Wasting Module

[tbhallett]

Fixes #542

[EvaJanouskova]

Hi @thewati, I can see you did some priority changes (commit cea20e0), here is a print screen of some changes made beside adding the undernutrition among the treatments in RF_PriorityRanking_ALLPOLICIES.xlsx, RMNCH sheet within this PR. (Because it is the xlsx file, I can't see which changes you made in the commit.)

Are these changes suggested by you? Are we still going to make these changes? I'm not sure who and why suggested that. Red is current version in master, green is what it is suggested to be changed to in this PR.

[EvaJanouskova]

@thewati, here is the version from the old master, which is the starting point of this branch:
ResourceFile_PriorityRanking_ALLPOLICIES_wasting_module_masterbase.xlsx

And here is the version from this branch:
ResourceFile_PriorityRanking_ALLPOLICIES_wasting_module.xlsx

You can review all suggested changes by comparing these versions.

[EvaJanouskova]

In terms of discussion today in stand-up call about how to resolve merge conflict due to changes in generic first appointment HSI events ....

Thanks a lot, @matt-graham! This is really helpful!

Hi @matt-graham, the Documentation check fails:
File "/home/runner/work/TLOmodel/TLOmodel/.tox/docs/lib/python3.11/site-packages/tlo/methods/wasting.py", line 33, in <module> class Wasting(Module, GenericFirstAppointmentsMixin): File "/home/runner/work/TLOmodel/TLOmodel/.tox/docs/lib/python3.11/site-packages/tlo/methods/wasting.py", line [55](https://github.com/UCL/TLOmodel/actions/runs/10066494565/job/27827994771?pr=543#step:6:56)2, in Wasting individual_properties: IndividualProperties, ^^^^^^^^^^^^^^^^^^^^ NameError: name 'IndividualProperties' is not defined

I tried to define it the same way as it is in stunting, but it doesn't seem to be working. Shouldn't the TYPE_CHECKING be turned on for wasting somewhere, or smt like that?

[thewati]

Hi @thewati, I can see you did some priority changes (commit cea20e0), here is a print screen of some changes made beside adding the undernutrition among the treatments in RF_PriorityRanking_ALLPOLICIES.xlsx, RMNCH sheet within this PR. (Because it is the xlsx file, I can't see which changes you made in the commit.)

Are these changes suggested by you? Are we still going to make these changes? I'm not sure who and why suggested that. Red is current version in master, green is what it is suggested to be changed to in this PR.

Hi @EvaJanouskova , I had a look at both files and I remember that commit. In that commit, I believe we added 3 treatment IDs called Undernutrition_Feeding_Supplementary, Undernutrition_Feeding_Inpatient, and Undernutrition_Feeding_Outpatient in the Naive sheet. I am not sure who changed or suggested the changes to the priorities. That commit did not touch the priorities you have highlighted. @mnjowe would you have an idea on the priorities Eva has highlighted?

[matt-graham]

In terms of discussion today in stand-up call about how to resolve merge conflict due to changes in generic first appointment HSI events ....

Thanks a lot, @matt-graham! This is really helpful!

Hi @matt-graham, the Documentation check fails: File "/home/runner/work/TLOmodel/TLOmodel/.tox/docs/lib/python3.11/site-packages/tlo/methods/wasting.py", line 33, in <module> class Wasting(Module, GenericFirstAppointmentsMixin): File "/home/runner/work/TLOmodel/TLOmodel/.tox/docs/lib/python3.11/site-packages/tlo/methods/wasting.py", line [55](https://github.com/UCL/TLOmodel/actions/runs/10066494565/job/27827994771?pr=543#step:6:56)2, in Wasting individual_properties: IndividualProperties, ^^^^^^^^^^^^^^^^^^^^ NameError: name 'IndividualProperties' is not defined

I tried to define it the same way as it is in stunting, but it doesn't seem to be working. Shouldn't the TYPE_CHECKING be turned on for wasting somewhere, or smt like that?

Ah that's because you need to import IndividualProperties from tlo.population - as this is only required for type hint you can do within the if TYPE_CHECKING block

[EvaJanouskova]

In terms of discussion today in stand-up call about how to resolve merge conflict due to changes in generic first appointment HSI events ....

Thanks a lot, @matt-graham! This is really helpful!

