and 1 partial ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #160      +/-   ##
==========================================
- Coverage   85.89%   85.81%   -0.09%     
==========================================
  Files           9        9              
  Lines         695      691       -4     
  Branches       79       78       -1     
==========================================
- Hits          597      593       -4     
  Misses         89       89              
  Partials        9        9

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morganle-48
morganle-48 reviewed Jan 19, 2026
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@yiwen-h yiwen-h merged commit 25e28ed into main Jan 19, 2026
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@yiwen-h yiwen-h deleted the 151_153_refactor-time-until-death-calculations branch January 19, 2026 16:30
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Do not use min() to truncate time_to_death Create reusable function for calculation of time_until_death

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