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joehcollinstdm32tbhallett
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Updates/fixes to MNH modules following on from Joe's PhD (#1251)
* prepare HIV and TB modules for PR * merge in edited hiv and tb files * remove hv_vmmc_counter property * check tb and hiv tests * flake8 checks * Change clustering of tb in hiv+ Change tb mortality rate to 2011-2018 values (increased) Add infant NVP Change relative proportions of imported vs transmitted tb Tb active case poll assigns cases within that month (not that year) Same for importation event which runs monthly Importation rate and transmission rate roughly calibrated * use parameter for importation rate not value * HIV infant NVP - cap repeat visits at 5 return blank appt footprint if child is not eligible * test runs * cap repeat infant NVP appts at 5 track repeat visits within event call * add referred_from and repeat_visits arguments to HSI_Hiv_StartInfantProphylaxis * edit infant NVP follow-up date * fixes to failing tests * fixes to failing tests * Updates to resource files with amended parameter values and new parameters added * Edits to antenatal healthcare code to ensure that coverage of inpatient interventions can be manipulated by scenario files. Also added fix which prevents higher coverage of AN inpatient care significantly increasing stillbirths * edit ipt coverage rates to ensure sims can run to 2099 * edit test_hiv_tb_scenarios.py to get correct IPT coverage for children * refer ART to level 2 if unsuccessful at level 1a reset baseline active tb across 2010, transmission poll starts 2011 * change importation rate to 10/100,000 mdr importation rate 1.86% of this * add fix to test_hiv_tb_scenarios.py * edits to pregnancy_supervisor.py in order to conduct sensitivity analysis with min/max availability of antenatal care * fix error caused by resetting ps_antepartum_haem * updating pregnancy_helper_functions.py. Fixes to repeat risk of death application, analysis functionality added. * added updated call to check_if_delayed_careseeking * update labour.py analysis event and analysis parameters * update labour.py logging and remove redundant parameters * final labour.py updates * fix error in labour_lm.py * small updates in postnatal_supervisor.py including removing redundant properties * removing redundant properties * removing redundant properties * Adding sensitivity scenario scripts * updating analysis scripts * updates to met_need.py * fixes to analysis_utility_functions.py to produce required outputs * finalising calibration analysis scripts * updating scenario files params * increased CFR for uterine rupture as MMR for that comp is low * fixes to paed continual ART referrals * fixes to paed continual ART referrals * check hv_art status correctly in TestAndRefer * Fixes to failing tests from maternal health modules * add catch if person is HIV diagnosed, do not schedule another HIV test in the TB test event * add condition not to run TB test in HIV HSI if TB already diagnosed * add condition don't run newborn testing if newborn_outcomes registered * HIV test not repeated if last test within one week in TB testing, no referral for HIV test if previous HIV test within one week edit tests to use new property tb_date_tested remove TB property tb_ever_tested * test_tb.py change end-date in test_basic_run_with_default_parameters as no active cases after 2011 with very small population * test_tb.py change end-date in test_basic_run_with_default_parameters as no active cases after 2011 with very small population * Comments added to newborn_outcomes.py to remember to update * update to stillbirth and APH calibration * use random date scheduling for TB screening HSI * updates to baseline and uhc scenarios to do analysis for abstract * correct parameter value error for treatment effect of IFA supplementation * correct parameter value error for treatment effect of blood transfusion for anaemia * add fix to test_tb.py to make prop_smear_positive=1 for purposes of test * edits to sepsis calibration and to calibration script * edits to sepsis calibration and to calibration script * update calibration script seed * fixed error in parameters introduced during calibration. update calibration script * fixed error in parameters introduced during calibration. update calibration script * update to fix parameter calibration * final specifications for scenario files * Updated resource files with parameter changes * Fix to labour.py to ensure surgery for failed RP treatment. Fix that caused variation between runs when doing SBA min analysis. Updates to comments * Fixed DALY weight acquisition for newborns. Update logic for ROP * Small fixes and logging updates to pregnancy_supervisor.py * updates to analysis scripts * updates to calibration scripts * fix failing newborn test relating to new retinopathy logic * updated seeds for scenario files * fixed error in quantiles * fixed error in quantiles * fixed error in quantiles * fixed error in quantiles * fixed error in quantiles * updated scenario files * updated analysis scripts * update prob_delay_ parameter * update rr_still_birth_ur parameter * update retionopathy and miscarriage params * update resus treatment effects * updated mean_birth_weights params * updates to consumables * updates to consumables * update enceph_cfr_multiplier * add in logic for the effect of obesity on potl * add in updated newborn resus logic * add in updated newborn resus logic * add in updated newborn resus logic * cord care provisional on birth kit consumables * update KMC logic * update KMC logic * update KMC logic * update neonatal pnc logic so care seeking is higher for all neonates with complications * update logic relating to ANC qual parameters * update so that inpatient care level corresponds with referal level * update so that inpatient care level corresponds with referal level * update calibration file * update analysis event in pregnancy supervisor * fix to error in newborn outcomes * fix to error in newborn outcomes * fix to error in newborn outcomes * calibration updates * calibration updates * calibration updates * calibration updates * calibration updates * calibration updates * calibration updates * calibration updates * calibration updates * calibration updates * fixes to tests * fixes mistake to cs baseline assumption * fixing errors * fixing errors for pph incidence * fixing errors for pph incidence * fixed obstructed labour error * fix to cause delay in PPH treatment * analysis script update * analysis script update * flake8 * remove unneeded logic from did_not_run functions * fix * tidying branch * tidying comments * flake8 * update to calibration script * update to thesis analysis script * typo * fixed classification of post term pregnancies * fixed application of anaemia risk * fixed effect of delays on PPH interventions * additional fix to anaemia logic * calibration scripts * calibration scripts * calibration scripts * fixed syntax error * removed uncalled parameters. Updated ResourceFile_Improved_Healthsystem_And_Healthcare_Seeking.xlsx to remove parameters that no longer exsist * Updated ResourceFile_Improved_Healthsystem_And_Healthcare_Seeking.xlsx to remove parameters that no longer exsist * Updated ResourceFile_Improved_Healthsystem_And_Healthcare_Seeking.xlsx to remove parameters that no longer exsist * Fixes for failing tests * Removal of all internal delay/squeeze factor logic from the MNH modules * removed uncalled parameter from resource file * fix MNH calibration script to meet new pandas requirements * fix MNH analysis script to meet new pandas requirements * add fix to calibration script to correctly output births * flake8 * update priority policy resource file to include new treatment ids * flake8 * flake8 * fix failing health system test --------- Co-authored-by: tdm32 <[email protected]> Co-authored-by: Tim Hallett <[email protected]>
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‎resources/ResourceFile_AntenatalCare.xlsx

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‎src/scripts/maternal_perinatal_analyses/analysis_scripts/analysis_utility_functions.py

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