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Analysis of expanding HCW by cadre#1415

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BinglingICL wants to merge 248 commits intomasterUCL/TLOmodel:masterfrom bs/expand_hcwUCL/TLOmodel:bs/expand_hcwCopy head branch name to clipboard

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Commits

Commits on Jul 5, 2024

• try to add one scenario of expanding hcw

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• try to add the scenario script

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• todo

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Commits on Jul 6, 2024

• input scenario data for increasing Clinical and Pharmacy cadres

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• input scenario data for increasing Clinical and Pharmacy cadres

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• update the scenario script

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Commits on Jul 7, 2024

• recover the 'custom' sheet in the resource file to fix test failure

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• update the scenario file

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• update comments

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Commits on Jul 10, 2024

• update baseline scenario

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• Reduce the running period to 2010-2030

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Commits on Jul 11, 2024

• try create scenarios given a budget

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Commits on Jul 12, 2024

• update the selection of scenarios

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• rename file

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• reduce individual increase to 4 options per cadre

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• reduce individual increase to 3 options per cadre

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Commits on Jul 15, 2024

• try increasing the individual increase of each cadre into 6 options

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• update todo

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Commits on Jul 16, 2024

• try increasing the individual increase of each cadre into 11 options

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Commits on Jul 17, 2024

• calculate minute salary per cadre per level

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• create parameters for the HR expansion function

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• design steps for the HR expansion function

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• update steps

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• add todo

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Commits on Jul 18, 2024

• create hr minute salary data

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• write the hr expansion function

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• update the minute salary file

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• save the minute salary data

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Commits on Aug 5, 2024

• calculate the current cost distribution of the four cadres

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• create the resource file for hr expansion scenarios base on fractions of extra budget

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• update resource file

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• update scenario file

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• todo in test_healthsystem

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• Merge branch 'refs/heads/master' into bs/expand_hcw

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• clean the data preparation file

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• fix checks failure

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• fix checks failure

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• fix checks failure

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• fix checks failure

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• renaming the scenario file

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• fix failing tests

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Commits on Aug 6, 2024

• creat the test of the hr expansion function

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Commits on Aug 12, 2024

• calculate scale up factor outside healthsystem module

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Commits on Aug 13, 2024

• local run that takes 12 hours

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• save and read pickle file

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• create logger for hr scale up factor

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• Revert "local run that takes 12 hours"

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Commits on Aug 14, 2024

• update the scenario script

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Commits on Aug 16, 2024

• a run for only two scenarios

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Commits on Aug 19, 2024

• scale to effective capabilities

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• rename file

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• rename long run class in scenario file

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• update test

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Commits on Aug 20, 2024

• initiate the analysis script - learn from Tim's branch 1414

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• extract more results

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• initial plots and todo

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• change to 10 runs per draw

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• fix failing checks

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Commits on Aug 21, 2024

• plot dalys by cause

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• get comparison results

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• plot comparison results

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Commits on Aug 22, 2024

• update logger format of scale up factors

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• check if scale to effective capabilities = True will change 2019 capabilities

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• Revert "update logger format of scale up factors"

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• get hr scale up factors

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• get current hr count by cadre

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• get hr salary and update scale up factors

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• get extra staff and extra cost

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Commits on Aug 23, 2024

• mannual calculation of total cost and total staff counts for each year and each scenario

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• calculate total cost and staff counts by the end of target period

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Commits on Aug 27, 2024

• Calculate and plot ROI and CE

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• fix failing checks and plot deaths averted

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• add todo

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• prepare scenarios of fractions that reflect current cost distribution among two/three/four cadres

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• instead of save and reload extra budget fractions data, try directly import the results from a script

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• rename file

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• update todo list

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• update todo list

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• temporarily fix param_names to be consistent with latest scenario run output, so that the analysis can run

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• delete unnecessary file

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• fix failed checks

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Commits on Aug 28, 2024

• name logger elements consistently

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• update todo

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• update plot name

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• update todo

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• plot numbers of staff and budget

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Commits on Aug 29, 2024

• update todo

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• update todo

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• update todo

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Commits on Sep 3, 2024

• turn up scale to effective capabilities

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Commits on Sep 4, 2024

• update the preparation file to also expand all other cadres

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Commits on Sep 5, 2024

• update the function to expand officer type

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• update the logger

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• update test

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• update scenario run settings

