Adding ITN_use effect and the treatment seeking probability

[OD1992]

@goldingn

Hello Nick I Have made some update in NGA_example.Rmd file:

-- I add the TS proba when I defining the clinical_incidence because I consider that not everyone infected goes to hospital to be tested/diagnosed.

-- I have added the ITN use effect as a covariate with negative effect (supposing beta_itn>0).

Thanks to review that.

[goldingn]

Hi Ousmane,

I'm having trouble tracking down. the changes you are referring to. In the future, could you please try to do the following?

1. use informative commit messages that say what you have changed in each commit
2. use links to specific sections of code (click on the line numbers in github and you can copy a link from the address bar, or right-click to copy a 'permalink') so you can point me to what you are referring to.
3. ask more specific questions in your issues so I can tell what you need help with

I think you are referring to a change to this line of code: https://github.com/OD1992/epiwave.mapping/blob/master/NGA_example.Rmd#L1231
which used to read:
clinical_case_incidence <- g(q_star * infection_incidence)
and now reads:
clinical_case_incidence <- g(q_star * infection_incidence*all_s_ts)

Can you explain to me what you are trying to achieve with this change, and why you think this is the correct way to implement it? There are equations explaining what all of these model parameters are and how they work. Perhaps you could write out the equations and explanation here for your change?

Note that the equations say that "In this case, c_{i} gives the incidence of all clinical episodes regardless whether those cases would be recorded in a health system."
c_{i} is equivalent to the object clinical_case_incidence in the code. So does it make sense to include treatment seeking in this term, or should it instead be rolled into the reporting fraction r ?

[OD1992]

Hi Nick, Sorry for this late response because I was on paternity leave the last two weeks. Now, I am back with a lot of work deadlines including our model. Nigeria NMP wants to get output at least the end of May. Consequently, it is so important to get some preliminary results for them. Right: *we should roll the care seeking into the reporting fraction **r*. Also, I am preparing an Abstract for the ASTMH on this topic ( https://docs.google.com/document/d/1mNKfqpzRIQ6O1A96QMmZYaUd3GZ4SgdmkQeVMv2-7q4/edit?usp=sharing). Feel free to modify this document. I am ok to have regular meetings in order to have a good track on this work, if it works for you. Let me know your thoughts. Best wishes, Ousmane Le jeu. 20 mars 2025 à 06:00, Nick Golding ***@***.***> a écrit :

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Hi Ousmane, I'm having trouble tracking down. the changes you are referring to. In the future, could you please try to do the following? 1. use informative commit messages that say what you have changed in each commit 2. use links to specific sections of code (click on the line numbers in github and you can copy a link from the address bar, or right-click to copy a 'permalink') so you can point me to what you are referring to. 3. ask more specific questions in your issues so I can tell what you need help with I think you are referring to a change to this line of code: https://github.com/OD1992/epiwave.mapping/blob/master/NGA_example.Rmd#L1231 which used to read: clinical_case_incidence <- g(q_star * infection_incidence) and now reads: clinical_case_incidence <- g(q_star * infection_incidence*all_s_ts) Can you explain to me what you are trying to achieve with this change, and why you think this is the correct way to implement it? There are equations explaining what all of these model parameters are and how they work. Perhaps you could write out the equations and explanation here for your change? Note that the equations say that "In this case, c_{i} gives the incidence of all clinical episodes regardless whether those cases would be recorded in a health system." c_{i} is equivalent to the object clinical_case_incidence in the code. So does it make sense to include treatment seeking in this term, or should it instead be rolled into the reporting fraction r ? — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A4HCQXM22BCYLBGW55Z22IT2VJKRBAVCNFSM6AAAAABZBCI42OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDOMZZGI4TCNBZHE> . You are receiving this because you authored the thread.Message ID: ***@***.***> [image: goldingn]*goldingn* left a comment (idem-lab/epiwave.mapping#6) <#6 (comment)> Hi Ousmane, I'm having trouble tracking down. the changes you are referring to. In the future, could you please try to do the following? 1. use informative commit messages that say what you have changed in each commit 2. use links to specific sections of code (click on the line numbers in github and you can copy a link from the address bar, or right-click to copy a 'permalink') so you can point me to what you are referring to. 3. ask more specific questions in your issues so I can tell what you need help with I think you are referring to a change to this line of code: https://github.com/OD1992/epiwave.mapping/blob/master/NGA_example.Rmd#L1231 which used to read: clinical_case_incidence <- g(q_star * infection_incidence) and now reads: clinical_case_incidence <- g(q_star * infection_incidence*all_s_ts) Can you explain to me what you are trying to achieve with this change, and why you think this is the correct way to implement it? There are equations explaining what all of these model parameters are and how they work. Perhaps you could write out the equations and explanation here for your change? Note that the equations say that "In this case, c_{i} gives the incidence of all clinical episodes regardless whether those cases would be recorded in a health system." c_{i} is equivalent to the object clinical_case_incidence in the code. So does it make sense to include treatment seeking in this term, or should it instead be rolled into the reporting fraction r ? — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A4HCQXM22BCYLBGW55Z22IT2VJKRBAVCNFSM6AAAAABZBCI42OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDOMZZGI4TCNBZHE> . You are receiving this because you authored the thread.Message ID: ***@***.***>