Code

Costing Module#1279

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Commits on Feb 20, 2024

• create example scenario for costing script

  

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• Merge remote-tracking branch 'origin/master' into sakshi/costing

  

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• update example scenario

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• update example scenario

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• reduce scenario size

  

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• add costing script

  

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Commits on Feb 21, 2024

• Update HR costing

  

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Commits on Feb 22, 2024

• add resource file

  

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Commits on Feb 28, 2024

• Merge remote-tracking branch 'origin/master' into sakshi/costing

  

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• move costing resourcefile to costing folder

  

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• differentiate between financial and economic costs

  

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• account for scaling factor

  

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• compare with real budget data

  

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• Revert "account for scaling factor"

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• update economic cost calculation

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Commits on Mar 5, 2024

• scaling factor is not needed

  

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Commits on Mar 7, 2024

• update dataframe names + add description for easier readability

  

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• first stab at calculating consumables costs

  

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Commits on Mar 11, 2024

• add financial cost of consumables

  

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• update scenario for azure run

  

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• update scenario for azure run

  

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• add consumable scenario

  

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Commits on Mar 13, 2024

• update HR financial cost

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• update HR economic cost

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• update consumable cost calculation

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• add latest version of costing resource file

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• add latest version of costing resource file

  

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Commits on Mar 24, 2024

• add latest version of costing resource file

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• update Gentamycin (units)

  

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Commits on Mar 25, 2024

• update item quantities for HIV prep and infant prep

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Commits on Mar 26, 2024

• update 1g to 1mg for Albendazole (Item code 52)

  

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• update units for gloves from 1 glove to "1 pair of gloves"

  

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Commits on Mar 27, 2024

• update item quantities for TB drugs

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• add conditions for each IPT recommendation

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Commits on Mar 28, 2024

• add prices for ARVs

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• add Isoniazid/Rifapentine to ResourceFile_Consumables_Items_and_Packages.csv

  

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Commits on Apr 3, 2024

• add Isoniazid/Rifapentine to all relevant RFs

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Commits on Apr 4, 2024

• Merge remote-tracking branch 'origin/master' into sakshi/costing

  

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• Update costing file

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Commits on Apr 5, 2024

• Update to the functionality for requesting consumables across the MNH modules to allow for clearer requesting of units of consumables for costing (correct number of units not yet implemented for al…

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• fixes to failing tests

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• linting

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• linting

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• Update cost estimation method and net inflow estimation

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Commits on Apr 10, 2024

• change cotrimoxazole units to mg

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• Merge branch 'consumables/editing_units_required' into consumables/editing_units_required_hiv

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• merge in updated unit costs

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• create framework for costing equipment

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Commits on Apr 11, 2024

• added dosage for amitriptyline antidepressant treatment

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• added dosage for epilepsy treatment

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• fix error in postnatal_supervisor.py leading to failing test

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• units added for care_of_women_during_pregnancy.py

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• units added for care_of_women_during_pregnancy.py

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• units added for labour.py

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• fix failing test. initial doses for newborn outcomes/postnatal supervisor

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Commits on Apr 17, 2024

• fix failing test. initial doses for newborn outcomes/postnatal supervisor

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Commits on Apr 18, 2024

• Merge remote-tracking branch 'origin/consumables/editing_units_required_hiv' into consumables/editing_units_required

  

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• delete temporary ~ file created

  

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• update units of safety box to "1 disposed syringe (100 syringes per box)"

  

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Commits on Apr 22, 2024

• Merge remote-tracking branch 'origin/master' into sakshi/costing

  

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Commits on Apr 23, 2024

• add table describing costing method to RF

  

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Commits on Apr 26, 2024

• update cost data for HR

  

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• minor updates to make script run

  

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Commits on May 3, 2024

• update HR costing method and RF

  

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Commits on May 6, 2024

• add HR costs other than salary

  

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Commits on May 7, 2024

• update calculation and extraction of consumable costs

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• update cost validation method

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• minor update for validation code

  

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• temporarily add large consumable availability file before moving it to dropbox

  

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Commits on May 11, 2024

• update consumable costing

  

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• update costing method intro in the RF

  

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Commits on May 14, 2024

• adapt use of do_scaling to behave as user expects.

