Code

Wasting Module#543

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tbhallett wants to merge 234 commits intomasterUCL/TLOmodel:masterfrom hallett/wasting_moduleUCL/TLOmodel:hallett/wasting_moduleCopy head branch name to clipboard

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Commits

Commits on Apr 6, 2022

• add test_wasting.py

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• add wasting.py

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• edit hsi_generic_first_appts.py

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Commits on Oct 5, 2023

• made some changes in wasting to ensure all tests in test_wasting are running without errors. added wasting analysis file to get more understanding of the current outputs before applying some major …

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• Merge branch 'master' into hallett/wasting_module

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Commits on Oct 6, 2023

• getting things running in the current wasting state and generate some outputs

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• not import but important

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Commits on Oct 9, 2023

• Linter Changes

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Commits on Oct 10, 2023

• added more treatment ids to color map

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Commits on Oct 11, 2023

• Updated policies excel and wasting dependencies python files

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Commits on Oct 12, 2023

• module dependencies, cause of death color map, linting

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Commits on Oct 13, 2023

• Merge branch 'master' into hallett/wasting_module

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Commits on Oct 17, 2023

• HSI event name should include module name

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Commits on Oct 20, 2023

• changed some logic, linting, progress individuals to SAM instead of killing them

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• code cleaning

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Commits on Oct 23, 2023

• fixed line error

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Commits on Nov 3, 2023

• added oedema reset to Wasting Natural Recovery

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• Remove progression to severe following treatment failure for MAM.

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Commits on Dec 4, 2023

• re-structuring wasting module, activated HSI events, modified some parameter values in wasting resource file

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• Merge remote-tracking branch 'origin/hallett/wasting_module' into hallett/wasting_module

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Commits on Dec 5, 2023

• added a new sheet as per same file in master

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• Merge branch 'master' into hallett/wasting_module

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• addressing the test membership error

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• update

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• Merge remote-tracking branch 'origin/hallett/wasting_module' into hallett/wasting_module

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• Worked on graphs

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• Wasting Graphs

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• Merge remote-tracking branch 'origin/hallett/wasting_module' into hallett/wasting_module

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Commits on Dec 7, 2023

• remove hard-corded parameters and add them to resource file, reformat graphs, address flake8 79 characters length limit

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• run from simulation

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• Merge remote-tracking branch 'origin/hallett/wasting_module' into hallett/wasting_module

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Commits on Dec 11, 2023

• resolving test health system error, changed values in resource file for plotting

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• correcting imports

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Commits on Dec 19, 2023

• linting

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Commits on Jan 4, 2024

• Merge branch 'master' into hallett/wasting_module

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• removing unnecessary semicolon

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Commits on Jan 8, 2024

• Merge branch 'master' into hallett/wasting_module

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Commits on Jan 29, 2024

• General changes after review 1

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Commits on Jan 31, 2024

• Updated Priority Ranking Policies resource file

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• Stunting Rollback

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• Treatment_ID update

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Commits on Feb 1, 2024

• Update src/tlo/analysis/utils.py

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Commits on Feb 2, 2024

• Added Dalys reported test, Treatment_ID naming and other fixes

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• Merge remote-tracking branch 'origin/hallett/wasting_module' into hallett/wasting_module

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Commits on Feb 5, 2024

• removing unused death parameters and linear model, restructuring linear models and wasting tests

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• Merge branch 'master' into hallett/wasting_module

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• addressing failing tests

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• resolving checks error

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• isort error

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Commits on Feb 6, 2024

• small fixes in wasting analyses, test and main module

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• use "left" not left when assigning inclusive value in linear models

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• remove misleading comment

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Commits on Feb 12, 2024

• Merge branch 'master' into hallett/wasting_module

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Commits on Feb 13, 2024

• addressing eva's comments and suggestions

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• Merge branch 'master' into hallett/wasting_module

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• Merge branch 'master' into hallett/wasting_module

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Commits on Feb 15, 2024

• resolving conflicts

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• Merge branch 'master' into hallett/wasting_module

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• RF_Wasting: CSV instead of XLSX

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• RF_Wasting: comments added

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• wast: parameters re-ordered, comments adjusted

