add covid19 vaccination info #197
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Summary of the missing optional fields for the brazil-followup parser:
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Summary of the missing optional fields for the brazil-followup parser:
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Thanks @ekamau! I'm happy with this now, maybe @sadiekelly could review too before this is merged? |
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Thanks Pip! great!
…On Tue, Oct 31, 2023 at 11:26 PM Pip Liggins ***@***.***> wrote:
Thanks @ekamau <https://github.com/ekamau>! I'm happy with this now,
maybe @sadiekelly <https://github.com/sadiekelly> could review too before
this is merged?
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sadiekelly
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Hi @ekamau I've added a few comments to various parsers. I can also do a double check across all studies to make sure we haven't missed anything. |
Vaccination data is provided in CVPSICL MLW_COVID19LMIC, although not defined in the data dictionary. The variable name c19_vacc indicates whether the patient has received a vaccine. dose_date gives the date of the most recent dose (I think). Previous vaccine doses are indicated in prev_vaccs but with no date |
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For PHOSP, data are collected on vaccinations in the PSQ form. This I think is similar situation to ISARIC Tier 1 and brazil follow up where data are only collected at follow up, so I think we can use this. psq_vac_first_yn indicates whether the patient has received a covid19 vaccine. Date of first dose is psq_vac_first_date and date of second dose psq_vac_sec_date |
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South Africa has vaccination status in the variable Vaccinated. Dates are given in First Dose Date, Second Dose Date and Booster Dose Date |
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Summary of the missing optional fields for the brazil-followup parser:
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Summary of the missing optional fields for the brazil-followup parser:
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@ekamau @sadiekelly - the reason the most recent edits are failing (or at least one of them) is that you're trying to add context notes to the subject table, which doesn't allow them. I wasn't present for the discussion about where to put vaccination data (subject vs observation) but if we think context notes are important, vaccinations will have to become observations. Otherwise we can update the docs to say that if a single date is provided, it should be the date of the most recent dose (if that's correct?). |
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Thanks Pip - yes, that's correct. Sorry I couldn't pin-point where the
errors were coming from. You are right. We could add capability for context
in the schema or update the docs as you see fit.
…On Mon, Nov 6, 2023 at 11:13 AM Pip Liggins ***@***.***> wrote:
@ekamau <https://github.com/ekamau> @sadiekelly
<https://github.com/sadiekelly> - the reason the most recent edits are
failing (or at least one of them) is that you're trying to add context
notes to the subject table, which doesn't allow them. I wasn't present for
the discussion about where to put vaccination data (subject vs observation)
but if we think context notes are important, vaccinations will have to
become observations. Otherwise we can update the docs to say that if a
single date is provided, it should be the date of the most recent dose (if
that's correct?).
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Adding context to the subject table doesn't feel like a sensible option to me - as a wide format table this would just look like another column (e.g. vaccination_context) which we haven't done for other attributes and if we open that up as an option, it could all get out of hand (where would it stop!). For now I think we should just ignore the context, I'll comment it out in the parser so we can retain the info. When moving to OMOP/ our eventual data storage option, we can re-evaluate whether the way the vaccination data is stored allows for context-like notes. |
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Summary of the missing optional fields for the brazil-followup parser:
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Summary of the missing optional fields for the brazil-followup parser:
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@pipliggins @ekamau thanks! I think this sounds sensible. Maybe add an explanation in the docs that the vaccination dates are not necessarily inclusive of all received doses; a single date would often be the date of most recent dose but we don't know for sure, a second dose date may have been missed or unknown at the time of data collection |
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added attributes for covid19 vaccinations - #186 . For the datasets I could find.