Hi @matt-graham, the Documentation check fails: File "/home/runner/work/TLOmodel/TLOmodel/.tox/docs/lib/python3.11/site-packages/tlo/methods/wasting.py", line 33, in <module> class Wasting(Module, GenericFirstAppointmentsMixin): File "/home/runner/work/TLOmodel/TLOmodel/.tox/docs/lib/python3.11/site-packages/tlo/methods/wasting.py", line [55](https://github.com/UCL/TLOmodel/actions/runs/10066494565/job/27827994771?pr=543#step:6:56)2, in Wasting individual_properties: IndividualProperties, ^^^^^^^^^^^^^^^^^^^^ NameError: name 'IndividualProperties' is not defined
I tried to define it the same way as it is in stunting, but it doesn't seem to be working. Shouldn't the TYPE_CHECKING be turned on for wasting somewhere, or smt like that?

Ah that's because you need to import IndividualProperties from tlo.population - as this is only required for type hint you can do within the if TYPE_CHECKING block

@matt-graham, The following is in the code:

if TYPE_CHECKING:
    from tlo.methods.hsi_generic_first_appts import HSIEventScheduler
    from tlo.population import IndividualProperties

Do you mean smt else?

[matt-graham]

@matt-graham, The following is in the code:

if TYPE_CHECKING:
    from tlo.methods.hsi_generic_first_appts import HSIEventScheduler
    from tlo.population import IndividualProperties

Do you mean smt else?

Sorry I missed that you already had the import in the code. It looks like the issue is actually that you are missing a

from __future__ import annotations

(see here for explanation of why required).
line at top of file

[EvaJanouskova]

@matt-graham, The following is in the code:

if TYPE_CHECKING:
    from tlo.methods.hsi_generic_first_appts import HSIEventScheduler
    from tlo.population import IndividualProperties

Do you mean smt else?

Sorry I missed that you already had the import in the code. It looks like the issue is actually that you are missing a

from __future__ import annotations

(see here for explanation of why required). line at top of file

Yes, this seems as what could cause the errors! Thank you @matt-graham!!

Great explanation. It's a cool trick you use there.

[mnjowe]

Hi @thewati, I can see you did some priority changes (commit cea20e0), here is a print screen of some changes made beside adding the undernutrition among the treatments in RF_PriorityRanking_ALLPOLICIES.xlsx, RMNCH sheet within this PR. (Because it is the xlsx file, I can't see which changes you made in the commit.)

Are these changes suggested by you? Are we still going to make these changes? I'm not sure who and why suggested that. Red is current version in master, green is what it is suggested to be changed to in this PR.

Hi @EvaJanouskova , I had a look at both files and I remember that commit. In that commit, I believe we added 3 treatment IDs called Undernutrition_Feeding_Supplementary, Undernutrition_Feeding_Inpatient, and Undernutrition_Feeding_Outpatient in the Naive sheet. I am not sure who changed or suggested the changes to the priorities. That commit did not touch the priorities you have highlighted. @mnjowe would you have an idea on the priorities Eva has highlighted?

I agree to your point @thewati. In this PR we were aiming at adding treatment IDs from wasting module only. @EvaJanouskova if there are merge conflicts that require manual way of merging commits I can help. I guess we just need to copy original file from master and manually add the three treatment IDs @thewati has mentioned above. Thanks

[EvaJanouskova]

@marghe-molaro, Could you please confirm the updates in Priorities?

There are 3 new lines added in all sheets:

• Undernutrition_Feeding_Supplementary
• Undernutrition_Feeding_Inpatient
• Undernutrition_Feeding_Outpatient

The values are always same for all 3 lines.
In most sheets the values are:

Priority	FT_if_5orUnder	FT_if_pregnant	FT_if_tbdiagnosed	FT_if_Hivdiagnosed
0	-1	-1	-1	-1

The only exception is the Naive sheet, where the values are:

Priority	FT_if_5orUnder	FT_if_pregnant	FT_if_tbdiagnosed	FT_if_Hivdiagnosed
2	-1	-1	-1	-1

Are these fine with you?

[marghe-molaro]

Hi @EvaJanouskova,

For the LCOA_EHP and EHP_III you would need to double check with @sakshimohan.

The Naive values look correct, but not the ones for the other sheets.

