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Initial Version of Scenario definition and other associated amendments needed for the "Horizontal vs Vertical"-type Analysis, #1288

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Initial Version of Scenario definition and other associated amendments needed for the "Horizontal vs Vertical"-type Analysis, #1288

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@tbhallett tbhallett commented Mar 4, 2024 •
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Developments to enable next generation of analyses, wherein we modify sets of parameters representing "Health System Strengthening" interventions and "Expansion of Vertical Programs". This is needed for the FCDO/GF analysis and planned ROI of HSS.

Includes giving the ScenarioSwitcher the functionality to make changes midway through the simulation.

@tbhallett
refactoring:
5fb9301 
* put the helper function for switching scenario into same file a ScenarioSwitcher class
* put tests for class and helper function together

(next step will be to rename and mock-up extended functionality)
@tbhallett tbhallett added this to In progress in PR priorities via automation Mar 5, 2024
@tbhallett tbhallett moved this from In progress to Ready for EM review in PR priorities Mar 5, 2024
@tbhallett tbhallett changed the title Development of ScenarioSwitcher Scenario definition and other associated amendments needed for the "Horizontal vs Vertical"-type Analysis Mar 26, 2024
@tbhallett tbhallett mentioned this pull request Apr 3, 2024
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tbhallett commented Apr 3, 2024 •
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Hi @tdm32, @marghe-molaro and @sakshimohan

Here's a first draft of the 'vertical vs horizontal' programs. @marghe-molaro is running in its current form on Azure, which will be a very useful "sanity check" for the health system strengthening interventions. 🤞

job_id = "horizontal_and_vertical_programs-2024-04-03T160928Z"

The main file is scripts/comparison_of_horizontal_and_vertical_programs/scenario_comparison_of_horizontal_and_vertical_programs.py.

@tdm32 -- you'll see some placeholders for putting in the changes for the HIV / TB and Malaria modules. Please could you propose a PR for merging into this branch that would make that work?

We can then run the whole thing again, and mock-up some figures (drawing heavily on the designs for the overview paper).

@tbhallett tbhallett changed the title Scenario definition and other associated amendments needed for the "Horizontal vs Vertical"-type Analysis Initial Version of Scenario definition and other associated amendments needed for the "Horizontal vs Vertical"-type Analysis, Apr 24, 2024
@tbhallett tbhallett marked this pull request as ready for review April 24, 2024 15:14
@tbhallett tbhallett moved this from Ready for EM review to Ready to merge in PR priorities Apr 24, 2024
@tbhallett tbhallett moved this from Ready to merge to Ready for EM review in PR priorities Apr 25, 2024
@tbhallett
restore scenario_comparison_of_horizontal_and_vertical_programs (re…
38cfc52 
…moving comments used to select certain scenarios to be run).
@tbhallett
Merge branch 'refs/heads/master' into hallett/analysis_for_vertical_a…
254613b 
…nd_horizontal_progs

# Conflicts:
#	src/tlo/methods/healthsystem.py
#	src/tlo/methods/scenario_switcher.py
#	tests/test_analysis.py
@tbhallett
first draft of figures
ac01da8
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tbhallett commented May 20, 2024 •
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Initial figures:

Additional_DALYs_Averted_vs_Baseline_2020-2030
Additional_Deaths_Averted_vs_Baseline_2020-2030
All_Scenarios:_DALYs_2020-2030
Deaths_2020-2030

Questions / To-dos

  • Full package has less impact than perfect healthcare seeking alone -- why? It should have at least the same impact, as the full package includes perfect healthcare seeking. Maybe run the package without the impact of increased healthcare seeking.
  • Why is 'perfect clinical practice' having a 'negative' impact on health? Is it due to this being in Mode 2 and it causing a proliferation of appointments that overwhelm the system? [Try it in Mode 1 / Try it with much larger incrrease in HRH]
  • The benefits of increased human resource for health seem small. Are they the same as that found originally by Margherita?
  • Add in equipment scenario.
  • Add in scenario for switch to funded HR scenario
  • Add in switch for consumables vital/essential
  • Add in switch for equipment availability
  • Change the consumables definition in Perfect Availability of Medicines & other Consumables to reflect update consumables scenarios.
  • Add in HIV/TB/Malaria scenarios

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@tbhallett, we have now tracked down the origin of the discrepancy in the two batches of rescaled mode 2 runs (see Issue #1348), down to a merger of master into the branch in this commit d56042f

It would be good to double check whether this could have affected this PR/the results you have shared too.

@tbhallett
Merge branch 'refs/heads/master' into hallett/analysis_for_vertical_a…
a0af398 
…nd_horizontal_progs

# Conflicts:
#	resources/healthsystem/consumables/ResourceFile_Consumables_Item_Designations.csv
#	resources/healthsystem/human_resources/scaling_capabilities/ResourceFile_dynamic_HR_scaling.xlsx
#	src/tlo/methods/consumables.py
#	src/tlo/methods/healthsystem.py
#	tests/test_consumables.py
@tbhallett
update scenario file
9a2f71a
@tbhallett
update scenario file
31758e1
@tbhallett
include "scale_to_effective_capabilities": True
28d7c8c
@tbhallett
linting
0712781
@tbhallett
linting
cb478f1
@tbhallett
reduce number of draws
243690f
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Second run is: horizontal_and_vertical_programs-2024-06-06T214004Z

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@marghe-molaro marghe-molaro marghe-molaro approved these changes

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@tdm32 tdm32

@tbhallett tbhallett

@sakshimohan sakshimohan

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