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Abie enhanced consistent rates#59

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aflaxman wants to merge 55 commits intomainfrom
abie_enhanced_consistent_rates
Draft

Abie enhanced consistent rates#59
aflaxman wants to merge 55 commits intomainfrom
abie_enhanced_consistent_rates

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@aflaxman aflaxman commented Oct 27, 2025

Title: Summary, imperative, start upper case, don't end with a period

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aflaxman and others added 30 commits September 30, 2025 14:55
@aflaxman
Initial commit of moud approach to consistent rates, for adapting to AD
4e84dc0
@aflaxman
Refactor model parameters and update data handling for dementia rates…
1c4808d 
… in consistent rates generation
@aflaxman
Refactor consistent rates module: enhance type hints, improve data ha…
ff4bd7f 
…ndling, and ensure numerical stability in calculations
@aflaxman
Refactor ode_model parameters and update age range in generate_consis…
a87c963 
…tent_rates for improved clarity and accuracy
@aflaxman
tweak key names to be slightly clearer
c7062b6
@aflaxman
code cleanup and run a bit faster for iterative development
35ff3f6
@aflaxman
BUG: square components of ode error to prevent big positive and negat…
5826f18 
…ive errors from balancing out
@aflaxman
remove clipping for size of dementia compartment (D) in ODE
c964b7b
@aflaxman
Reorganize code to make it easier to explain (I hope!)
49f6338
@aflaxman
add stuff to make the consistent rate code more easily usable
4d29b84
@aflaxman
Merge remote-tracking branch 'origin/main' into abie_consistent_rates
f615d88
@aflaxman
ENH: Use consistent rates in sim
8b5187a
@aflaxman
Incorporate consistent rate generation into into make_artifacts tool
7391b97
@aflaxman
pin artifact requirements to allow successful building of consistent …
03fd1a4 
…artifacts
@aflaxman
Merge branch 'main' of github.com:ihmeuw/vivarium_csu_alzheimers into…
2117076 
… abie_consistent_rates
@aflaxman
Better initialization of AD states
3524927 
This Includes a bug fix for the conditional prevalence of AD Dementia
@aflaxman
include data for mixed dementia
a084b78
@aflaxman
include data for dementia severity
c055183
@aflaxman
use mixed dementia and severity splits in consistent model
bf14006 
and clean up code to use data_keys instead of hardcoding artifact keys
@aflaxman
make delta fractions sum to one, add excess mortality to moderate dem…
4e2f0ea 
…entia state
@aflaxman
tweaks and bug fixes suggested by chatgpt
06357c6
@aflaxman
minor tweaks while iterating
d0b96d9
@aflaxman
update model to include severity and mixed dementia
9b17649
@aflaxman
add lost line to make_artifacts
d1b660e
@aflaxman
keep trying, but seems like something is wrong in the mixed
317f6ce
@aflaxman
remove mixed dementia, get pretty good results
83c2372
@aflaxman
add mixed dementia (just for simulants who develop mixed dementia dur…
216b033 
…ing bbbm-ad or mci-ad state
@albrja
Test final run code
1063d30
@albrja
Merge branch 'main' into final_runs
8381562
@albrja
Add config for runs
1937714
aflaxman and others added 16 commits November 1, 2025 18:38
@aflaxman
adding severity-specific emr
fd44bda
@aflaxman
isort, black
1dbff2b
@aflaxman
increase pop_size and tweak mixed_dementia prevalence; maybe the mixe…
5af6f23 
…d prevalence tweak will stop bbbm from dropping a lot in first ten years of sim
@aflaxman
remove mixed dementia initial prevalence
d16c145
@aflaxman
dial down volume of run so that it routinely succeeds
7dcf384
@aflaxman
resolve conflicts in merged fix for bbbm-ad state initialization and …
c579073 
…tweak psim params to make it run reliably
@albrja
Merge branch 'main' into final_runs
166eb47
@albrja
Update config
2824d3b
@aflaxman
make this match final runs
9e3689c
@aflaxman
v1 experiment: smooth first and second differences of h_S_to_BBBM age…
60ca9cc 
… pattern
@aflaxman
add increasing prior
4fe4521
@aflaxman
Remove Mixed Dementia
f3619ee 
I was having some trouble, and I think the incidence-not-hazard is part of it
so I'm stripped out the Mixed Dementia state from the calibration and from the
vivarium model.  If/when I get to add it back in, I must also remember to include
it in the CSMR, which is another piece that is missing currently
@aflaxman
tweaks to better match old vals
7d967ad 
including a major oversight, failing to include p_ad_dementia as a calibration target in the ODE
which I sort of think would be unnecessary, but really seems to make a big difference
@aflaxman
add 40 year olds to ODE calibrations
89f8b40 
black and isort, too
@aflaxman
pretty acceptable results :)
5c496fd
@aflaxman
settings I used to make all the artifacts on 2025-11-16
7f74fc4
@aflaxman aflaxman marked this pull request as ready for review November 18, 2025 17:50
@aflaxman aflaxman marked this pull request as draft November 20, 2025 17:50
@aflaxman aflaxman marked this pull request as ready for review November 20, 2025 17:57
@aflaxman aflaxman marked this pull request as draft January 9, 2026 18:46
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@albrja albrja Awaiting requested review from albrja albrja is a code owner

@hussain-jafari hussain-jafari Awaiting requested review from hussain-jafari hussain-jafari is a code owner

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@aflaxman @albrja

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