For "Default" and "Test" and "Test Mode 1" you can go for (0, -1, -1, -1, -1).
In the case of "RMNCH" I believe these may need to be prioritised as mainly concerning under 5 care (@tbhallett should confirm this) in which case I would go for (5, 3, -1, -1, -1)
In the case of ClinicallyVulnerable, go for (3, 2, 2, 2, 2)
For VerticalProgrammes and CVD you can go for (3, -1, -1, -1, -1)

[EvaJanouskova]

Hi @EvaJanouskova,

For the LCOA_EHP and EHP_III you would need to double check with @sakshimohan.

The Naive values look correct, but not the ones for the other sheets.

For "Default" and "Test" and "Test Mode 1" you can go for (0, -1, -1, -1, -1). In the case of "RMNCH" I believe these may need to be prioritised as mainly concerning under 5 care (@tbhallett should confirm this) in which case I would go for (5, 3, -1, -1, -1) In the case of ClinicallyVulnerable, go for (3, 2, 2, 2, 2) For VerticalProgrammes and CVD you can go for (3, -1, -1, -1, -1)

Thanks @marghe-molaro. @sakshimohan and @tbhallett, could you please confirm the above? Thank you!

[tamuri]

Determinism test is failing because this uses the old (and now removed) way of logging. log needs arguments key and data.

[tbhallett]

Let's just delete this obsolete line then!

[EvaJanouskova]

@tamuri, Why the test_determinism is not failing on my computer?

[sakshimohan]

Hi @EvaJanouskova,
For the LCOA_EHP and EHP_III you would need to double check with @sakshimohan.
The Naive values look correct, but not the ones for the other sheets.
For "Default" and "Test" and "Test Mode 1" you can go for (0, -1, -1, -1, -1). In the case of "RMNCH" I believe these may need to be prioritised as mainly concerning under 5 care (@tbhallett should confirm this) in which case I would go for (5, 3, -1, -1, -1) In the case of ClinicallyVulnerable, go for (3, 2, 2, 2, 2) For VerticalProgrammes and CVD you can go for (3, -1, -1, -1, -1)

Thanks @marghe-molaro. @sakshimohan and @tbhallett, could you please confirm the above? Thank you!

Hi @EvaJanouskova . Is there a more detailed description of the three interventions which I could refer to, to assign them the right priority?

[EvaJanouskova]

Hi @EvaJanouskova,
For the LCOA_EHP and EHP_III you would need to double check with @sakshimohan.
The Naive values look correct, but not the ones for the other sheets.
For "Default" and "Test" and "Test Mode 1" you can go for (0, -1, -1, -1, -1). In the case of "RMNCH" I believe these may need to be prioritised as mainly concerning under 5 care (@tbhallett should confirm this) in which case I would go for (5, 3, -1, -1, -1) In the case of ClinicallyVulnerable, go for (3, 2, 2, 2, 2) For VerticalProgrammes and CVD you can go for (3, -1, -1, -1, -1)

Thanks @marghe-molaro. @sakshimohan and @tbhallett, could you please confirm the above? Thank you!

Hi @EvaJanouskova . Is there a more detailed description of the three interventions which I could refer to, to assign them the right priority?

@sakshimohan, See the description in the write-up, page 8.

[EvaJanouskova]

@tbhallett, We may need to include some equipment for the wasting module. Would it be fine to address this later, or do you need it for another project asap, in which case I should incorporate any equipment that comes to mind at this moment within this PR?

[tbhallett]

@tbhallett, We may need to include some equipment for the wasting module. Would it be fine to address this later, or do you need it for another project asap, in which case I should incorporate any equipment that comes to mind at this moment within this PR?

Thanks Eva. It seems a good idea to me to add in the declarations now, if they are coming to mind. You can always add more later if it turns out you missed some. We are going to run the full model for the costing calculations with this module included soon, so I would say please include things if you can.

[sakshimohan]

(3, -1, -1, -1, -1)

Thanks @EvaJanouskova.

For EHP, you can go for (2, -1, -1, -1, -1) for all three treatment_ID s.
For LCOA:

• (2, -1, -1, -1, -1) for Undernutrition_Feeding_Supplementary, and Undernutrition_Feeding_Outpatient;
• (4, -1, -1, -1, -1) for Undernutrition_Feeding_Inpatient.