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• wast & test_wast: property renamed un_acute_malnutrition_tx_start_date -> un_am_tx_start_date

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• wast: read parameters from CSV

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• wast: properties descriptions adjusted

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• RF_Wast: note updated

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• wast: minor changes (param moved; comment added)

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• RF_Wast: rename col 'more notes' to 'old values'; avoid multiple rows in a cell

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Commits on Feb 19, 2024

• RF_Wast: added REF to some old values

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• wast: comments adjusted

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• wast: setting properties in the order they are defined

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• wast: TODO

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Commits on Feb 20, 2024

• wast: tidy up the get_prob_severe_wasting_or_odds_wasting fnc; TODO incl.

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• wast: descriptions and comments adjusted

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Commits on Feb 22, 2024

• Updated proportion, prob/odds function_name, rng

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• Merge remote-tracking branch 'origin/hallett/wasting_module' into hallett/wasting_module

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• Updated proportion, prob/odds function_name, rng

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Commits on Feb 26, 2024

• Merge remote-tracking branch 'origin/hallett/wasting_module' into hallett/wasting_module

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Commits on Mar 1, 2024

• Fix prob_odds function_name, rng

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• Merge branch 'master' into hallett/wasting_module

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• Merge remote-tracking branch 'origin/hallett/wasting_module' into hallett/wasting_module

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• wast: fix a bug; rm TODOs

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Commits on Mar 5, 2024

• Standardize progression to sev wasting

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• fixing the bug. return proportion not product

  mnjowe

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• changing all appearance of '115-<125mm' to '[115,125)mm'

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• Merge remote-tracking branch 'origin/hallett/wasting_module' into hallett/wasting_module

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• adding random number generator to linear model

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Commits on Mar 6, 2024

• squeeze single row output

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Commits on Mar 16, 2024

• plotting wasting prevalence by age group and year

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• Merge branch 'master' into hallett/wasting_module

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Commits on Mar 17, 2024

• added footnote, fixed isort error

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Commits on Mar 25, 2024

• RF_Wast, wast: CSV instead of XLSX

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Commits on Jul 19, 2024

• added wasting scenario run file for azure

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Commits on Jul 23, 2024

• Merge branch 'master' into hallett/wasting_module

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• PEP8

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• Merge remote-tracking branch 'origin/master' into hallett/wasting_module

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• Merge branch 'EvaJ/wasting/first_suggestions' into hallett/wasting_module

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Commits on Jul 24, 2024

• RF_Wast, wast: [115,125) -> [115-125) (comma confuses the data as it separates individual columns); wast: minor updates in comments

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• wast: fix the imports of HSIEventScheduler and IndividualProperties

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Commits on Jul 25, 2024

• RF_PriorityRanking_ALLPOLICIES: priorities changed for undernutrition_ in RMNCH, ClinicallyVulnerable, VerticalProgrammes, and CVD as suggested by Margherita

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• test_wast: input params of sim.modules['SymptomManager'].has_what fixed

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Commits on Jul 29, 2024

• wast: duplicated logger setup rm; logger arguments added

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Commits on Jul 30, 2024

• Merge branch 'master' into hallett/wasting_module

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• wast: fix MUAC distribution for moderate wasting; apply choice fnc to get MUAC distribution for each WHZ category

  EvaJanouskova

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• RF_PriorityRanking_ALLPOLICIES: priorities changed for undernutrition in EHP_III, and LCOA_EHP as suggested by Sakshi

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Commits on Jul 31, 2024

• wast: apply fixed to be used on rows

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• test_wast: update checking of scheduled hsi events; outpatient and inpatient care for SAM cases depend on coverage

  EvaJanouskova

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• wast: simplified setting of oedema status

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• wast: returns rm from fnc descriptions if no return, outdated params rm from fnc descriptions

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Commits on Aug 2, 2024

• wast: update the var/fnc names to reflect what they store/do (esp. do not confuse MAM with moderate wasting etc)

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• [no ci] wast: update the par names to reflect what they represent

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• Merge branch 'master' into hallett/wasting_module

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• RF_Wast: update the par names to reflect what they represent

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Commits on Aug 6, 2024

• wast: assert added as stated in comment + minor changes (out of loop calculation of value independent of loop var; fnc description and comments updated)