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• change data type to fix json error

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• update logger

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• scale down minute salary when scale up to effective capabilities

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• update logger

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• update scenario run file

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• Merge remote-tracking branch 'refs/remotes/origin/master' into bs/expand_hcw

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Commits on Sep 6, 2024

• add comments in test

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• submit a run with 3 draws

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Commits on Sep 7, 2024

• assert to make sure the input the officer types match the defined

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• test minute salary scale down

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Commits on Sep 11, 2024

• add comment on creating alternative scenarios

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Commits on Sep 12, 2024

• temporary update plots for 3 scenarios

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• distribute extra budget for Other group matching their cost distribution

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• Merge branch 'refs/heads/master' into bs/expand_hcw

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• submit a run of all 33 scenarios

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• fix checks failure

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Commits on Sep 17, 2024

• plot extra staff by cadre

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Commits on Sep 18, 2024

• plot extra cost by cadre

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Commits on Sep 20, 2024

• initial plots for all scenarios

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• initial plots for all scenarios

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Commits on Sep 23, 2024

• update comments

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• fix failing checks

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• add scenario settings with historical scaling from 2019 to 2024 and expansion by cadre from 2025 to 2030 - todo: might need update scenarios of extra budget allocation and HRH cost growth rate

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Commits on Sep 24, 2024

• annotate bar plot for DALYs averted

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Commits on Sep 25, 2024

• plot for treatment counts

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Commits on Sep 26, 2024

• update scenario colors

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• plot yearly dalys and staff

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• adjust figsize

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• reverse legend order

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• minor ajdust

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Commits on Oct 2, 2024

• update scenario names

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• try plot 3D plots using 4D data

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Commits on Oct 4, 2024

• update the 3D plot

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• try multiple linear regression

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Commits on Oct 7, 2024

• try extract more results and plot to understand the results

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• anova analysis and more plot

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Commits on Oct 9, 2024

• plot never ran appts and hcw time gap/needed to run those appts

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Commits on Oct 10, 2024

• update data prepare file

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• plot more and delete some

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Commits on Oct 11, 2024

• plot more never ran appts results

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Commits on Oct 15, 2024

• check summary logger Capacity

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Commits on Oct 16, 2024

• plot never ran appts info

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• minor formatting

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• extract fraction of hcw time used

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Commits on Oct 17, 2024

• plot fraction of hcw time used

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Commits on Oct 19, 2024

• extract and plot results of hcw time by cadre and treatment

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Commits on Oct 20, 2024

• minor update

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• plot time used increased of C + P scenario

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Commits on Oct 21, 2024

• more plots of time used increased of C + P scenario

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• more plots

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Commits on Oct 22, 2024

• comment results and plots, which may be less relevant

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• reformat

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• add todo for new loggers

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• Merge remote-tracking branch 'refs/remotes/origin/master' into bs/expand_hcw

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• fix failing checks

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• prepare the "better scenario" indicated by never ran services cost gap

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• undo the changes for historical scaling

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• to test the "best" scenario

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• fix series have no columns

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Commits on Oct 23, 2024

• fix the issue of running only one scenario

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Commits on Oct 24, 2024

• try add suumary logger of fraction of time used by officer, level and district

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• add fraction of time used by officer, level and district to summary counter

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• try add summary logger of appt num by appt and facility id

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• modify summary logger of appt num by appt and facility id

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• modify summary logger of appt num by appt and facility id

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• a possible issue

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• add summary logger of fraction of time used by officer district

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Commits on Oct 25, 2024

• try fixing error of non-usual facilities

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• add a small comment on rescaling capabilities

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• add todo tasks for RescalingHRCapabilities_ByDistrict

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Commits on Oct 28, 2024

• plots for representative scenarios inc. the gap allocation

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• update comments

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• recover the plot of treatments, service demand, etc.

