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Updates to ROI analysis #1711

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Updates to ROI analysis #1711

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@sakshimohan sakshimohan commented Sep 26, 2025 •
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This PR updates the scripts abd RF used to produce the results for the following papers -

  1. Estimating System-Wide Healthcare Costs Using a Health System Model: Application to the Thanzi La Onse Model of Malawi
  2. System-Wide Investments Generate Health and Enhance HIV, TB and Malaria Control in Malawi

@sakshimohan
Changes to accommodate revised scenarios
fe02734 
- Note that Xpert costs no longer need to be estimated separately.
@sakshimohan sakshimohan marked this pull request as ready for review September 26, 2025 11:21
@sakshimohan sakshimohan marked this pull request as draft September 26, 2025 11:21
@sakshimohan
first take - Frontier plot
ce1a216
@sakshimohan
corrections to Scenario dictionary
1a502d0
@sakshimohan
improve legend positioning in Cost effectiveness plane plots
a05d982
@sakshimohan
remove horizontal lines from ROI plots and formatting changes to CEA …
2a467dc 
…Plane
@sakshimohan
remove horizontal lines from ROI plots and formatting changes to CEA …
39bf753 
…Plane

+ Add ROI bar plots at two implementation cost assumptions
@sakshimohan
move all the functions up
72ae25b 
+ fix calculation of roi at upper bound ASC
+ formatting fixes to plots
@sakshimohan
update the order in which scenarios appear in extracted csvs
603d0be
@sakshimohan
remove superfluous imports
b175cb6
@sakshimohan
new results folder
766a452
@sakshimohan
Add consumables plot + change title of ROI plots
94c8ae9
@sakshimohan
formatting edits to consumables plot
54b818a
@sakshimohan
fix issues with negative costs/health impact when estimating ICERs an…
60c6523 
…d ROIs
@sakshimohan
edit roi bar plots for inset figures
d9b2560
@sakshimohan
update scenarios and results folder for latest outputs
d232355
@sakshimohan
fix treemap plot - previously summed across the three stats
e5c68ab
@sakshimohan
update results extracts
4bfe316
@sakshimohan
update results folder for costing_validation
09bbac6
@sakshimohan
add per capita estimates
72a4f3e
@sakshimohan
add per capita estimates
7665f3a
@sakshimohan
change input_cost central measure to median
4e36b92
@sakshimohan
generate heatmap plots of consumable availability
d205840 
(Note that the RF should be taken from  branch - tara/gff_hss_and_htm_scale_up
@sakshimohan
- update the calculation of ICERs to be based on summary stats rather…
c2d855e 
… than runs
@sakshimohan
add frontier in the main CEA plot
920d7c0
@sakshimohan
update costing scripts to accept latest scenario runs.
cdf9466
@sakshimohan
add the estimate of HSI counts and update the statements on HIV consu…
1095943 
…mable costs.
@sakshimohan
Add CSB++ to the list of nutritional consumables.
68f106d
@sakshimohan
Update the cost of SAM medicines and scale down the cost of F-75 ther…
adb99c9 
…apeutic milk
@sakshimohan sakshimohan requested review from tbhallett and removed request for tbhallett December 19, 2025 16:49
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sakshimohan commented Dec 19, 2025

Will request review once the manuscript has been accepted in its current form

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