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• wast & analysis_wast: logging key updated to reflect prevalence props not counts are logged

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• wast & test_wast: MAM/SAM corrected to mod/sev wasting

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• wast & test_wast: DALY calculations corrected

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• wast: minor changes (comments, debug messages adjusted)

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Commits on Aug 8, 2024

• wast: minor changes (params descriptions adjusted)

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Commits on Aug 9, 2024

• wast & RF_wast: probs corrected

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• wast & test_wast: PollingEvent name specified

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• wast: MUAC, oedema, clinical state of acute malnutrition, and complications if SAM updated only when WHZ changed

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Commits on Aug 23, 2024

• wast & test_wast: natural recovery -prepared for future (to improve also severe wasting, not used yet), -clear symptoms moved to clinical_acute_malnutrition_state(), -recovery date only if recovere…

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• wast, RF_Wast & test_wast: treatment -lengths as parameters, -var names updated, -duplicated code of treatments for SAM simplified; event names updated to follow naming convention

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• wast: actual mean for wasting incidence lm corrected

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Commits on Aug 24, 2024

• wast: track incidence only (it is not incidence if they remained non-wasted)

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Commits on Oct 8, 2024

• wast: return wasted always as series (even if 1 bool retuned) when initialise_population

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• Merge remote-tracking branch 'origin/master' into hallett/wasting_module

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• wast: progress/recovery from moderate wasting schedule only for new cases

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• wast: split get_prob_severe_wasting_or_odds_wasting() fnc into two separate fncs

  EvaJanouskova

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• wast: fix wasting_prevalence_props calculations (logged)

  EvaJanouskova

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Commits on Oct 9, 2024

• wast: typo

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• Merge remote-tracking branch 'origin/master' into hallett/wasting_module

  EvaJanouskova

  committed
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• wast & test_wast: fix and simplify calculation of proportion_normalWHZ_with_oedema by calculating prob_normal_whz once when population initiated

  EvaJanouskova

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Commits on Oct 10, 2024

• wast: more descriptive names (consistent with other names)

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Commits on Oct 11, 2024

• analysis_wast: rm note, update axis label

  EvaJanouskova

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• RF_wast: more precise value of proportion_oedema_with_WHZ<-2

  EvaJanouskova

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• scenario_wast: create 2 scenarios incl. wasting - minimal and full_model, keep original scenario

  EvaJanouskova

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• scenario_wast_full|minimal_model: scenarios updated

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• analysis_wast: renamed -> .._with_sim_running

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• analysis_wast: new analysis script analysis without running sim, to analyse outputs from a separate scenario run (scenario_wasting_minimal|full_model)

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• scenarios wast: names udpated in comments

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• scenarios wast: start and end dates corrected

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• scenario_wast_min_model: 1 year sim & 2K pop

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Commits on Oct 14, 2024

• scenario_wast_orig: match modules with minimal_model

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• scenario_wast_orig: add name of scenario to output filename

  EvaJanouskova

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• undernutrion_analyses folder renamed -> stunting_analyses

  EvaJanouskova

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• wast: print rm

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Commits on Oct 15, 2024

• analysis_wast: update the analysis script to analyse sim run from Azure + minor updates (save all figures as png, and save all figures together in one pdf)

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• analysis_wast: PEP 8

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• analysis_wast: save both png and pdf for each figure & all_figures in one pdf (pages of size of figs)

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• analysis_wast: save figs into simulation results folder

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• scenario_wast_full|minimal_model: sim 2010-2030(incl), 20K pop, 10 runs

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  c7c3497

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• analysis_wast: PEP 8

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  ef9cb70

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• scenario_wast_full|minimal_model: up to 2023-01-02 (wasting log after each year finished, on 01-01)

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  065d1f4

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Commits on Oct 17, 2024

• wast: clinical acute malnutrition categories written together

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  5695d74

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• analysis_wast: footnote corrected

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  4601dc6

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• Merge remote-tracking branch 'origin/master' into hallett/wasting_module

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  a7fdda8

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• wast: tidy up

  Show description for c328ddb
  

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• analysis_wast: title corrected

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  3deb9f7

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Commits on Oct 22, 2024

• wast: increase care_seeking_odds_ratio for SAM symptom, so almost everyone with SAM will get the treatment

