Param Revamp - HIV

[mmsuarezcosta]

Files

Files changes:

• parameters.csv
• scaleup_parameters.csv
  • It is important to review the modifications I have made to this file. I have updated to the standard parameters.csv format, thus the column target_value has been renamed value, and the max and mins have been changed to prior_min and prior_max. The logic is that anything within the scale_up file is a target by definition, so it is not required to label the value itself as target.

Files used in hiv module that require refactoring (request for @mnjowe to support in future iterations):

• hiv_prevalence.csv
• time_since_infection_at_baselin.csv
• MoH_numbers_tests.csv, spectrum_treatment_cascade.csv (they contain historical data, so refactoring may not be required)

Calibration Data Files

• LHC_samples.csv
• unaids_infections_art2021.csv
• unaids_mortality_dalys2021.csv
• children0_14_prev_AIDSinfo.csv
• unaids_program_perf.csv
• DHS_prevalence.csv
• MoH_number_art.csv
• MPHIA_incidence2020.csv
• MPHIA_prevalence_art2020.csv
• MoH_numbers_tests.csv (also used in HIV.py)

Files Not Used in Code (May be legacy - consider deleting)

• calibration_from_aids_info.csv
• MoH_CPT_IPT2020.csv
• unaids_pmtct2021.csv
• MPHIA_incidence2020.csv (output_plots.py references 2015 version that doesn't exist, consider updating reference)
• MPHIA_prevalence_art2020.csv (output_plots.py references 2015 version that doesn't exist, consider updating reference)

Parameters

Assumptions

• mean_months_between_aids_and_death
• mean_months_between_aids_and_death_infant
• rr_fsw (discrepancy in write-up value 20 and parameter.csv value of 25)
• rr_behaviour_change
• proportion_reduction_in_risk_of_hiv_aq_if_on_prep
• mean_months_between_aids_and_death_infant

Undetermined, calibration

I cross-checked the write-up and notes in the parameter CSV file to determine which I believed to be calibrated.

• hiv_testing_rate_adjustment, treatment_initiation_adjustment,vs_adjustment: believe all these are calibrated based on write-up and parameter documentation in code
• Circumcision parameters (prob_circ_after_hiv_test, increase_in_prob_circ_2019, prob_circ_for_child_before_2020, prob_circ_for_child_from_2020): Based on write-up, vmc was calibrated to national rates, so I have labeled all these as calibrated
• aids_tb_treatment_adjustment: believe it is calibrated because of adjustment label
• Other testing rate probabilities (e.g. prob_hiv_test_at_anc_or_delivery) I have marked as local, but they may have been adjusted for calibration.

Hard-Coding

• Any values the LinearModels I have left hard-coded. Example:

        predictors = [
            Predictor("age_years").when("<15", 0.0).when("<49", 1.0).otherwise(0.0),
            Predictor("sex").when("F", p["rr_sex_f"]),

• Consumables and equipment

Notes (Future development)

• More thoroughly review designation of local and universal (I did not have time to exhaustively review)

[marghe-molaro]

Thanks @mmsuarezcosta, this looks good to me, and I think is ready for @tdm32's review!