PR to record the prevalence of disease/condition, still births, neonatal death, maternal mortality #1455
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Could create it within the healthburden module, but am unable to access logs? Or what is directly produced from the modules themselves.
… module (Get_Current_Prevalence). Also have it so that this is run every month alongside the Get_Current_Dalys logger
Adding in disease modules gradually
Co-authored-by: Tim Hallett <[email protected]>
…into rmw/log_prevalence_all_disease
… freuquency parameter was set as, is now just passed in as an argument
…ta type or another.
…module, then calling it in the write_to_log and write_to_log_prevalence functions
…s module, then calling it in the write_to_log and write_to_log_prevalence functions - Added logic to healthburden too to ensure that if None is returned the logging etc is skipped (in accordance with it being in the base class).
- Added assertion to check if a module that uses the healthburden module has a report_prevalence function
(Based on conversation yesterday) - changed so that it is no longer in base class (as not all modules are disease modules), but there is an assertion checking to see that if something uses the healthburden module, it must have the report_prevalence function |
# Conflicts: # src/tlo/core.py
Reformatted test so now they log at the same rate
…lthburden are not included
Changed so that the MMR, Live Births etc returns None only if Simplified Births are used
… last month. Fixed issue so that only comparing actual times (not NaT)
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The point prevalence is recorded for a number of modules and conditions within modules (Alri, BladderCancer, BreastCancer, CardioMetabolicDisorders ( chronic_ischemic_hd, chronic_kidney_disease, chronic_lower_back_pain, diabetes, hypertension), COPD, Depression, Diarrhoea, Epilepsy, Hiv, Labor (Intrapartum stillbirth), Malaria, Measles, NewbornOutcomes, OesophagealCancer, OtherAdultCancer, PostnatalSupervisor, PregnancySupervisor (Antenatal stillbirth), ProstateCancer, RTI, Schisto, TB, Demography (maternal_deaths, newborn_deaths).
Additional questions:
- Okay to calculate the prevalence of diarrhoea? It is a not really a disease in its own right, more of a symptom
- For some modules (RTI), may be more accurately described by calculating incidence, rather than prevalence. Is that useful/okay? Or should it be skipped?
Other notes:
- COPD is defined as ch_lung_function > 3.
- Have not included events in the CardioMetabolic Module (ever_heart_attack and ever_stroke) as would be a cumulative incidence living people who have had such events