  EvaJanouskova

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  d463b56

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• wast: follow-up MAM treatment after SAM treatment when recovered to MAM

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  88bc3f0

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• wast: *new MAM, SAM cases start with 'none' treatment (not only wasting cases);

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  5b5d8a2

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Commits on Oct 27, 2024

• wast & test_wast: new HSI_Wasting_GrowthMonitoring; other events renamed

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  d96b53a

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Commits on Oct 28, 2024

• wast: rm duplicated setting of tx_start_date

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  5ae5958

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Commits on Oct 29, 2024

• wast: diagnosis any rnd day within the month; fasten run by excluding well group from seeking care sooner

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  c7adae1

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• wast: priority=2 for HSI_Wasting_GrowthMonitoring

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  164f055

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• wast: comment corrected

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  fa8cf23

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• RF_PriorityRanking_ALLPOLICIES: Undernutrition_GrowthMonitoring added

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  c2028d6

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Commits on Oct 30, 2024

• Merge remote-tracking branch 'origin/master' into hallett/wasting_module

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  e7023be

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• Revert "RF_PriorityRanking_ALLPOLICIES: Undernutrition_GrowthMonitoring added"

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  14a8e11

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• RF_PriorityRanking_ALLPOLICIES: Undernutrition_GrowthMonitoring added; lowest_priority_considered mv to the bottom

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  4f8190c

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• hs: enforce_priority_policy() fnc updated to work for individual & population hsi_event.target

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  17e7f20

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• scenario_wast_full_model|minimal_model|orig: till the end of 2030 no more no less

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  7da7768

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• Revert "hs: enforce_priority_policy() fnc updated to work for individual & population hsi_event.target"

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Commits on Nov 9, 2024

• wast & RF_Wast: used coverage wasn't treatment coverage, hence rm

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  dbcd577

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Commits on Nov 10, 2024

• wast: HSI_Wasting_GrowthMonitoring changed to IndividualScope (incl. TODOs)

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  35acc35

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• Merge remote-tracking branch 'origin/master' into hallett/wasting_module

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  36001f2

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• wast: improved code readability

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  cfa03aa

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• wast & RF_Wast: parameters added and used

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  committed
  d4e9322

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Commits on Nov 12, 2024

• wast: vars names and description updated

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  a1542f3

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Commits on Nov 13, 2024

• scenario_wast_min_model: use simplified_births

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  fb0e8a5

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Commits on Nov 15, 2024

• wast: minor (tidy up)

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  committed
  d36304a

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• RF_Wast & test_wast: parameter names udpated

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  1ea06b4

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• wast: minor (comment updated)

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  277ede2

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• test_wast: minor (superfluous assert rm)

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  committed
  11985b1

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• scenario_wast_min_model: contraception module not needed

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  committed
  e61f1b7

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• equipment: description updated

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  committed
  4baf50a

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• wast: diagnosis code completed

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  e116ac8

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Commits on Dec 3, 2024

• wast & test wast: property un_am_bilateral_oedema renamed to un_am_nutritional_oedema (for consistency with write-up)

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  172725d

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• wast: initial & on birth properties setup (not need to set up dates to pd.NaT)

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  0938207

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• test_wast: correct asserts

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  add465d

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• wast: apply mod wast incidence only if not on tx, and reset recovery date

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  committed
  57458f8

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Commits on Dec 6, 2024

• wast: joining the conditions when the Event should not run into one if statement

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  committed
  8935a5d

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• wast: if on tx, and discharge date scheduled, they shouldn't have die from SAM

  EvaJanouskova

  committed
  ad8a143

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• wast: minor (HSI_Event description updated)

  EvaJanouskova

  committed
  85ada27

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• wast: set discharge date only if not destined to die; do not reset with recovery to MAM, they may not get the follow-up tx

  EvaJanouskova

  committed
  6cbd18d

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• test_wast: tx coverages were rm

  EvaJanouskova

  committed
  f42e82b

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• wast: rm unused local vars

  EvaJanouskova

  committed
  bec0769

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Commits on Dec 7, 2024

• wast: footprint assignment simplified; dates properties: tidy up description; death date assigned only when happening, reset recovery date when malnutrition state changes to MAM/SAM

