Complete ALRI Module

[tbhallett]

• [x] PR 1: with loose-end tied up from the initial version:

• 'daly_very_severe_ALRI' is never used: is that right?

• There are no probabilities describing the risk of onset of the complication "empyema". There is the risk of empyema being delayed onset (i.e. prob_pleural_effusion_to_empyema) and also the risk that "empyema" leads to sepsis (prob_empyema_to_sepsis). However, for simplicity we only have two phases of complication (initial and delayed), so this is not represented at the moment. I am not sure if it should be or not.

• The risk of death is not affected by delayed-onset complications: should it be?

• Check that every parameter is used and remove those not used (from definition and from excel). I think that are several not being used (e.g prob_respiratory_failure_to_multiorgan_dysfunction and r_progress_to_severe_ALRI) -- perhaps left over from an earlier version? Also, please could you tidy-up ResourceFile_Alri.xlsx? If there are sheets that need to remain in there, it would be good if you can explain what each is for on the sheet (and delete anything that is not needed).

• Is it right that 'danger_signs' is an indepednet symptom? It seems like this is something that is determined in the course of a diagnosis (like in diarrhoea module).

• [x] PR 2: Provide basic functionality of HSI:

• Provide edits the Generic_HSI_First_Appts that cause a child that is showing symptoms of ALRI disease to have run on them a function inside the Alri module called something like assess_child(self, person_id)

• Let that function call do_treatment for that child

• [x] PR 4: Elaborate the HSI system to the extent needed.

• [x] PR 5: Follow-up events for those with treatment failure, in the same stream of HSI events

• [x] PR 6: Update consumables item cloxacillin following its addition in the spreadsheet

• [x] PR 7: Analyse mortality data and input in the model parameters

• [x] PR 3 : Achieve a basic calibration of the model for incidence and deaths, adjusting healthcare seeking behaviour and efficacy of treatment accordingly.

• [x] PR 8: Achieve calibration of the model for HSI outputs.

• [ ] PR 9: Have pulse oximeter in the consumables list (determine cost per unit of use)

• [x] PR 10: Update effect of oxygen on different IMCI severities, and oral antibiotics on non-hypoxaemic severe pneumonia, following clinical advice.

[inesll]

• [ ] PR 1: with loose-end tied up from the initial version:
• 'daly_very_severe_ALRI' is never used: is that right?
• There are no probabilities describing the risk of onset of the complication "empyema". There is the risk of empyema being delayed onset (i.e. prob_pleural_effusion_to_empyema) and also the risk that "empyema" leads to sepsis (prob_empyema_to_sepsis). However, for simplicity we only have two phases of complication (initial and delayed), so this is not represented at the moment. I am not sure if it should be or not.
• The risk of death is not affected by delayed-onset complications: should it be?
• Check that every parameter is used and remove those not used (from definition and from excel). I think that are several not being used (e.g prob_respiratory_failure_to_multiorgan_dysfunction and r_progress_to_severe_ALRI) -- perhaps left over from an earlier version? Also, please could you tidy-up ResourceFile_Alri.xlsx? If there are sheets that need to remain in there, it would be good if you can explain what each is for on the sheet (and delete anything that is not needed).
• Is it right that 'danger_signs' is an indepednet symptom? It seems like this is something that is determined in the course of a diagnosis (like in diarrhoea module).
• [ ] PR 2: Provide basic functionality of HSI:
• Provide edits the Generic_HSI_First_Appts that cause a child that is showing symptoms of ALRI disease to have run on them a function inside the Alri module called something like assess_child(self, person_id)
• Let that function call do_treatment for that child
• [ ] PR 3 : Achieve a basic calibration of the model for incidence and deaths, adjusting healthcare seeking behaviour and efficacy of treatment accordingly.
• [ ] PR 4: Elaborate the HSI system to the extent needed.

Yes, this is excellent!! Thanks very much Tim! :)

[tbhallett]

Great work on all this @inesll.

I suppose the last thing about the oximeter is a long-term fix, so I'll put this onto the backlog now.