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• add new pre-service training unit costs

  

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• Merge remote-tracking branch 'origin/hallett_update_use_of_scaling_factor' into sakshi/costing

  

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• fix failing test. initial doses for newborn outcomes/postnatal supervisor

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• fixed error in labour. COPD consumable unites

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• remove consumable packages from diarrhoea.py

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• diarrhoea.py consumable units

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Commits on May 15, 2024

• cmd.py consumable units

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• rti.py consumable units

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Commits on May 16, 2024

• Merge remote-tracking branch 'origin/master' into sakshi/costing

  

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• Merge branch 'refs/heads/master' into consumables/editing_units_required

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Commits on May 17, 2024

• alri.py consumable units plus fixed error in diarrhoea.py

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Commits on May 20, 2024

• drop level = 5 staff from the calculation of health worker salaries

  

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• co: get item codes of consumables from item names and define number of units per case in the module (using new chosen units)

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Commits on May 21, 2024

• Merge remote-tracking branch 'origin/master' into sakshi/costing

  

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• Add cystoscope, endoscope and prostate specific antigen test

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• Merge remote-tracking branch 'origin/consumables/editing_units_required' into consumables/editing_units_required

  

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Commits on May 22, 2024

• co: alternative consumables chosen by probs

  

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Commits on May 29, 2024

• co: 21 tablets per packet for both types of pills (informed by Emi)

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• co: update TODOs

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• cancer_cons: consumables updated and required units per case defined (as nmbs of chosen units)

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Commits on May 30, 2024

• change cost of contraception consumables

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• Merge remote-tracking branch 'origin/master' into sakshi/costing

  

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• [no ci] cancer_cons: rm outdated TODOs

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• [no ci] co: rm resolved TODOs

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• Merge remote-tracking branch 'origin/consumables/editing_units_required_EvaJ/Contraception' into consumables/editing_units_required

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• co: rm TODOs as opened an issue to resolve them (#1384)

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• update cost of trocar

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• add cancer consumables to ResourceFile_Costing.xlsx

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• include OHT 2016 costs for Biopsy needle and Specimen container

  

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• cancers: missing arguments added

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• add availability data cancer consumables

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• Merge remote-tracking branch 'origin/consumables/editing_units_required' into consumables/editing_units_required

  

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Commits on Jul 18, 2024

• first draft of equipment cost calculation

  

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Commits on Jul 23, 2024

• correct equipment use extraction in order not to mask levels 3,4,5 which don't belong to any district

  

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Commits on Aug 15, 2024

• clean HR costing and add figures

  

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Commits on Aug 21, 2024

• add the cost of item codes 19 and 20

  

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• correct the costs being extracted from OneHealthTool

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Commits on Aug 29, 2024

• update costing of consumables dispensed and add a plot

  

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• add bar plot of the cost of the top 10 consumables

  

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Commits on Aug 31, 2024

• add count of facilities from HHFA to master facility list

  

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• update calculation of the cost of excess stock

  

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Commits on Sep 3, 2024

• minor changes to extract correct cost values into scenario_cost.csv

  

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Commits on Oct 7, 2024

• Update HR costs in account for multiple draws and runs

  

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Commits on Oct 10, 2024

• update consumables costing to allow for multiple runs and draws

  

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• Update pre-service training costs in the costing RF + add RM R7 data

  

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Commits on Oct 11, 2024

• Update pre-service and in-service training cost calculation

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Commits on Oct 14, 2024

• Update equipment cost calculation to account for each draw and run

  

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• Add stacked bar plot

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Commits on Oct 15, 2024

• Add ROI and maximum ability to pay calculation and plots

  

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• rename cost_of_excess_consumables_stocked

  

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Commits on Oct 16, 2024

• update the cost of item_code 20 "Suture, catgut, chromic, 0, 150 cm" - the CMST price needed to be divided by 12

  

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• Update plots

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Commits on Oct 17, 2024

• fix line plot so that it does not change the scenario_cost

  

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• create calibration data for consumables

  