  EvaJanouskova

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  b949156

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• wast & test_wast: update names of tx programmes to be in line with write-up

  EvaJanouskova

  committed
  30ba983

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Commits on Dec 10, 2024

• scenario_wast_min_model: 30K pop, 2010-2030 for 1st round calibration

  EvaJanouskova

  committed
  745d548

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• Merge remote-tracking branch 'origin/master' into hallett/wasting_module

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  8dd0ba0

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Commits on Dec 11, 2024

• RF_Wast: prob_death_after_SAMcare updated (substantially lower), hence prob_mam_after_SAMcare increased

  EvaJanouskova

  committed
  92e3ed8

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• analysis_wast: minor (tidy up comments)

  EvaJanouskova

  committed
  66cf53c

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• analysis_wast: combine deaths of both genders together

  EvaJanouskova

  committed
  ce8b0ec

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• wast: log both mod & sev wasting prevalence (instead of overall prev.) + log prevalence in above 5 years old

  EvaJanouskova

  committed
  5601969

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• wast & analysis_wast: tidy up

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  committed
  a41986d

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• wast: rm above5 prevalence logging

  EvaJanouskova

  committed
  85f5253

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• Merge remote-tracking branch 'origin/master' into hallett/wasting_module

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  committed
  03ddcca

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Commits on Dec 12, 2024

• analysis_wast: incidence - fix legend names, prevalence - mod & sev wasting

  EvaJanouskova

  committed
  7666291

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• wast: calculation of under5s for prevalence logging fixed

  EvaJanouskova

  committed
  037d40d

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• wast: log wasting prev in 5y+ olds

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  committed
  86b4c85

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Commits on Dec 29, 2024

• analysis_wast: prev by age grp - plot mod/sev wast separately, for year 2020,

  EvaJanouskova

  committed
  46a3f58

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• analysis_wast: incidence mod:wast props - tidy up

  EvaJanouskova

  committed
  e515e0d

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• wast: add logging of under5s pop size

  EvaJanouskova

  committed
  0c4468b

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• analysis_wast: tidy up update of df

  EvaJanouskova

  committed
  f77381e

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• wast: log pop sizes (mod/sev/total)

  EvaJanouskova

  committed
  ecb01f2

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• analysis_wast: incidence - plot nmbs of new cases instead of props mod:wast incidence cases.

  EvaJanouskova

  committed
  ca519f9

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• wast: log avg length of wasting

  EvaJanouskova

  committed
  3554a40

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• wast: log initial prevalence

  EvaJanouskova

  committed
  4fcd605

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• wast: length logging - sev wasted cannot be on MAM tx

  EvaJanouskova

  committed
  3fdd9da

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• analysis_wast: plot avg length of wasting by recovery options

  EvaJanouskova

  committed
  d1d2cce

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• analysis_wast: prints rm

  EvaJanouskova

  committed
  d1582c1

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• analysis_wast: add plot init prevalence by age grp

  EvaJanouskova

  committed
  e81f630

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• wast: log length for above5 too

  EvaJanouskova

  committed
  dd59b08

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• analysis_wast: higher upper y-axis limit for length of not yet recovered

  EvaJanouskova

  committed
  0cb7c4c

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• wast: minor (properties description updated)

  EvaJanouskova

  committed
  0d82002

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• wast: logging adjusted to avoid division by zero

  EvaJanouskova

  committed
  f13b169

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• wast & RF_Wast & test_wast: natural death due SAM scheduled when SAM developed; natural recovery from severe wasting if not dying;date_of_outcome_for_untreated_wasting's fnc input parameter changed…

  Show description for 3ac6565
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  3ac6565

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• wast: tidy up

  EvaJanouskova

  committed
  8164ed6

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• wast: log wasting_length_avg only at debug level

  EvaJanouskova

  committed
  067062f

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• scenario_wast_min_model: setup as for status quo

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  committed
  0a4dee7

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• Merge branch 'master' into hallett/wasting_module

  Show description for e9d897f
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  committed
  e9d897f

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• RF_PriorityRanking_ALLPOLICIES: after-merge update

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  committed
  f388ae8

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