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• plots against current allocation scenario

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• Revert "plots against current allocation scenario"

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• minor reformat

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Commits on Oct 29, 2024

• calculate time used

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Commits on Oct 30, 2024

• format scenario grouping and coloring

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• format scenario grouping and coloring

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• plot for time info

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Commits on Nov 3, 2024

• plot for CNP permutation scenarios

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Commits on Nov 5, 2024

• log the capabilities

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Commits on Nov 6, 2024

• comment and uncomment some lines

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Commits on Nov 7, 2024

• no need to log the year of scale up in HRH expansion HSI

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• turn on historical scaling for years 2020-2024

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• recover the scaling factors in historical scaling for years 2020-2024

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  117a916

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• fix failing checks

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• fix failing checks

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• update scenario run settings

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Commits on Nov 8, 2024

• update scenario run settings and TBC

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• update param_names

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Commits on Nov 11, 2024

• Merge remote-tracking branch 'refs/remotes/origin/master' into bs/expand_hcw

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• update comment

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Commits on Nov 12, 2024

• format labels

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• update scenario run settings and first run to test historical scaling only

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• Merge remote-tracking branch 'refs/remotes/origin/master' into bs/expand_hcw

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Commits on Nov 14, 2024

• update 3D plot

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Commits on Nov 19, 2024

• correct type

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• update analysis file to run new results

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• update comment of the "gap" strategies

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• Merge remote-tracking branch 'refs/remotes/origin/master' into bs/expand_hcw

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Commits on Nov 21, 2024

• update regression

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• Merge remote-tracking branch 'refs/remotes/origin/master' into bs/expand_hcw

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• set the "gap" allocation strategy for defaul + historical scaling

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• to run the "gap" allocation strategy for defaul + historical scaling

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• fix failing checks

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Commits on Nov 29, 2024

• run 5 more runs for baseline of baseline draws excl. "gap" strategy

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• run for sensitivity analysis - baselines + no expansion - to get gap strategy

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Commits on Dec 2, 2024

• update the preparation file to incorporate historical scaling, which does not change the extra budget fracs

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  2c9f2ed

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• get the expected hrh increase rate

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• get yearly hrh count from logger

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Commits on Dec 6, 2024

• record the gap strategies for main and sensitivity analysis

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• correct typo

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• rerun gap strategy for main analysis as the proportions has changed due to another 5 runs of no expansion

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• run all non-gap strategies for more budget

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• run all non-gap strategies for less budget

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Commits on Dec 11, 2024

• calculate average yearly increase rate per cadre during 2025-2034

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• reduce runs per draw to 5

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• Merge remote-tracking branch 'refs/remotes/origin/master' into bs/expand_hcw

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• run default_cons for sensitivity analysis

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Commits on Dec 12, 2024

• update analysis file to include budget growth rate

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Commits on Dec 14, 2024

• Merge remote-tracking branch 'refs/remotes/origin/master' into bs/expand_hcw

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• run max hs function for sensitivity analysis

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• the 17th decimal of some cadre's minute salary has changed - due the same change to HRH capabilities

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Commits on Dec 20, 2024

• use standard error for CI

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• update analysis script

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Commits on Jan 6, 2025

• try plot 3D-plot on avg. increase rate

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Commits on Jan 9, 2025

• add more info to staff cost 2024

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Commits on Jan 14, 2025

• add in optimal strategies

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• comments on DALYs causes and treatment types grouping

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• prepare the scenario script to run the "optimal" strategy

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• Merge remote-tracking branch 'refs/remotes/origin/master' into bs/expand_hcw

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• fix checks errors

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• fix checks errors

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• run 10 runs for the "optimal" strategy, as all other strategies has 10 runs in the main analysis

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Commits on Jan 22, 2025

• update plots

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Commits on Jan 27, 2025

• prepare sample and predict

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• update plot

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• comment the sample preparation and prediction relevant

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• save results data

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Commits on Jan 28, 2025

• update plot

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Commits on Jan 30, 2025

• update regression model

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Commits on Feb 3, 2025

• update plot

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Commits on Feb 4, 2025

• update regression model tests

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• update plot

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Commits on Feb 7, 2025

• update the preparation file

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• 3D plot for strategy sample

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• Revert "3D plot for strategy sample"

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Commits on Feb 10, 2025

• update preparation script

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Commits on Feb 13, 2025

• temporary change to utils for this analysis only

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• update plot

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• Revert "temporary change to utils for this analysis only"

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• fix check error

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