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Commits on Oct 18, 2024

• update the unit cost of 'chlorhexidine', 'vacuum, obstetric' and ' Suture, catgut, chromic, 0, 150 cm'

  

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Commits on Oct 20, 2024

• add cost of item 188

  

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• fix equipment costs + calibration_data for consumables, HR and equipment

  

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• calibration plot (work in progress)

  

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Commits on Oct 21, 2024

• update ARV costs based on TDF/3TC/DTG regimen (previously ABC/3TC/DTG)

  

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• update calibration plots

  

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• correct in-service training costs

  

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• replace calibration scatter plots with dot plots

  

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• add cost of vitamin b-12

  

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• use life span to calculate equipment replacement costs

  

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• update the unit_cost of IRS

  

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Commits on Oct 22, 2024

• add costs of IRS and bednets

  

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• stylistic updates

  

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• update staff count estimation - use healthsystem.summary logger

  

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Commits on Oct 23, 2024

• update hr and consumable costs to be calculated by run.

  

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Commits on Oct 24, 2024

• update all costs to be in the same format and add two levels of disaggregation to the scenario costs - 'Facility_Level' & groups (such as consumable name) corresponding to the cost_category

  

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• make cost estimation a function

  

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Commits on Oct 28, 2024

• update the calculation of HR costs

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• rename script

  

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Commits on Oct 30, 2024

• move cost validation script out from main cost_estimation script

  

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• add supply chain costs

  

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• move scenario specific costing to a new script

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Commits on Oct 31, 2024

• update the unit cost of O2, blood and IRS to include supply chain costs

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• update function to produce stacked bar chart summaries of cost

  

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Commits on Nov 1, 2024

• clean figure name and title for stacked bar charts

  

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• clean line plots of trend in cost

  

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• update line plot to allow for disaggregation

  

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• update the order of the legend

  

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• add condition so that disaggregation is only possible if one draw is plotted.

  

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  committed
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• update the calculation of max_ability_to_pay_for_implementation

  

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Commits on Nov 4, 2024

• update the plots for ROI and maximum ability to pay

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• add function to summarize costs

  

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• Move ROI plot to main cost_estimation script

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• add other cost plot to GF analysis

  

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Commits on Nov 5, 2024

• wrap the x-tick labels in the stacked bar plots

  

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• correct supply chain costs

  

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• correct supply chain costs

  

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  7900a8f

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Commits on Nov 6, 2024

• manual fix for depo and oxygen costs

  

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• Allow for x tick labels to be taken from a dictionary in stacked bar plots

  

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• update stacked bar plots to plot scenario names as x tick labels

  

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• create a function to get_monetary_value_of_incremental_health

  

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• create a function to discount costs

  

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  740a669

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• update roi plots to account for negative increment costs or cost savings

  

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• add VSL version of ROI

  

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• remove gap between bar plots

  

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Commits on Nov 7, 2024

• get all scripts running as expected

  

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• update chosen_cet to one from Lomas et al, 2023

  

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• add functionality to plotting more than one ROI curve on one plot

  

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• update xticklabels to letters

  

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Commits on Nov 10, 2024

• update xticklabels to letters

  

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  95ad850

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• add figures for GF report

  

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• Update ylim on ROI plots

  

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Commits on Nov 11, 2024

• add global fund ROI figure

  

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Commits on Nov 19, 2024

• update ROI figure title

  

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• update consumables cost from 'available' to 'used'

  

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  6675886

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• new analysis scripts for GF and FCDO analysis

  

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  123a4f9

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• remove unnecessary packages

  

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  2694cf8

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• add description

  

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  8747a65

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• update discounting code to overcome pandas warning

  

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  4838ee2

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• update the cost of IRS and bednets

  

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  6ecb422

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• update dict for figures

  

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  856bd34

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• update y_lim options for roi plot

  

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• add vertical lines at 0, 1b, 3b in combined ROI plot

  

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  2d4b887

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• make vertical lines in ROI plots flexible

  

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  2b2b4d9

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Commits on Nov 20, 2024

• add a way to estimate projected health spending and include it in ROI plots in the X-tick labels

  

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  2f1e036

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• add health spending projections assumptions

  

