Updates to Costing and ROI analysis

[sakshimohan]

This PR updates the scripts and 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 (ACCEPTED - Applied Health Economics and Health Policy - January 2026)
2. System-Wide Investments Generate Health and Enhance HIV, TB and Malaria Control in Malawi (REVISION Submitted - Nature Communications - December 2025)

[sakshimohan]

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

[sakshimohan]

Hi @tbhallett @tdm32 - Could we merge this PR into master ahead of the publication of the costing paper? The changes are only to analysis scripts -

1. The scripts under src/scripts/costing which i. provide functions for cost analyses, ii. run the analyses for the costing manuscript
2. src/scripts/costing/manuscript_analysis/scenario_full_system_cost.py - Scenario script for the costing paper
3. roi_analysis_horizontal_vs_vertical.py - analysis script for the revised ROI paper with Nature Comms
4. resources/costing/ResourceFile_Costing_Consumables.csv - Minor updates to the costing RF for consumables.

[tdm32]

Hi @tbhallett @tdm32 - Could we merge this PR into master ahead of the publication of the costing paper? The changes are only to analysis scripts -

1. The scripts under src/scripts/costing which i. provide functions for cost analyses, ii. run the analyses for the costing manuscript
2. src/scripts/costing/manuscript_analysis/scenario_full_system_cost.py - Scenario script for the costing paper
3. roi_analysis_horizontal_vs_vertical.py - analysis script for the revised ROI paper with Nature Comms
4. resources/costing/ResourceFile_Costing_Consumables.csv - Minor updates to the costing RF for consumables.

Hi @sakshimohan , I can review this next week. You can add a tag to your working branch with all of these up-to-date scripts and add that to the paper as master will always move on so you would probably want to link to the exact version used to produce your results.

[sakshimohan]

Hi @tbhallett @tdm32 - Could we merge this PR into master ahead of the publication of the costing paper? The changes are only to analysis scripts -

1. The scripts under src/scripts/costing which i. provide functions for cost analyses, ii. run the analyses for the costing manuscript
2. src/scripts/costing/manuscript_analysis/scenario_full_system_cost.py - Scenario script for the costing paper
3. roi_analysis_horizontal_vs_vertical.py - analysis script for the revised ROI paper with Nature Comms
4. resources/costing/ResourceFile_Costing_Consumables.csv - Minor updates to the costing RF for consumables.

Hi @sakshimohan , I can review this next week. You can add a tag to your working branch with all of these up-to-date scripts and add that to the paper as master will always move on so you would probably want to link to the exact version used to produce your results.

Thanks, @tdm32. That makes sense. I'll follow up with Asif on how to add a tag.

[sakshimohan]

Hi @tdm32. I've now submitted the final version of the costing manuscript to AHEHP with the Zenodo link for the final costing updates. When you get a chance, could you please approve this PR? I imagine the journal will still take a few weeks to process/edit the final version, so no immediate rush.