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  4593d30

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• add projected health spending to all xticklabels in ROI plots

  

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• add proportion of health spend as data labels on bar plots

  

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Commits on Nov 21, 2024

• change output folder for cost_validation

  

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  472f9d7

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• get consumable names from a different RF

  

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  de06a81

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• merge in changes from master

  

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  584eb9a

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• discount_rate in the estimate_cost function used incorrectly

  

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  862a092

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• minor fixes to plots

  

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  43f50db

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• update discounting function

  

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  7d209a1

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• discount malaria costs

  

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  6f2c5ea

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Commits on Nov 25, 2024

• update stacked bar plot legend position and ylim

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• add draft facility operating costs

  

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  6490726

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Commits on Nov 26, 2024

• allow ROI plots with set colours for each draw

  

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  ceb0ccb

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• update RF to apply historical scaling to HR

  

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  6937153

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• update costing scenarios - real world and perfect health system

  

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  417bc58

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• convert facility operations cots to annual costs

  

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  74b42fb

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• pre-define color pallettes for cost categories

  

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  0a42b72

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• edit figure name

  

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  f8a70f2

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• add draft script to generate outputs for costing overview paper

  

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  60fd3d0

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• merge in changes from master - consumables and HR logging

  

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  63f748b

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• merge in changes from master - scenario

  

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• merge in changes from master - util

  

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  c5967c8

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Commits on Nov 29, 2024

• update the categorisation of blood and oxygen to 'medical consumables' from 'other'

  

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  8e620b9

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• add treemap

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  12e605e

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• update treemap saved figure name

  

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  5644b97

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Commits on Dec 2, 2024

• update treemap to fix the colourmap for consumables and adjust fontsize

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  a98d6ec

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• fix outputfile path input

  

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  08dd2da

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• correct facility operation cost estimation - remove district disaggregation

  

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  90c2138

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• validate facility operation costs

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  377d4ca

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• updates for facility operating costs validation

  

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  27c5a5c

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Commits on Dec 4, 2024

• disaggregate Rm consumables costs

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  67bc720

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• minor fixes to calibration data

  

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  da548b7

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• change the cost of oxygen back from OHT 2016 cost

  

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  a2cc253

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Commits on Dec 9, 2024

• update the cost of disposable male circumcision kit to UNICEF catalogue prices

  

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  8f80a70

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• update tables to include all 4 scenarios

  

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  83e5857

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• add plot for inflow to outflow ratio

  

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  8f9e443

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Commits on Dec 10, 2024

• extract values for manuscript text

  

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  d6a7b0e

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Commits on Dec 13, 2024

• update facility operating unit costs based on further cleaning of the data

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Commits on Dec 15, 2024

• update stacked bar plot to add labels and error bars around the total value

  

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  cfde29c

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Commits on Jan 14, 2025

• update the cost of family planning commodities based on UNFPA prices

  

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  committed
  3f1bc7b

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• update the cost of vitamin A and K based on UNFPA prices

  

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  committed
  917b793

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• minor edits to consumable names to ensure that the names match with RF_Items_and_Packages

  

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  committed
  434a1be

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• minor edits to consumable names to ensure that the names match with RF_Items_and_Packages - sutures

  

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  027bfbf

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Commits on Jan 16, 2025

• improve look of calibration figures

  

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  378917e

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• update facility operation unit costs

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Commits on Jan 17, 2025

• Make adjustments to calibration RM data -

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• Adjust font size in stacked bar chart

  

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  392d4c2

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• Change time from 17 years to 8 years

  

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  e3b5dc3

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• update colour map for consumable treemap

  

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  8614156

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Commits on Jan 20, 2025

• add result for main text on HIV testing consumables cost across scenarios

  

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  9b94315

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• extract cleaned calibration table for appendix

  

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  99b29c5

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Commits on Jan 21, 2025

• edits to manuscript text extract

  

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  committed
  a57d97f

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Commits on Jan 22, 2025

• stacked bar - adjustments + only show CI > 0

  

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  6659f84

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• add temporary figure for lomas et al discount rates

  

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  21a6b61

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Commits on Jan 27, 2025

• clean consumables lists for calibration

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  b92e56f

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